Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Transdermal enhancement through rat skin of luciferase plasmid DNA loaded in elastic nanovesicles

Transdermal absorption of luciferase plasmid (pLuc) was enhanced by loading in elastic cationic liposomes and niosomes and the application of iontophoresis or the stratum corneum (SC) stripping method. Cationic liposomes (DPPC/Chol/DDAB at a 1:1:1 molar ratio) and niosomes (Tween61/Chol/DDAB at a 1:1:0.5 molar ratio) were prepared by the freeze-dried empty liposomes method. The elastic vesicles were prepared by hydrating the lipid or surfactant film by 25% of ethanol instead of distilled water. Gel electrophoresis of all nanovesicles showed the 100% pLuc entrapment efficiency. All nanovesicles loaded with pLuc showed larger vesicular sizes than the nonloaded vesicles of about 1.4 times for liposomes and 1.7 times for niosomes. The nanovesicles loaded with pLuc demonstrated less positive zeta potential than the nonloaded vesicles. The pLuc loaded in elastic vesicles kept at 4 ± 2 and 27 ± 2°C for 8 weeks gave the remaining pLuc of about 70 and 60% for liposomes and 85 and 73% for niosomes, respectively. For nonelastic vesicles kept at 4 ± 2°C, 56 and 61% of the remaining pLuc were observed for liposomes and niosomes, respectively, while at 27 ± 2°C, all pLuc were degraded. The deformability indices of the elastic liposomes and niosomes loaded with the pLuc were 16.64 ± 2.92 and 20.72 ± 0.82, whereas the nonelastic vesicles gave 9.35 ± 0.09 and 10.08 ± 0.12, respectively. Transdermal absorption through rat skin pretreated with SC stripping or treated with iontophoresis of pLuc loaded in nanovesicles by vertical Franz diffusion cells was investigated at 37°C. The cells were stopped and the skin and the receiving solution were withdrawn at 1, 3, and 6 hours and the pLuc contents in the stripped SC, whole skin (viable epidermis and dermis; VED), and the receiving solution were assayed by the modified gel electrophoresis and gel documentation. Without the SC stripping technique or iontophoresis, the pLuc loaded and nonloaded in nonelastic cationic liposomes or niosomes were not found in SC, VED, and receiving solution. The fluxes in the whole skin of pLuc loaded in nonelastic liposomes and niosomes with SC stripping and iontophoresis at 6 hours gave 2.73 ± 0.46 and 3.83 ± 0.73, and 7.01 ± 1.22 and 9.60 ± 1.31 g/cm²/h, respectively, while pLuc loaded in elastic liposomes and niosomes without the SC stripping and iontophoresis at 6 hours showed 2.79 ± 0.09 and 2.84 ± 0.04 g/cm²/h, respectively. The pLuc loaded in elastic niosomes or in nonelastic niosomes with iontophoresis was found in the receiving solution with a higher amount than that loaded in elastic liposomes or nonelastic liposomes with iontophoresis. The fluxes in the receiving solution of pLuc loaded in nonelastic liposomes and niosomes with iontophoresis at 6 hours were 6.71 ± 0.31 and 8.82 ± 0.28 g/cm²/h, respectively. For elastic liposomes and niosomes, the fluxes of the loaded pLuc in the receiving solution were the same, at about 1.9 g/cm²/h. Although pLuc loaded in nonelastic niosomes with iontophoresis gave the highest delivery of the plasmid in VED and receiving solution, a more promising applicable approach for gene delivery has been suggested to be the elastic niosomal systems, since no equipment is required.     

Ridge crest versus swale: contrasting plant–water relations and performance indexes in two understory plant species in a coastal maritime forest

Coastal-ridge plains are progradational landforms composed of elevated ridges and low-lying swales. The transitions between ridges and swales are steep, promoting dynamic shifts between xeric and mesic systems. Two understory plants that co-occur in ridge plains of North American mid-Atlantic maritime forests are Sabal minor and Ilex vomitoria. As coastal-ridge plains foster varying amounts of surface and sub-surface water driven largely by topography, the purpose of this study was to evaluate plant–water relations and chlorophyll a fluorescence in these two species. Ridge plants had lower leaf- and xylem-water potentials, lower osmotic potential (I. vomitoria), and lower symplastic water content (S. minor). Although there were no differences in potential- and effective-quantum yields, there were decreases in fluorescence performance index for ridge I. vomitoria and swale S. minor. While the data support potential water-stress conditions in ridge plants of both species, the data also suggest that I. vomitoria and S. minor use different physiological processes to tolerate hydrologically dynamic ridge–swale maritime forests.     

The plant cell pressure probe

The pressure probe is a micro manometer for the simultaneous direct recording and manipulation of plant cell hydrostatic pressure. It is used to map in space and time the turgor pressures of individual cells within tissues and organs of intact plants. This is used to study the hydraulic architecture of tissues, tissue movement and the responses of tissues to water stress. The approach can be augmented by simultaneous measurement of individual cell osmotic pressure. This permits the hydraulic driving forces across selectively permeable membranes and walls to be assessed fully. By manipulating manually the pressure, cell wall elasticity and its properties can also be mapped. Under some conditions this can be extended to plastic behaviour.     

Mechanics,Structure and Function of Biopolymer Condensates

The spontaneous nature of biopolymer phase separation in cells entails that the resulting condensates can be thermodynamic machines, which, in the process of condensing, can take on distinct forms themselves and deform neighboring cellular structures. We introduce here general notions of material and mechanical properties of protein condensates with an emphasis on how molecular arrangements and intermolecular interaction within condensates determine their ability to do work on their surroundings. We further propose functional implications of these concepts to cellular and subcellular morphology and biogenesis.     

Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse‐grained modeling

The PIEZO channels, a family of mechanosensitive channels in vertebrates, feature a fast activation by mechanical stimuli (eg, membrane tension) followed by a slower inactivation. Although a medium‐resolution structure of the trimeric form of PIEZO1 was solved by cryo‐electron microscopy (cryo‐EM), key structural changes responsible for the channel activation and inactivation are still unknown. Toward decrypting the structural mechanism of the PIEZO1 activation and inactivation, we performed systematic coarse‐grained modeling using an elastic network model and related modeling/analysis tools (ie, normal mode analysis, flexibility and hotspot analysis, correlation analysis, and cryo‐EM‐based hybrid modeling and flexible fitting). We identified four key motional modes that may drive the tension‐induced activation and inactivation, with fast and slow relaxation time, respectively. These modes allosterically couple the lateral and vertical motions of the peripheral domains to the opening and closing of the intra‐cellular vestibule, enabling external mechanical forces to trigger, and regulate the activation/inactivation transitions. We also calculated domain‐specific flexibility profiles, and predicted hotspot residues at key domain‐domain interfaces and hinges. Our results offer unprecedented structural and dynamic information, which is consistent with the literature on mutational and functional studies of the PIEZO channels, and will guide future studies of this important family of mechanosensitive channels.     

Altered dynamics upon oligomerization corresponds to key functional sites

It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse‐grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422–1434. © 2017 Wiley Periodicals, Inc.     

Thermodynamics of ABC transporters

ABC transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. However, despite such advances, the precise mechanisms that determine the energy-coupling between ATP hydrolysis and the conformational changes following substrate binding remain to be elucidated. Here, we present our thermodynamic analysis for both ABC importers and exporters, and introduce the two new concepts of differential-binding energy and elastic conformational energy into the discussion.We hope that the structural analysis of ABC transporters will henceforth take thermodynamic aspects of transport mechanisms into account as well.     

Physiological responses of different olive genotypes to drought conditions

Gas exchange rates, chlorophyll fluorescence, pressure–volume relationships, photosynthetic pigments, total soluble sugars, starch, soluble proteins and proline concentrations were investigated in five Olea europaea L. cultivars with different geographical origins (Arbequina, Blanqueta, Cobran?osa, Manzanilla and Negrinha) grown under Mediterranean field conditions. We found considerable genotypic differences among the cultivars. Comparing the diurnal gas exchange rates, we observed that Cobran?osa, Manzanilla and Negrinha had high photosynthetic rate than Arbequina and Blanqueta. The first group reveals to be better acclimated to drought conditions, and appears to employ a prodigal water-use strategy, whereas Blanqueta and Arbequina, with high water-use efficiency, appear to employ a conservative water-use strategy. The degree of midday depression in photosynthesis was genotype dependent, with a maximum in Arbequina and a minimum in Negrinha. The reductions in the photosynthetic rate were dependent from both stomatal and non-stomatal limitations. Elastic adjustment plays an important role as drought tolerance mechanism. The group of cultivars that employ a prodigal water-use strategy revealed high tissue elasticity, whereas Arbequina and Blanqueta revealed high tissue rigidity. We also identified the existence of drought tolerance mechanisms associated with soluble proteins accumulation in the foliage. The high levels of soluble proteins in Arbequina may represent an increased activity of oxidative stress defence enzymes and may also represent a reserve for post stress recovery. In all cultivars, especially in Manzanilla, free proline was accumulated in the foliage. The discussed aspects of drought stress metabolism may have an adaptative meaning, supporting the hypothesis that olive cultivars native to dry regions, such as Cobran?osa, Manzanilla and Negrinha, have more capability to acclimate to drought conditions than cultivars originated in regions with a more temperate climate, like Arbequina and Blanqueta.     

Iterative cluster-NMA: A tool for generating conformational transitions in proteins

Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of beta1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed.