The Effect of ß-Sheet Secondary Structure on All-ß Proteins by Molecular Dynamics Simulations.

The effect of ß-sheet ratio and chain length on all-ß proteins was investigated by MD simulations. Protein samples composed of different repeating units with various ß-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of ß-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the ß-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of ß-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding.

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein.

The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range. We concluded that the proteins with higher ratio or larger number of sequentially hydrophobic residues present more orientated and compact structure under a certain low temperature. It is attributed to the lower non-bonded potential energy between H-H residual pairs, especially more hydrophobic residues in a procession among the protein chain. Considering the microscopic structure of the protein, more residue contacts are achieved with the proteins with higher ratios and sequential H residues under the low temperature. Meanwhile, with the ratio and consecutive number of H residues increasing, the distribution of stem length showed a transition from exponential decline to unimodal and even multiple peaks, indicating the specific ordered structure formed. These results provide an insight into 3D structural properties of proteins from their residue sequences, which has a primary structure at molecular level and, ultimately, a practical possibility of applying in biotechnological applications.

A Study on the Through-Plane Permeability of Anisotropic Fibrous Porous Material by Fractal Stochastic Method.

The through-plane permeability is of great importance for understanding the transport phenomenon in anisotropic fibrous porous material. In this paper, a novel pore-scale model based on the equilateral triangle representative unit cell (RUC) and capillary bundle model is developed for the fluid flow through the anisotropic fibrous porous material according to fractal theory, and the effective through-plane permeability is presented accordingly. The digital structures of the fibrous porous material are generated by a fractal stochastic method (FSM), and the single-phase fluid flow through the 3D-reconstructed model is simulated by using the finite element method (FEM). It was found that the effective through-plane permeability depends on the fiber column size, porosity, and fractal dimensions for pore and tortuosity. The results show that the predicted through-plane permeability by the present fractal model indicates good agreement with numerical results and available experimental data as well as empirical formulas. The dimensionless through-plane permeability is positively correlated with the porosity and negatively correlated with the fractal dimensions for pore and tortuosity at certain porosity.

Effects of the Temperature and Salt Concentration on the Structural Characteristics of the Protein (PDB Code 1BBL).

The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stability of the protein immersed in salt solutions with different concentrations and temperatures. Our work demonstrates that the electrostatic potential energy and van der Waals energy of the system show the opposite changes with the influence of the external environment. Since the electrostatic potential energy changes more obviously, it is dominated in the non-bonding interactions. The structural parameters, such as the root mean square deviation and the radius of gyration, increased initially and decreased afterward with the increase of the salt concentration. The protein presented the loose structure with a relative low stability when it was immersed in a monovalent solution with a salt concentration of 0.8 mol/L. The salt concentration corresponding to the maximum value of structural parameters in the monovalent salt solution was double that in the divalent salt solution. It was also concluded that the protein presented a compact and stable structure when immersed in salt solutions with a high concentration of 2.3 mol/L. The analysis of the root mean square deviation and root mean square fluctuation of the protein sample also exhibited that the structural stability and chain flexibility are strongly guided by the effect of the temperature. These conclusions help us to understand the structural characteristics of the protein immersed in the salt solutions with different concentrations and temperatures.

Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies.

The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples' structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.

Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study.

The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field. The characteristic time when the jump occurs in the time evolution curves of root mean square deviation (RMSD) and radius of gyration Rg decreases with increasing electric strength, which demonstrates the rapidly conformational transition that occurs. The number of intra-protein hydrogen bonds, which is the key factor for stabilizing the protein structure, is related to the overall size of the protein. The value of the dipole moment and characteristic time are both influenced by the strength, but are independent of the direction of the external field. The protein sample becomes rotated with the electric field direction. These conclusions provide a theoretical realization of understanding the protein conformational transition in an electric field and the guidance for anticipative applications.

Translocation of a Polymer through a Crowded Channel under Electrical Force.

The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength F, the chain length N, and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ ~ F-α is observed. With the crowding extent ρ increasing, the scaling exponent α becomes large. It is found that, for noncrowded channel, translocation probability drops when the field strength becomes large. However, for high-crowded channel, it is the opposite. Moreover, the translocation time and the average translocation time for all segments both have exponential growth with the crowding extent. The investigation of shape factor 〈δ〉 shows maximum value with increasing of the number of segments outside s. At last, the number of segments inside channel Nin in the process of translocation is calculated and a peak is observed. All the information from the study may benefit protein translocation.

Liquid crystalline assembly of rod-coil diblock copolymer and homopolymer blends by dissipative particle dynamics simulation.

Liquid crystalline assembly of rod-coil diblock copolymers blended with coil or rod homopolymers is investigated by dissipative particle dynamics simulation, considering systematically the effect of the interactions between rods and coils, the volume fraction and length of the added coil or rod homopolymers. The addition of coil or rod homopolymers induces disorder-order or order-liquid crystalline transition. In rod-coil/coil blends, the solubilization of homopolymers will saturate at a certain amount of homopolymers and then the excess homopolymers will be segregated into the central regions of coil block domains, forming "wet-dry mixture" lamellae. The solubility capacity decreases with increasing homopolymer length, determined by the competition between the mixing entropy and the elastic entropy. In rod-coil/rod blends, due to the orientational interactions between rods, the length matched rod homopolymers directly interdigitate with rod blocks with less entropy loss, thus prompting the formation of a bilayer liquid crystalline phase. The rod domain spacing Dr remains unchanged and conversely the coil domain spacing Dc becomes thin, to occupy more interfacial area. With the addition of shorter rod homopolymers, the overall lamellar spacing D of blends monotonically increases with the volume fraction of homopolymers, similar to the case of rod-coil/coil blends. Generally, rod homopolymers have a more significant impact on the liquid crystalline assembly of the blends, compared with the coil homopolymers. Our results indicate that blending with coil or rod homopolymers into a rod-coil system is an effective method to induce liquid crystal phase transition and control the phase spacing of the ordered structure.

Self-assembly of cyclic rod-coil diblock copolymers.

The phase behavior of cyclic rod-coil diblock copolymer melts is investigated by the dissipative particle dynamics simulation. In order to understand the effect of chain topological architecture better, we also study the linear rod-coil system. The comparison of the calculated phase diagrams between the two rod-coil copolymers reveals that the order-disorder transition point (χN)ODT for cyclic rod-coil diblock copolymers is always higher than that of equivalent linear rod-coil diblocks. In addition, the phase diagram for cyclic system is more "symmetrical," due to the topological constraint. Moreover, there are significant differences in the self-assembled overall morphologies and the local molecular arrangements. For example, frod = 0.5, both lamellar structures are formed while rod packing is different greatly in cyclic and linear cases. The lamellae with rods arranged coplanarly into bilayers occurs in cyclic rod-coil diblocks, while the lamellar structure with rods arranged end by end into interdigitated bilayers appears in linear counterpart. In both the lamellar phases, the domain size ratio of cyclic to linear diblocks is ranged from 0.63 to 0.70. This is attributed to that the cyclic architecture with the additional junction increases the contacts between incompatible blocks and prevents the coil chains from expanding as much as the linear cases. As frod = 0.7, the hexagonally packed cylinder is observed for cyclic rod-coil diblocks, while liquid-crystalline smectic A lamellar phase is formed in linear system. As a result, the cyclization of a linear rod-coil block copolymer can induce remarkable differences in the self-assembly behavior and also diversify its physical properties and applications greatly.

Predicting protein structure from long-range contacts.

Short-range and long-range contacts are important in forming protein structure. The proteins can be grouped into four different structural classes according to the content and topology of alpha-helices and beta-strands, and there are all-alpha, all-beta, alpha/beta and alpha+beta proteins. However, there is much difference in statistical property for those classes of proteins. In this paper, we will discuss protein structure in the view of the relative number of long-range (short-range) contacts for each residue. We find the percentage of residues having a large number of long-range contacts in protein is small in all-alpha class of proteins, and large in all-beta class of proteins. However, the percentage of residues is almost the same in alpha/beta and alpha+beta classes of proteins. We calculate the percentage of residues having the number of long-range contacts greater than or equal to (>/=) N(L)=5, and 7 for 428 proteins. The average percentage is 13.3%, 54.8%, 41.4% and 37.0% for all-alpha, all-beta, alpha/beta and alpha+beta classes of proteins with N(L)=5, respectively. With N(L) increasing, the percentage decreases, especially for all-alpha class of proteins. In the meantime, the percentage of residues having the number of short-range contacts greater than or equal to N(S) (>/=N(S)) in protein samples is large for all-alpha class of proteins, and small for all-beta class of proteins, especially for large N(S). We also investigate the ability of amino residues in forming a large number of long-range and short-range contacts. Cys, Val, Ile, Tyr, Trp and Phe can form a large number of long-range contacts easily, and Glu, Lys, Asp, Gln, Arg and Asn can form a large number of long-range contacts, but with difficulty. We also discuss the relative ability in forming short-range contacts for 20 amino residues. Comparison with Fauchere-Pliska hydrophobicity scale and the percentage of residues having large number of long-range contacts is also made. This investigation can provide some insights into the protein structure.