Biophysical Interpretation of Evolutionary Consequences on the SARS-CoV2 Main Protease through Molecular Dynamics Simulations and Network Topology Analysis.

In this study, we present a combined analysis procedure between atomistic molecular dynamics (MD) simulations and network topology to obtain more understanding on the evolutionary consequences on protein stability and substrate binding of the main protease enzyme of SARS-CoV2. Communicability matrices of the protein residue networks (PRNs) were extracted from MD trajectories of both Mpro enzymes in complex with the nsp8/9 peptide substrate to compare the local communicability within both proteases that would affect the enzyme function, along with biophysical details on global protein conformation, flexibility, and contribution of amino acid side chains to both intramolecular and intermolecular interactions. The analysis displayed the significance of the mutated residue 46 with the highest communicability gain to the binding pocket closure. Interestingly, the mutated residue 134 with the highest communicability loss corresponded to a local structural disruption of the adjacent peptide loop. The enhanced flexibility of the disrupted loop connecting to the catalytic residue Cys145 introduced an extra binding mode that brought the substrate in proximity and could facilitate the reaction. This understanding might provide further help in the drug development strategy against SARS-CoV2 and prove the capability of the combined techniques of MD simulations and network topology analysis as a "reverse" protein engineering tool.

Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations.

The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0-32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.

The Relationship between the Morphology and Elasticity of Natural Rubber Foam Based on the Concentration of the Chemical Blowing Agent.

Concentrated natural latex was used to produce a rubber foam that is porous, elastic and well ventilated. The mechanical properties can be either soft or firm, depending on the formulation of the latex used. Briefly, concentrated natural latex was mixed with chemical agents to make the rubber foam on a laboratory scale using the Dunlop process. In this work, we changed the concentration of the chemical blowing agent in the latex. The morphological properties of the rubber foam were characterised using scanning electron microscopy, and the mechanical properties, or elasticity, were studied using compression experiments and the Mooney-Rivlin calculation. The results show that the concentration of the chemical blowing agent affects the morphological properties of the rubber foam but not the mechanical properties, indicating the heterogeneous structure of the rubber foam. The thermodynamic parameters (∆G and ∆S) and the internal energy force per compression force (Fu/F) of the rubber foam with various amounts of chemical blowing agent were also investigated. This study could be applied in the foam industry, particularly for pillow, mattress and insulation materials, as the present work shows the possible novel control of the morphological structure of the rubber foam without changing its mechanical properties. The difference in cell sizes could affect the airflow in rubber foam.

Current challenges in thermodynamic aspects of rubber foam.

Natural rubber (NR) foam can be prepared by the Dunlop method using concentrated natural latex with chemical agents. Most previous studies have focused on the thermodynamic parameters of solid rubber in extension. The main objective of this study is to investigate the effect of the NR matrix concentration on the static and dynamic properties of NR foams, especially the new approach of considering the thermodynamic aspects of NR foam in compression. We found that the density and compression strength of NR foams increased with increasing NR matrix concentration. The mechanical properties of NR foam were in agreement with computational modelling. Moreover, thermodynamic aspects showed that the ratio of internal energy force to the compression force, Fu/F, and the entropy, S, increased with increasing matrix concentration. The activation enthalpy, ∆Ha, also increased with increasing matrix concentration in the NR foam, indicating the greater relaxation time of the backbone of the rubber molecules. New scientific concepts of thermodynamic parameters of the crosslinked NR foam in compression mode are proposed and discussed. Our results will improve both the knowledge and the development of rubber foams based on the structure-properties relationship, especially the new scientific concept of the thermodynamical parameters under compression.

Performance of Nano- and Microcalcium Carbonate in Uncrosslinked Natural Rubber Composites: New Results of Structure-Properties Relationship.

Calcium carbonate (CaCO3) is one of the most important inorganic powders and is widely used as filler in order to reduce costs in the rubber industry. Nanocalcium carbonate reduces costs and acts as a semireinforcing filler that improves the mechanical properties of rubber composites. The objective of this study was to investigate the effect of nano-CaCO3 (NCC) and micro-CaCO3 (MCC) on the properties of natural rubber composites, in particular, new results of structure-properties relationship. The effects of NCC/MCC on the properties of rubber composites, such as Mooney viscosity, bound rubber, Mullins effect, and Payne effect, were investigated. The result of the Mullins effect of rubber composites filled with NCC was in good agreement with the results of Mooney viscosity and bound rubber, with higher Mooney viscosity and bound rubber leading to higher stress to pull the rubber composites. The Payne effect showed that the value of different storage moduli (ΔG') of rubber composites filled with 25 parts per hundred rubber (phr) NCC was the lowest due to weaker filler network, while the rubber supplemented with 100 phr NCC had more significant ΔG' values with increase in strain. The results of rubber composites filled with MCC showed the same tendency as those of rubber composites filled with NCC. However, the effect of specific surface area of NCC on the properties of rubber composites was more pronounced than those of rubber composites filled with MCC. Finite element analysis of the mechanical property of rubber composites was in good agreement with the result from the experiment. The master curves of time-temperature superposition presented lower free volume in the composites for higher loading of filler, which would require more relaxation time of rubber molecules. This type of nanocalcium carbonate material can be applied to tailor the properties and processability of rubber products.

Distinct ionic adsorption sites in defective Prussian blue: a 3D-RISM study.

Ferric hexacyanoferrate (FeHCF) or Prussian blue (PB) exhibits selective alkali ion adsorption and has great potential for use in various applications. In the present work, alkali ion (Li+, Na+, K+, and Cs+) and water configurations in defective PB (d-PB) were studied by using the statistical mechanics of molecular liquids. The three-dimensional (3D) distribution functions of the ions and water were determined by solving the 3D-reference interaction site model (RISM) equation of systems of a unit lattice of d-PB in electrolyte solutions, i.e., LiCl, NaCl, KCl, and CsCl. The results show the difference in the ion-water configurations and distributions between small (Li+ and Na+) and large ions (K+ and Cs+). The adsorption sites of Li+ and Na+ are located off-center and lie on the diagonal axis. By contrast, the larger ions, K+ and Cs+, are adsorbed at the center of the unit cell. The degree of dehydration due to the adsorption of alkali ions indicates that there was no water exchange during Li+ and Na+ adsorption, whereas two and three water molecules were removed after adsorption of K+ or Cs+ in the unit cell.

Molecular dynamics study of natural rubber-fullerene composites: connecting microscopic properties to macroscopic behavior.

Macroscopic and microscopic properties of fullerene (C60)-cis-polyisoprene (cis-PI) composites at varying fullerene concentrations were investigated using atomistic molecular dynamics (MD) simulations over microsecond time scales. Results show that the introduction of fullerenes into a polymer matrix increases density, bulk modulus and heat capacity while thermal expansivity decreases. The presence of fullerenes slowed the diffusion of both C60 and cis-PI. Moreover, increasing fullerene concentration results in ordering of the cis-PI chains at the cis-PI-fullerene interfaces and shrinking of bulk PI regions. Free energy calculations of fullerene dimerization suggest that fullerenes disperse at low and aggregate at high fullerene concentrations. Our multi-scaled analysis approach demonstrates the role of 'ordered' regions adjacent to the interface between cis-PI and fullerene in controlling the level of order and mobility of the cis-PI chains. The relationship between the microscopic behavior and the changes in mechanical and thermal properties are discussed. Our study is beneficial for further studies and development of advanced rubber technology for novel, cost-effective, material with very high stiffness and thermal endurance with optimizing conditions of filler contents.

A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase.

The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. The binding affinity or the binding free energy of ligand to receptor was found to be determined by a subtle balance of two major contributions that largely cancel out each other: the ligand-receptor interactions and the dehydration free energy. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50 ; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated residue, is the main source of high-level oseltamivir resistance. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site.

Molecular recognition explored by a statistical-mechanics theory of liquids.

"Molecular recognition" is one of the most important molecular processes for living systems in order to maintain their life, since most of the biological functions are initiated with the process. Understanding of the process is also important for designing a new drug. Firstly, it is important to find a target of a drug, which is in many cases a function of protein or DNA to be inhibited. Secondly, binding a drug molecule to the active site of a biomolecule itself is a "molecular recognition process". In the present article, we review our recent studies on the molecular recognition process, carried out by means of the 3D-RISM theory, a statistical mechanics theory of liquids. Studies on the conduction mechanisms in two types of molecular channels, aquaporin and the M2 channels, are reviewed.

Proton transport through the influenza A M2 channel: three-dimensional reference interaction site model study.

The three-dimensional distribution function (DF) and the potential of mean force (PMF) of water and hydronium ions in five protonated states of the influenza A M2 channel are calculated by means of the three-dimensional reference interaction site model (3D-RISM) theory in order to clarify the proton conduction mechanism of the channel. Each protonated state, denoted as iH, where i = 0-4, has a different number of protonated histidines, from 0 to 4. The DF of water in each state exhibits closed structures of 0H, 1H, and 2H and open structures in 3H and 4H. In the closed form, the DF and PMF indicate that hydronium ions are excluded from the channel. In contrast, the ion can distribute throughout the opened channel. The barrier in PMF of 3H, approximately 3-5 kJ/mol, is lower than that of 4H, 5-7 kJ/mol, indicating that 3H has higher permeability to protons. On the basis of the radial DFs of water and hydronium ions around the imidazole rings of His37, we propose a new mechanism of proton transfer through the gating region of the channel. In this process, a hydronium ion hands a proton to a non-protonated histidine through a hydrogen bond between them, and then the other protonated histidine releases a proton to a water molecule via a hydrogen bond. The process transfers a proton effectively from one water molecule to another.

Molecular selectivity in aquaporin channels studied by the 3D-RISM theory.

The three-deimensional distribution functions (3D-DFs) and potentials of mean force (PMFs) of small neutral molecules inside the two aquaporin channels, AQP1 and GlpF, are calculated based on the 3D-RISM theory, the statistical mechanics theory of molecular liquids, in order to investigate the permeability of those ligands through the channels. The ligands investigated are neon (Ne), carbon dioxide (CO(2)), nitric oxide (NO), ammonia (NH(3)), urea, and glycerol. Neon shows continuous distribution throughout the channel pore in AQP1 as is the case of water, although the PMF of Ne at the selective filter (SF) region is higher than that of water, indicating that the stability of molecules in the channel is determined not only by their size, but also by the charge distribution. The ligand molecules, CO(2), NO, urea, and glycerol, have a large barrier in PMF at the SF region in AQP1, indicating that the channel is not permeable by those ligands. On the other hand, NH(3) has only a small activation barrier, approximately 2.5 kJ/mol, to be overcome. Therefore, our theory predicts that a NH(3) molecule can be permeated through the AQP1 channel. In GlpF, all the ligands have negative PMF throughout the channel pore except for glycerol, which has a small barrier at the SF area, approximately 2.1 kJ/mol. The barrier can be readily overcome by the thermal motion. So, our results are quite consistent with the experiments for urea and glycerol, for which the corresponding data are available. The results obtained by the 3D-RISM theory show striking differences from those obtained by the MD simulations, especially in the case of GlpF. Possible causes of the difference in the results between the two methods are discussed.

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.

Selective ion binding by protein probed with the statistical mechanical integral equation theory.

Selective ion binding by human lysozyme and its mutants is probed with the three-dimensional interaction site model theory which is the statistical mechanical integral equation theory. Preliminary and partial results of the study have been already published (Yoshida, N. et al. J. Am. Chem. Soc. 2006, 128, 12042-12043). The calculation was carried out for aqueous solutions of three different electrolytes, CaCl2, NaCl, and KCl, and for four different mutants of the human lysozyme: wild type, Q86D, A92D, and Q86D/A92D, which have been studied experimentally. The discussion of this article focuses on the cleft that consists of amino acid residues from Q86 to A92. For the wild type of protein in the aqueous solutions of all the electrolytes studied, there are no distributions observed for the ions inside the cleft. The Q86D mutant shows essentially the same behavior with that of the wild type. The A92D mutant shows strong binding ability to Na+ in the recognition site, which is in accord with the experimental results. There are two isomers of the Q86D/A92D mutant, e.g., apo-Q86D/A92D and holo-Q86D/A92D. Although both isomers exhibit the binding ability to the Na+ and Ca2+ ions, the holo isomer shows much greater affinity compared with the apo isomer. Regarding the selective ion binding of the holo-Q86D/A92D mutant, it shows greater affinity to Ca2+ than to Na+, which is also consistent with the experimental observation.

Selective ion-binding by protein probed with the 3D-RISM theory.

Cations (Ca2+, Na+, K+) selectively bound by human lysozyme and its mutants are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.