What is the relationship between structure and function group of answer choices?

What are structure-function relations?

While the biological literature often uses the terminology “structure-function relationship,” its specific meaning is rarely defined. In general, a system’s activity often depends on its internal organization. Thus, we provide the following working definition: a structure-function relationship exists when the individual components of a system are arranged into a structure that allows the system to perform its activity. In everyday life, a useful structure-function relation is that the parts of the corkscrew are designed and put together so that we can easily open a bottle of Pinot Grigio. It is interesting to note that the above definition does not exclude the possibility that a structure is more complicated than it needs to be for a given function. The reason is that the extra baggage can allow for one or more additional functions. For example, the corkscrew can be part of a multitool, which can be configured to efficiently turn a screw or open a bottle of beer. As we shall see in Chapter 2, the ECM is modular, which means that various molecules are organized into a structure from smaller modules in order to support multifunctionality similar to a multitool. Furthermore, the definition itself may imply that the structure allows functional performance with near optimum efficiency. One must, of course, also specify what optimum efficiency is. For example, optimum efficiency of ATP production may be obtained by tuning production rate to satisfy demand because making more ATP than is used can be wasteful, but making less than required may result in failure of function. Since the mitochondrial structure influences ATP production rate [3], demand can affect structure, which in turn regulates function.

Structure-function relations are often reported in biochemistry and protein engineering. The specific 3D structure of a protein such as an enzyme plays a critical role in determining the function of the enzyme. Matrix metalloproteinase (MMP)-1 is a well-studied enzyme that is known to degrade type I collagen. However, MMP-1 plays a broad role in many processes in health, including development, tissue morphogenesis, and wound healing as well as during pathological tissue changes, such as cancer, pulmonary emphysema, and fibrotic disorders [5]. Computational modeling of the role of mutations in binding of MMP-1 to collagen has shown that the specific 3D structure of MMP-1 determines the strength of its activity against collagen [6]. This is a prime example of a structure-function relationship at the level of interactions between two proteins. Furthermore, the MMP-1 structure-function relation can be directly probed by introducing mutations at the catalytic site of the enzyme, which results in a change in structure and a corresponding decline in activity relative to the wild-type optimal one [7].

The structures in Fig. 1.1 are not random; indeed, the specific organization of the elements of each structure provides the basis of the relevant function. For example, the arrangement of collagen fibrils in the stroma achieves two functions: (1) it allows a strong ECM of the cornea of the eye with mechanical strength to withstand the ocular pressure as well as an occasional mechanical injury such as a punch and (2) the cornea allows light to enter the eye and hence it must be transparent. As we shall see in Chapter 11, these mechanical and optical functions are simultaneously met by an efficient organization of collagen fibrils as is evident in Fig. 1.1A. Furthermore, the role of proteoglycans in the development of corneal structure will also be explored.

The structural basis of contractile force generation is the cytoskeleton. In the presence of ATP, myosin motors walk on actin and, by pulling on neighboring filaments, force is generated. Different types of muscle generate varying amounts of specific force or contractile stress (force per cross-sectional area). For example, maximum contractile stress in rat diaphragm is larger in muscle types with a higher content of myosin cross bridges per unit sarcomere length [8]. Notice that more myosin motors create more cross-bridges and a denser structure, and hence, this is a simple structure-function relation. Alternatively, when the integrity of the cytoskeletal actin network in vascular smooth muscle cells is gradually compromised with the depolymerizing agent cytochalasin D, the force generation declines in a dose-dependent manner [9]. It is interesting to note, however, that the contractile stress produced by the slow diaphragm muscle fibers is less than that of the fast fibers even after accounting for the number of cross bridges available for force generation [8]. In this case, the structure responsible for the functionally different force generation is at the molecular level within the structure of the myosin motor itself. The large majority of the ATP that drives muscle contraction is produced in the mitochondria. As can be seen in Fig. 1.1B, mitochondria also form a network of clusters of varying sizes. It has been reported that the larger the fractal dimension of the mitochondrial cluster network, the larger the mitochondrial membrane potential and hence ATP production rate [10]. Since the fractal dimension is a structural measure of the complex space-filling capacity of an object [11], the fact that ATP production rate is a function of the fractal dimension represents an important structure-function relation in cellular metabolism.

The third example structure in Fig. 1.1C is related to lung stability and elasticity. The specific structure of more than 300 million alveoli in the human lung serves the basic function of the lung as an organ, namely, gas exchange via diffusion that requires a large surface area over a thin barrier with proper mechanical stability [12]. This fine structure is protected from collapse by a negative pressure (relative to atmospheric pressure) around the lung, which generates a positive trans-lung pressure and hence a tensile stress in the elastin-collagen network of the alveolar septal walls. During inspiration, a further decrease in the negative pressure (generated by ATP-driven muscle contraction) stretches the tissues to draw air into the structure, whereas during expiration, most of the work done on elastin by stretching the molecular structure is returned by passive contraction of the tissues due to the recoil of elastin. Thus, in this case, the specific structure in Fig. 1.1C allows gas exchange, whereas the elastin network provides tissue elasticity at the molecular level necessary for breathing.

Designer Cellulosomes

Designer cellulosomes have been proposed as a tool for understanding the structure–function relationship of cellulosome components and for subsequent biotechnological application in waste management and biofuel production.41–43 In designer cellulosomes, each chimeric enzyme is appended with a dockerin of divergent specificity that binds specifically to a matching cohesin of a chimeric scaffoldin. Thus, in contrast with mini-cellulosomes, designer cellulosomes allow precise incorporation of the different enzymes into the chimeric scaffoldin, and the composition of designer cellulosomes is homogeneous with respect to the enzyme content and the exact location of the enzymes within the complex (Figure 3(b)). The first demonstrations in the construction and use of artificial cellulosomes were reported in 2001.44 In this work, divalent designer cellulosomes were assembled with components of Clostridium cellulolyticum, and the complex exhibited enhanced degradation of microcrystalline cellulose. Two cohesins originating from different bacterial species and exhibiting divergent specificities were fused into a single polypeptide chain together with a CBM for targeting of the enzymes to the cellulosic substrate, thus forming the chimeric scaffoldin. Chimeric enzymes that contained matching dockerins were constructed in parallel, enabling their precise incorporation into the designer cellulosome complex.

Two factors that serve to enhance deconstruction of recalcitrant cellulosic substrates were defined: the enzyme targeting to the substrate surface via the CBM of the scaffoldin and the physical proximity effect of the enzyme components.45 In addition, the resulting enhancement in substrate deconstruction was shown to increase with the recalcitrance of the cellulosic substrate.46 Also, for more complex lignocellulosic substrates (wheat straw), the contribution of a large spectrum of enzymes (from different glycoside hydrolase families) specialized for the different subcomponents of the substrate was demonstrated.

The designer cellulosome approach also enabled fabrication of novel and inventive cellulosome geometries, and their activities on crystalline cellulosic substrates were compared with those of more conventional designer cellulosomes.47 This study established the negative influence of multiple CBMs in designer-cellulosome complexes in cellulose degradation, thus corroborating the results of a previous study,45 and further indicated that increased architectural restrictions and elevated levels of rigidity appeared to decrease the activity of the resultant designer cellulosomes. In one case, a family 6 fungus-derived cellulase was included into designer cellulosome modes together with standard cellulosomal enzymes.48 In this study, the two factors—targeting effect and proximity effect—were observed to occur separately and not in combination. The authors suggested that the origin of the enzymes from the different microbial systems may have been responsible for the apparent antagonism between the proximity and CBM targeting effects and that the benefit of combined effects may occur in designer cellulosomes composed only of bacterial enzymes. In fact, family 6 enzymes have not been observed to be a component of native cellulosomes. It is interesting to note that two family 6 enzymes—an endoglucanase and an exoglucanase—derived from the aerobic bacterium Thermobifidia fusca, were incorporated into designer cellulosomes.49 The endoglucanase performed well in the cellulosome mode, but the family 6 exoglucanase exhibited an “antiproximity” effect and was inappropriate for use as a component in designer cellulosomes.

The designer cellulosome approach was also used to examine the interplay of prominent cellulosomal and noncellulosomal cellulases from C. thermocellum on crystalline cellulose.50 In this case, the targeting effect was found to be the major factor responsible for the synergism among the enzyme combinations whereas the proximity effect appeared to play a negligible role. Thus, designer cellulosome complexes may exhibit both of these effects, either singly or in combination, depending on the characteristics (specific enzymes, composition and organization of scaffoldin, linker regions, etc.) of the individual system and its relationship to the status of the substrate. The phenomena that cause the synergistic effect seem to depend on the characteristics of the specific enzyme combination used to fabricate the designer cellulosome and the properties of the component parts vary with each study.

In 2006, the complete conversion of the free enzyme system of the aerobic thermophile bacterium T. fusca into the cellulosomal mode was initiated. This highly cellulolytic bacterium possesses a set of only six cellulases and four xylanases. This finite and manageable panel of enzymes allows the very attractive possibility of converting the entire enzymatic system into the cellulosomal mode, which eliminates the difficulties in selecting enzymes from a highly diverse set for inclusion into designer cellulosomes. At first, the cellulases were engineered into chimeric cellulosomal enzymes by replacing their native CBM with a dockerin of divergent specificity. Several designer cellulosome complexes exhibited enhanced cellulose-degrading activity as compared with the free wild-type enzyme degradation.49,51–53 The significance of linker length and dockerin position in enzyme design was examined,51 and it was established that linker length had apparently no influence on the activity of the chimaeras. However, the position of the dockerin in the chimeric enzymes appeared to be an important parameter.

The combined action of cellulases and xylanases together in the same designer cellulosome complex served to enhance the combined synergistic activities of the enzymes toward a natural complex wheat straw substrate.54 While preparing different classes of designer cellulosomes—those that contain only cellulases, those that contain only hemicellulases, and those of mixed composition—the advantages of using the mixture of enzymes in a single cellulosome for degradation of the wheat straw substrate were demonstrated, suggesting a strong proximity effect among cellulases and xylanases.55 Thus, the entire xylanolytic system of T. fusca was assembled into a defined designer cellulosome complex and its combined saccharolytic activity was compared versus that of the free xylanase system. The data demonstrated enhanced synergistic activities for the xylanolytic designer cellulosomes on the natural recalcitrant wheat straw substrate degradation.56 In parallel, another article reported the constructions of several divalent designer “xylanosomes” that performed higher xylanolytic activities on arabinoxylan and destarched corn bran when compared with that of the free enzymes.57

Very recently, the designer cellulosome technique was pushed to its apparent limit (six different chimeric dockerin-bearing enzymes from T. fusca bound at specific locations onto a hybrid scaffoldin).58 The artificial designer cellulosome complexes obtained were comparable in size with natural cellulosomes. Evidence for proper assembly and stability was provided, and their enzymatic activity on raw substrates (pretreated on not) was compared with those of the free enzyme system and of natural cellulosomes. The action of these designer cellulosomes on untreated wheat straw exhibited a 1.6-fold enhancement toward the combination of wild-type enzymes and was 33–42% as efficient as the natural cellulosomes of C. thermocellum. The reduction of substrate complexity by pretreatment of the wheat straw substrate allowed complete conversion of the substrate into soluble saccharides by native cellulosomes. However, the pretreatment removed the advantage of the designer cellulosomes because the free enzymes displayed higher levels of activity, indicating that enzyme proximity between these selected enzymes was less significant on pretreated substrates.

An overview of the methodologies essential for designing and examining cellulosome complexes was published recently.59

4.2.5 Fatigue tests

Besides static tensile loading tests, dynamic tests are also in use; however, there is less literature about structure–function relationships of tendon and ligament tissue under dynamic conditions than under static conditions. Fatigue loading tests under high loads are not only interesting in terms of elucidating fatigue-induced tendon or ligament injuries, but also with regard to the usually monotonic increase in peak strains found with increasing cycles and the structural changes causing this observed behavior. Combinations of fatigue tests with imaging methods such as polarized light imaging may help to reveal the structural changes that lead to increasing peak strains during fatigue loading, for example as discussed for the changes in the crimp pattern (Freedman et al., 2015). Murine PT were used and the changes in crimp frequency and amplitude were assessed as a function of time (cycle number) and of locality (mid-substance versus insertion site; center versus lateral) during fatigue loading and polarized light imaging. The experimental conditions and the loading protocol are summarized in Fig. 4.8. As a result, cycle number was a significant factor for peak strain, tangent stiffness, hysteresis, and laxity at all different localities tested. While fatigue loading, peak strain, tangent stiffness, and laxity increased, the hysteresis decreased. As for the crimp pattern, crimp frequencies decreased and crimp amplitudes increased with increasing cycles at 0.1 N (representing the toe region in a typical load–displacement curve). As such, nondestructive real-time monitoring during fatigue loading at low cost elucidated biomechanical changes in correlation to structural changes—which may be used as a tool in diagnostics (Freedman et al., 2015).

It is not just tendon and ligament tissues that may be subjected to fatigue tests. In order to test tendon replacement (bio)-materials for their suitability to act as substitutes at corresponding defect sites, dynamic biomechanical testing may be of interest. For example, Altman et al. examined silk as an optional material for tissue engineering of anterior cruciate ligament (ACL). They assessed the fatigue performance of single silk fibers at different temperatures (37°C and 90°C-treatment in order to remove the glue-like sericin) as well as hierarchically fabricated 6-corded ACL matrix (Altman et al., 2002). Single pull-to-failure testing was performed at a strain rate of 100%/s. Cycles to failure at ultimate tensile strength, 1680 and 1200 N, were determined using a H-sine wave function at 1 Hz.

Microscale physiological functions

If the previous section appeared as a laundry list of binding possibilities, this section will, as a compensation, provide only a few selected examples of structure-function relationships at the molecular scale. To start, let us first examine the force-extension relation of HA. Using an optical tweezer, a system that utilizes laser light to trap particles [83], single HA molecules were attached by covalent cross-links to two amino-modified polystyrene beads and stretched at a constant rate of 45 nm/s at room temperature [84]. The extension of the HA molecule was determined as the distance between the two beads, a larger immobilized and a smaller monitored by interferometry, whereas the force was computed as the product of the bead-trapping stiffness and the displacement of the small bead. A typical force-extension curve is shown in Fig. 8.6A.

To interpret the experimental results, two versions of the worm-like chain (WLC) model were fitted to the measured force (F)-extension (x) data. The first is the approximate solution to the polymer stretching problem (Eq. 3.5), which was proposed to describe the deformation of a continuously bendable thin rod [85]:

(8.1)F=kBTlp141−xLc2−14+xLc

where lp is the persistence length, Lc is the contour length, T is the absolute temperature, and kB is the Boltzmann constant. Recall from Chapter 3 that the elasticity of the molecule is determined by lp, which is related to the correlations along the backbone of the chain. However, this model only includes entropic unfolding coupled with bending, but not stretching since the force diverges as x → Lc. The second model takes into account the possibility that the molecule can be stretched beyond its contour length [86]. The corresponding force-extension relation is given by the following formula (Eq. B3.30):

(8.2)x=Lc1−12kBTFlp+FS

where the parameter S is the chain’s molecular spring constant in units of force. Interestingly, the two models provided similar estimates of both lp and Lc with values of 4.5 ± 1.2 nm and 2.65 ± 1.44 μm from Eq. (8.1) and 4.4 ± 1.2 nm and 2.60 ± 1.41 μm from Eq. (8.2), respectively. The histograms of lp are also similar from the two models (Fig. 8.6B). The mean value of S from Eq. (8.2) was 5716 ± 4007 pN. The surprisingly large standard deviation may be due to the fact that the setup was not able to probe large enough forces where chain elasticity in elongation would significantly contribute. Nevertheless, an average spring constant of HA can be estimated as k=SLc=2.16 mN/m. While this number depends on Lc, in Chapter 3, we obtained an expression for Young’s modulus of the WLC (Eq. 3.7):

(8.3)Y=4lpkBTπRe4

where Re is the equivalent or axially averaged radius of the molecule, assuming a cylindrical shape. Since in the extended and partially relaxed state, AFM measurement-based diameter estimates of HA chains are between 0.5 and 0.6 nm, Eq. (8.3) predicts that Y is between 2.9 and 6 GPa. It may be surprising that these values are similar to the stiffness of the collagen molecule, which is a triple helix reinforced by hydrogen bonds (see Chapter 3). Notice, however, that Eq. (8.3) is most sensitive to small changes in radius because Re in the denominator is raised to the power 4. The values of Re can depend on various factors such as the hydration level, the tonicity of the solution, and it also fluctuates along the chain. This only shows the difficulty of applying continuum mechanical concepts such as that in Eq. (8.3) to phenomena at the molecular scale. It is also important to remember that many PGs and proteins bind to HA in the ECM in vivo and the mode of deformation is not uniaxial stretch. Indeed, the HA-hyalectan network in cartilage undergoes mostly compression and the HA-containing pericellular coating of endothelial cells, called glycocalyx, in the vasculature primarily receives shear stresses.

A useful method to study the properties of thin polymer layers in compression is the AFM. To determine the compressive modulus of a layer of HA, an interesting method was developed that combined the AFM technology with reflection interference contrast microscopy (RICM) [87]. The AFM was employed to determine the force applied to an approximately 500-nm-thick layer of HA attached to a glass slide during gradual compression from the top while an inverted microscope was used to detect reflected light from the probe. As the spherical AFM tip approached the glass compressing the HA layer, characteristic circular Newtonian fringe patterns developed in the RICM images as a function of the distance between the tip of the colloidal probe and the glass surface (see the setup in Fig. 8.7A). Knowing the geometry and the wavelength of the light, the absolute distance between the probe and the top surface of the glass can be calculated from the circular fringe patterns. The compressive strain is simply obtained as the change in thickness over the undeformed thickness of the layer. The calculation of stress is much more involved and requires considering the energy of the compressed layer treated as a polymer brush. We do not reproduce these calculations here; rather, just present the final results. Fig. 8.7B shows the stress-strain curve of the HA layer. As the probe starts to compress the layer, the stress first increases linearly with a slope of 0.17 kPa (red dashed-dotted line), which is also the low-strain Young’s modulus Y in compression. As the compression progresses, the stress increases nonlinearly and the corresponding Y is depicted in the inset reaching a maximum value of 2 kPa for a strain of ~ 0.75. These values are six orders of magnitude smaller than the estimated value of Y of a single molecule in axial stretching. Thus, under compression, the HA layer behaves as an extremely soft material. The mechanism behind the tiny value of the modulus is that the tethered HA chains occupy a highly folded configuration and can easily fold and buckle further under compressive forces. The reason is that the 500 nm layer thickness is about 6 times smaller than the contour length of HA molecules (Lc = 2.86 μm) with a molecular weight of 1.08 MDa [87].

Since these experiments were carried out at physiological conditions including proper ionic strength and pH, the layer and its properties may be considered a reasonable model of the pericellular matrix. However, the modulus of chondrocyte pericellular matrix in healthy cartilage was found to be ~ 40 kPa [88]. Although it does not appear to be clear what the reasons are behind this difference of ~ 20-fold, recall that there is a million-fold difference in Y when a single HA molecule is stretched and when thousands of HA molecules are compressed. Thus, one possibility that may explain the difference in stiffness between a real pericellular matrix and the HA layer is the mode of deformation. The AFM probing the HA layer generates compression. On the contrary, the modulus of excised chondrocyte pericellular matrix was measured using the micropipette aspiration technique, which imposes a different mode of deformation on the matrix certainly involving both compression and stretching. Another possibility is that the HA layer does not contain PGs. Using the optical tweezers method, the force-extension relation of a single HA chain decorated with aggrecans was studied during both compression and elongation [89]. Although modulus values were not derived from the raw data, interesting insight is still available. When the aggregate was compressed, there was no detectable force between 0.7Lc and 0.3Lc, indicating that in this regime, a collapse or buckling phenomenon took place, possibly similar to the low strain modulus region of the pure HA layer in Fig. 8.7B. Continuing compression below 0.3Lc generated a nonlinearly increasing force resisting further deformation. The interesting finding is that the same experiment on pure HA developed measurable resistance to compression only below 0.05Lc. This then suggests that the presence of PGs in the pericellular matrix significantly adds to the stiffness of the matrix. The Poisson-Boltzmann model of PGs, described in some detail in Chapter 7, suggested that electrostatic forces arising from the repulsion between neighboring charged GAGs along the PG backbone account for about half of the equilibrium compressive modulus of cartilage, which, at the macroscale, provides the physiological stiffness of cartilage tissue resisting compression [90]. Based on these arguments, the likely scenario is that HA serves as the organizing structural unit while the presence of PGs, and especially their GAG side chains, elevate the stiffness of the pericellular matrix from 2 kPa of the HA layer to 40 kPa.

As a complex 2–5-μm-thick structured layer around the cell, the pericellular matrix plays many important biological functions. For example, finite element modeling suggests that the pericellular matrix provides a protective stress shielding, but it can also amplify compressive strains reaching chondrocytes [91]. More generally, the pericellular matrix participates in transducing both mechanical and biochemical cues to the cell [92]. Thus, HA and the aggregating PGs are important determinants of the microscale structure and function of cartilage and other tissues. However, in an unexpected twist of discovery, our old network friend decorin from Chapter 7 has recently emerged and found to orchestrate many of the mechanical and biological functions of the pericellular matrix in cartilage [93]. It would not be too surprising, if decorin also influenced pericellular matrixes in other tissues.

3.2.4 Examples for operando studies of doped SnO2 sensing materials

Operando studies of gas-sensing materials provide insights in the relation between the structure, material properties and the function of the gas-sensing materials. The understanding of structure-function relationships enables the knowledge-based design of gas-sensing materials as an alternative to the trial-and-error-based development of sensing materials. The potential of this approach is demonstrated by investigations on the gas detection mechanism of undoped and doped SnO2 gas-sensing materials, which will be discussed in the following section.

Understanding the working principle of undoped, that is, pristine, SnO2 is the basis for investigations on doped, that is, noble metal loaded, SnO2 sensing materials. The current model for undoped SnO2 was successively improved based on theoretical calculations/modeling and experimental results obtained with operando methods. The detection of reducing gases on undoped SnO2 is based on the reaction of the analyte gas with preadsorbed oxygen (Fig. 3.18A). This reaction is based on the ionosorption of atmospheric oxygen, which causes an electron depleted surface layer. The extent of this depletion layer depends on the concentration of ionosorbed surface oxygen, which is determined by the adsorption and desorption of atmospheric oxygen and the reaction of ionosorbed oxygen with the reducing gas [212]. However, undoped SnO2 also responds to reducing gases in the absence of oxygen. The presence of reducing gases causes an electron accumulation layer, which initially was ascribed to the formation of analyte gas related donor species, for example, CO+ or H+, in the absence of atmospheric oxygen [304,317]. The transition from depletion to accumulation controlled conduction is demonstrated by simultaneous work function and resistance measurements (see Fig. 3.16). The formation of such an accumulation layer in ambient conditions, that is, in the presence of oxygen and water vapor, casted doubts on the existence of an analyte gas related donor species. In order to determine the nature of the electronic donor species, which causes the accumulation layer, the surface chemistry of undoped SnO2 was studied by operando IR spectroscopy. The spectra revealed that in dry and humid air, as well as in the absence of oxygen, the gas reception is based on the same surface reactions, namely the reaction of the analyte gases (CO, H2, and H2O) with surface oxygen forming oxygen vacancies, which act as electron donor. The surface concentration of oxygen vacancies depends on the reduction of the surface by the analyte gases and the (re-)oxidation by atmospheric oxygen [257]. If the surface concentration of oxygen vacancies is lower than in the bulk of the SnO2 grains, a depletion layer is formed, while when the concentration of oxygen vacancies at the surface exceed the one in the bulk an accumulation layer is formed. The gas reception via the reduction of the SMOX sensing material is also shown for WO3 [265] and In2O3 [230,231] by using operando IR or Raman spectroscopy, respectively. This reception mechanism can be altered or completely changed by the presence of noble metal loadings (Fig. 3.18).

The influence of noble metal loadings on SMOX sensing materials is rather complex, but the general sensitization mechanisms are distinguished: A solely chemical sensitization, for example, by the improved adsorption and spill-over of the reactive species, or a dominantly electrical effect based on the electronic coupling of noble metals with the SMOX; the latter case may also involve changes of the chemical reactions [294,319,320].

Loading SnO2 with Au particles is a well understood example for a spill-over sensitization mechanism, which solely changes the chemical processes without affecting the electronic properties of the SMOX [284,321]. It was found, using operando XAS, that Au is always present in the metallic state and that the oxidation state is not affected by the composition of the atmosphere [284,321]. The presence of these metallic Au clusters improves the CO oxidation and CO sensing [284]. The sensitization by an electronic interaction, that is, charge transfer, between SnO2 and the Au clusters was excluded by operando work function measurements and, like for undoped SnO2 (Fig. 3.16), the flat-band situation is found in nitrogen. Thus, there are no intrinsic electronic states and the space charge layer at the grain surface is determined by the ionosorption and the reactions of surface oxygen species [284]. The comparative study of undoped and different Au-doped SnO2 materials shows, that there is a strong enhancement of the oxygen ionosorption rather than an improved CO adsorption [321]. This is in line with operando XAS and DRIFTS measurements, which indicate an interaction of O2 with Au and an increased oxidation of the SnO2 surface, but do not show adsorbed CO species [321]. The sensitization mechanism of Au on SnO2 is summarized in Fig. 3.18B: O2 is adsorbed on metallic Au clusters and subsequently dissociated, transferred to and ionized by SnO2; the increased concentration of surface oxygen increases the reactivity of the surface and consequently the sensor signals, while the basic reception and transduction mechanism of undoped SnO2 is not changed.

Significant changes in the chemical and electronic properties are observed in the case of Pt-doped SnO2 materials. The changes, and consequently the gas-sensing performance, depend on the Pt structure, which is determined by the introduction method for the noble metal. Taking sol-gel-made SnO2 as an example, the Pt precursor can be introduced before [322] or after [323] the calcination of the as prepared powder. If Pt is introduced before the calcination, the sensor signals to CO are only slightly affected by humidity and are decreased compared to the ones of undoped SnO2 in dry conditions, but in humid air higher than the ones of undoped SnO2 [289]. However, if Pt is introduced after the calcination, the sensor signals to CO in dry air are significantly lower than the ones of undoped SnO2, but in humid air the materials show the highest sensor signals to CO [289]. The fundamental difference of both Pt-doped SnO2 materials is found in the Pt structure: The evaluation of the EXAFS revealed, that if Pt is introduced before the calcination, Pt is atomically distributed in the SnO2 lattice [227], while if Pt is introduced after the calcination it forms a separate Pt oxide phase, which is in close contact with the supporting SnO2 [289]. XANES spectra recorded during the temperature programmed reduction (Fig. 3.12, left and middle) show, that in case of the atomically distributed Pt, no reduction is observed, since Pt is incorporated in the bulk and the surface of SnO2 [227], while the Pt oxide clusters are easily reduced and reoxidized [289], since they are in close contact with the atmosphere and thus at the surface of the SnO2 grains. In both cases, the operando XANES spectra recorded during gas sensing show no reduction of Pt (Fig. 3.12, right) [227,289].

The electronic and chemical effect of both Pt structures is different. In the case of atomic Pt sites, Pt, on the one hand, acts as an electron acceptor decreasing the concentration of free charge carriers and thus increasing the resistance of the material [130]. On the other hand, the Pt incorporated in the SnO2 surface acts as a reactive site increasing the surface reactivity [259]. Operando DRIFTS combined with analysis of the exhaust gases showed, that the atomically distributed Pt (Fig. 3.18C) increases the adsorption of CO and activates lattice oxygen bound to Pt [259]. The selective enhancement of CO adsorption on Pt and the increased reactivity explain the low impact of water vapor on the CO sensor signals. In the case of Pt oxide clusters on the SnO2 surface, operando DRIFTS and further resistance measurements show that the reaction takes dominantly place on the Pt oxide clusters, which are electronically coupled with SnO2, so that changes of the Pt oxide clusters’ stoichiometry change the electronic interface of Pt oxide and SnO2 and, thus, the resistance of SnO2 (Fermi-level control mechanism) [324]. In dry air, the oxidation of CO on the Pt oxide clusters causes only small changes in the stoichiometry due to the feasible reoxidation of Pt oxide. Consequently, there are only small changes in the resistance of SnO2. However, in humid air, the reoxidation is inhibited and the stoichiometry of the Pt oxide clusters is changed, releasing electrons back to SnO2, which were trapped in the Pt oxide clusters, and thus lowering the resistance of SnO2 (Fig. 3.18D). The Fermi-level control mechanism and the lack of changes in the Pt oxide phase in dry air explain the observed gas-sensing behavior of the material.

In summary, these examples demonstrate the advantage of combining suitable ex situ, in situ and operando methods to investigate the structure-function-relationships of gas-sensing materials and, thus, provide the basis to prepare tailor-made gas-sensing materials. And yet, these examples represent only a small fraction of all the different SMOXs, dopants and structures. A general understanding of the structure-function-relationships of SMOX-based gas sensors will still require extensive and systematic attempts to study gas-sensing materials by the above described methods.

8.1 Introduction: What is Materiomics?

Materials science is a well-established discipline that is familiar to many. It can be characterized as the study of how a material’s structure determines its properties (structure–function relationship) and how this understanding can be used to achieve desirable performance through appropriate processing/synthesis. An example is the control of the mechanical properties of a metal through the manipulation of the microstructure using appropriate heating, cooling, and mechanical deformation. This is a process practiced from the formation of the first wrought iron items such as nails by blacksmiths through to advanced aerospace alloys. Composites then emerged slowly over centuries to give us our existing toolkit of high-performance structural materials. The accumulated knowledge in these material systems now allows the aerospace engineer to “dial up” the materials from their database to design whole plane or individual component on a computer. In tissue engineering of scaffolds, in addition to mechanical property information we are interested in cellular adhesion, immune compatibility, cell adhesion density, phenotype, and so forth. This information is not available for the researcher who would like to “dial up” the appropriate materials to develop a device that is capable of, for example, manipulating cells to develop into a vascularized functioning organ.

The emerging field of materiomics offers a holistic approach to material systems that aims to merge materials science and biological methodologies in order to open new opportunities to discover novel and improved materials with reduced development times (Table 8.1). Materiomics studies the relationships between molecular, physicochemical, and/or processing properties of materials and their characteristics and functions. For example, the process of bone tissue growth on a calcium phosphate scaffold under controlled conditions is a materials science and biological problem, whereas understanding how bone can be grown on any material is a materiomics problem (Groen et al., 2013).

Table 8.1. A List of Key Terminology Associated with Materiomics and the Development of New Biomaterials

The TerminologyDefinitionBiomaterialsA synthetic material for application in biologyCombinatorial spaceA range of materials created by combining a smaller number of base components at various ratiosComputational modeling in materiomicsUsing statistical methods or computer-based methods to simulate and predict the behavior of materials and biological systems such as proteinsHigh-throughput screeningA method of experimentation whereby experiments are parallelized, usually through the automation of experimental procedures, such that several tests can be achieved in the time it would conventionally take to perform a single testMaterials discoveryScreening a materials space (often a combinatorial space) to discover a material optimal for a particular applicationMaterials or chemical spaceAll or a subset of materials of chemistries that exist or could theoretically be producedMathematical descriptorA mathematically derived number that describes a molecular, compositional, or physical property of a materialOntologiesControlled vocabularies that precisely describe in terms computers can understand, multiple aspects of materials, such as composition, synthesis, processing, and propertiesPolymer libraryA collection of different polymersPolymer microarrayAn experimental platform that allows hundreds to thousands of unique materials to be expressed on one support, e.g., a microscope slide, at addressable locationsSynergistic effectsWhereby a combination of components produces a property that could not be predicted from assessing the properties of the individual components

Abstract

There is a wide variety of collagen suprastructures in the body, which serve fundamental functions in different tissues both at the microscale and at the macroscale. Utilizing quantitative modeling, these structure-function relationships are discussed in three specific tissues: tendon, bone, and skin. Despite the observed strong tissue specificity, some general conclusions can be drawn, which include adaptive control of microscale stiffness for the regulation of cellular processes, optimal stiffness, toughness, and force transmission at the mesoscale and macroscale, and protection against rupture and failure at the organ and organism levels. Many of these functions are supported by not only the suprastructures, but how the suprastructures respond to mechanical forces, namely, unfolding and realignment of wavy collagen fibrils and fibers. This suggests that a wide spectrum of nonlinear recruitment processes is available for the collagenous extracellular matrix to be smart and becomes what life wants it to be.

5.5 Tissue engineering

Tissue engineering is an interdisciplinary field that has attempted to utilize a variety of processing methods with synthetic and natural polymers to fabricate scaffolds for the regeneration of tissues and organs. The study of structure-function relationships in both normal and pathological tissues has been coupled with the development of biologically active substitutes or engineered materials. The fibrillar collagens, types I, II, and III, are the most abundant natural polymers in the body and are found throughout the interstitial spaces where they function to impart overall structural integrity and strength to tissues. The collagen structures, referred to as extracellular matrix (ECM), provide the cells with the appropriate biological environment for embryologic development, organogenesis, cell growth, and wound repair. In the native tissues, the structural ECM proteins range in diameter from 50 to 500 nm. In order to create scaffolds or ECM analogues, which are truly biomimicking at this scale, one must employ nanotechnology. Recent advances in nanotechnology have led to a variety of approaches for the development of engineered ECM analogues. To date, three processing techniques (self-assembly, phase separation, and electrospinning) have evolved to allow the fabrication of nanofibrous scaffolds. With these advances, the long-awaited and much anticipated construction of a truly “biomimicking” or “ideal” tissue engineered environment or scaffold, for a variety of tissues, is now highly feasible [27].

Since there is no consensus on the gold standard for creating analogues to the native ECM, all three and even combinations of these processing techniques have been utilized to produce nanofibrous structures. Researchers used both electrospinning and phase separation to create submicron diameter fibers with pores or pits on the order of 100 nm. The appeal of nanofibers in tissue engineering is their structural similarity to native ECM; however, ECM has not only a structural role but also a functional one. This network creates a dynamic, three-dimensional microenvironment in which cells are maintained. Signals are transmitted between the cell nucleus and the ECM enabling communication between both for cell adhesion, migration, growth, differentiation, programmed cell death, modulation of cytokine and growth factor activity, and activation of intracellular signaling. In addition, the interactions between cell receptors and ECM molecules are critical for wound healing and the development of nature's provisional matrix for cellular migration, proliferation, and subsequent tissue remodeling. The influence of the ECM on cellular activities occurs via binding of specific factors to specific ECM molecules and binding of ECM molecules to cell surface receptors known as integrins, which then influence local release of growth factors or separation of molecules (for cell attachment, spreading, and growth) [28,29].

Current nanolevel processing techniques have been developed with the goal of mimicking ECM geometry. All three of the aforementioned techniques are capable of producing fibers with submicron diameters. Efforts have also been made to go beyond geometry and attempt to truly mimic the ECM in terms of physiological ability. By engineering material properties of synthetic polymer structures and surfaces, they can be made more conducive to cell adhesion and function. On the other hand, natural polymers may already contain/present signaling capabilities required by cells. Thus, materials utilized as nanofibers in tissue engineering include a variety of synthetic and natural polymers that offer advantages and disadvantages. There have been investigations into the use of xenogeneic and allogeneic ECM as tissue engineering devices, but the problems associated with this approach include age-related factors, cell lysis, and calcification. The polymers electrospun should offer the advantages of being readily available and having known degradation times and mechanical strengths. However, these synthetic polymers lack an ultrastructure that mimics ECM; thus, we are also electrospinning natural polymers, that is, native ECM proteins, as previously mentioned, for tissue engineering applications. Yet, even natural polymers have some disadvantages, including immunogenicity and variations in mechanical properties, degradation, and reproducibility [29].

The mechanical properties of the scaffolds, including tangential modulus and stress and strain to failure, can be tailored by controlling the geometry and orientation of the fibers in the scaffolds. The authors have evaluated the mechanical properties of the different PGA electrospinning concentrations in both aligned and random fiber orientation scaffolds. The overall results exhibit a correlation between the fiber diameter and orientation and the elastic modulus and strain to failure. Additionally, it has been shown that the greater surface-area-to-volume ratio of smaller fibers results in a faster loss of strength during degradation. When an initially tough (high strength and elasticity) and fast degrading material is desired, PGA is a good choice. However, the higher rate of degradation may result in sharp increases in localized pH, which may cause unwanted tissue responses if the region does not have a high buffering capacity or sufficient mechanisms for the rapid removal of metabolic waste. Biocompatibility studies have been performed by the authors, in which PGA and acid-treated PGA were evaluated in cell culture and in an animal model. Both fiber diameter and acid pretreatment influenced the in vitro and in vivo cellular responses. The acid pretreatment improved biocompatibility via a hypothesized mechanism of surface hydrolysis of ester bonds, thereby exposing carboxylic acid and alcohol groups. This may improve binding that, in turn, may improve the ability of cells to adhere to the surface [30].

When a single polymer does not have the properties desired for a tissue engineering application, a copolymer or blend (simple mixture) of polymers may be employed to achieve the desired geometric, mechanical, and biodegradation properties. Electrospinning again allows the ability to produce nanofibers of such a copolymer or blend. The incorporation of glycosaminoglycans (GAGs) into an ECM analogue during electrospinning could potentially be an important aspect in truly mimicking the native ECM. GAGs serve a variety of functions including linking collagen structures and binding growth factors. The specific GAGs of physiological and tissue engineering scaffold significance are hyaluronic acid, dermatan sulfate, chondroitin sulfate (most abundant GAG in tissues), heparin, heparan sulfate, and keratan sulfate [31–33].

The mechanical properties of the electrospun collagen-blended vascular prosthetics (Fig. 5.4) fall within the ranges of the corresponding values for traditional vascular materials. Human dermal fibroblasts seeded onto the PDO/collagen type III scaffolds displayed favorable cellular interactions; the cells migrated into the thickness of the scaffolds containing collagen but merely migrated on the seeded surface of the 100% PDO scaffold [34].

Electrospun materials composed of nanofibers have a high surface-area-to-volume ratio. This is potentially an important consideration when designing a hemostatic product. A high surface-area-to-volume ratio increases the surface area available for blood components to interact with to initiate clot formation. A fibrinogen scaffold with an average fiber diameter of 700 nm, dimensions of 60 × 60 × 0.7 mm, and weighing approximately 0.08 g has an estimated total surface area of approximately 3300 cm2. This translates into a relative surface-area-to-volume ratio of 1300 cm2/cm3 or a relative surface-area-to-weight ratio of 4.1 m2/g [34].

Development of functional tissue engineering products requires an appropriate scaffolding to mimic the native ECM. Current research in tissue engineering is approaching a major breakthrough in the treatment of injury and disease due to the ability to routinely create ECM analogous nanofibers. Since the inception of the field of tissue engineering, many methods have evolved from the simple concept of placing cells in a degradable scaffold to building native tissues either in vivo or in vitro. These advances come on the heels of advances in the life sciences that provide critical information about the nature and development of tissues and diseases. Ultimately, engineers must match applications, materials, and fabrication processes to best meet the needs of the tissue they wish to build. It is anticipated that nanotechnology will be a key component in the development of the next generation of scaffolds, particularly with respect to the fabrication component [35,36].

Recently, nanomaterials derived from natural renewable resources have drawn much attention in the nanotechnology research thrust. Lignocelluloses are composed of cellulosic nanofibrils that can be disintegrated by chemical, mechanical, and enzymatic methods in order to obtain nanocellulose. Further, nanocellulose can also be synthesized by bacterial method in a suitable culture. Nanocelluloses have many interesting properties (viz., nanodimension, renewability, low toxicity, biocompatibility, biodegradability, easy availability, and low cost) that make them ideal nanomaterials for diverse applications. Various methods of nanocellulose preparation and their properties, surface modifications of nanocellulose, and applications of nanocellulose in the diverse fields of tissue regeneration have been explored. Some typical nanocellulosic tissues are shown in Fig. 5.5 [36].

Nanocellulosic materials have many interesting properties (such as nontoxicity, biodegradability, renewability, and biocompatibility) that make them ideal candidates for many potential applications. Nanocellulose can be extracted from the lignocellulosic biomass by using various methods that influences their properties. There are enormous potential for the nanocellulosic materials that includes nanocomposites membrane, hybrid film, hydrogel, and aerogel that are few of many to states. Cellulose nanomaterials could have wide applications in food packaging energy, water treatment, biomedical filed, etc. Further, nanocellulose derived from the bacterial synthesis has proved as a promising biomaterial for various biomedical applications such as tissue engineering, drug delivery, wound dressing, and cardiovascular applications. It is hoped that comprehensive further research for the utilization of huge renewable lingo cellulosic biomass for the preparation of nanomaterials could be useful in diverse applications [36].

17.7 Conclusion

The development of catalysts that can achieve a high activity and selectivity for the ORR is imperative to ensure a broader commercial viability of PEFCs. The techniques discussed in this chapter provide insights into some of the fundamentals needed to understand the structure–function relationships of the catalyst. The development of catalyst materials for PEFCs is an evolving field, and the examples provided herein are only a fraction of what has been developed and demonstrated in the literature. This chapter highlights the achievements in the field to demonstrate the diversity of these advancements and to inspire further development of new catalyst materials and structures. A particular focus herein is on tuning the composition and structure of the catalyst to minimize the amount of Pt and to maximize its utilization. An overall aim is to decrease the cost of PEFCs to enable their widespread adoption.

Optimization of PEFCs requires more than fine tuning the design and components of the fuel cell. Further correlations of experimental results with theory are required to continue to guide the field. Additional detailed studies and ongoing scientific research are still required to assess the individual components of the fuel cell to improve its overall performance and durability. It is imperative to remember the variations in the properties between different materials and different structures when developing and evaluating potential catalysts. Trends specific to a particular composition, as an example, are often overlooked in favor of comparing and contrasting results with the trends observed for Pt NPs. These trends do not, however, always hold true for all catalyst compositions and structures. Although Pt is currently the benchmark PEFC catalyst, a lot of room remains to develop catalysts that can outperform Pt in both acidic- and alkaline-based systems. It will require that the fundamental properties of these catalysts are taken into consideration when designing alternatives.

It is often necessary to break away from the confines of conventional development and explore new directions to produce the best possible results. We hope that the information presented in this chapter will aid you in your own pursuit of PEFC catalysts with improved performance and durability. Furthermore, we hope that the optimization of these catalysts can increase the economic feasibility and commercial viability of PEFCs and improve their competitiveness in the marketplace when compared to fossil fuel-based energy sources.

What is the relationship between a structure and a function?

What is the relationship between structure and function quizlet?

Which best describes the relationship between structure and function?

What is the relationship between structure and function human biology?