EFFECTS OF SECONDARY STRUCTURE ON ELASTIC BEHAVIOR OF PROTEIN-LIKE CHAINS

The elastic behavior of protein-like chains was investigated by using the Pruned-Enriched-Rosenbluth Method (PERM).Three typical protein-like chains such as all-α,all-β,and α+β(α/β) proteins were studied in our modified orientation dependent monomer-monomer interaction (ODI) model.We calculated the ratio of /N and shape factor <δ*> of protein-like chains in the process of elongation.In the meantime,we discussed the average energy per bond ＜U＞/N,average contact energy per bond ＜U＞c/N,average helical energy per bond ＜U＞h/N and average sheet energy per bond ＜U＞b/N.Three maps of contact formation,α-helix formation,β-sheet formation were depicted.All the results educe a view that the helix structure is the most stable structure,while the other two structures are easy to be destroyed.Besides,the average Helmholtz free energy per bond ＜A＞/Nis was presented.The force f obtained from the free energy was also discussed.It was shown that the chain extended itself spontaneously first.The force was studied in the process of elongation.Lastly,the energy contribution to elastic force fu was calculated too.It was noted that fu for all-β chains increased first,and then decreased with x0 increasing.     

三维吸附紧密高分子单链的力学性质研究

采用PERM(pruned-enriched Rosenbluth method)算法,研究了吸附在界面附近的紧密高分子链力学行为.发现当界面的吸附能比较大时,紧密高分子链从紧贴于吸附界面到逐渐远离的过程中,其外形会经历4种典型的变化.同时紧密高分子链的尺寸大小如/N、xy/N、z/N,形状参数<δ*>,热力学性质如每个键的平均自由能A/N,平均相互作用能/N等,甚至所受外力的大小都会同时做出相应的变化,其出现变化的位置也一致.特别是随着紧密高分子链离开吸附界面的过程中,作用于高分子链上的外力明显出现几个力学平台,这与实验得到的结果完全一致.同时还研究了弱吸附能的情况,在这种情况下实验是很难进行的.     

ELASTIC BEHAVIOR OF PROTEIN-LIKE SINGLE CHAIN

The conformational properties and elastic behaviors of protein-like single chains in the process of tensile elongation were investigated by means of Monte Carlo method. The sequences of protein-like single chains contain two types of residues: hydrophobic (H) and hydrophilic (P). The average conformations and thermodynamics statistical properties of protein-like single chains with various elongation ratio λ were calculated. It was found that the mean-square end-to-end distance r increases with elongation ratio,λ. The tensor eigenvalues ratio of : decreases with elongation ratio λ for short (HP)x protein-like polymers, however, the ratio of : increases with elongation ratioλ,especially for long (H)x sequence. Average energy per bond increases with elongation ratioλ, especially for(H)x protein-like single chains. Helmholtz free energy per bond also increases with elongation ratioλ. Elastic force (f), energy contribution to force (fU) and entropy contribution to force (fs) for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.     

Polymer translocation through a nanopore. II. Excluded volume effect

Following our previous study of a Gaussian chain translocation, we have investigated the transport of a self-avoiding chain from one sphere to another sphere through a narrow pore, using the self-consistent field theory formalism. The free energy landscape for polymer translocation is significantly modified by excluded volume interactions among monomers. The free energy barrier for the placement of one of the chain ends at the pore depends on the chain length N nonmonotonically, in contrast to the N-independence for Gaussian chains. This results in a nonmonotonic dependence of the average arrival time [tau0] on N for self-avoiding chains. When the polymer chain is partitioned between the donor and recipient spheres, a local free energy minimum develops, depending on the strength w of the excluded volume interaction and the relative sizes of the donor and recipient spheres. If the sizes of spheres are comparable, the average translocation time tau (the average time taken by the polymer, after the arrival at the pore, to convert from the donor to the recipient) increases with an increase in w for a fixed N value. On the other hand, for the highly asymmetric sizes of the donor and recipient spheres, tau decreases with an increase in w. As in the case of Gaussian chains, tau depends nonmonotonically on the pore length.     

Polymer translocation through a nanopore: a two-dimensional Monte Carlo study

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For LR(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.     

Elastic behavior of adsorbed polymer chains

Elastic behaviors of single polymer chains adsorbed on the attractive surface are first investigated using Monte Carlo simulation method based on the bond fluctuation model. We investigate the chain size and shape of adsorbed chains, such as mean-square radius of gyration S2, mean-square bond length b2, shape factors sf(i) and delta*, and the orientation of chain segments P2, to illuminate how the shape of polymer chains changes during the process of tensile elongation. There are some special behaviors of the chain size and shape at the beginning of elongation, especially for strong attraction interaction. For example, mean fraction of adsorbed segments decreases abruptly in the region of small elongation ratio and then decreases slowly with increasing elongation ratio. In fact, the chain size and shape also changes abruptly for small elongation ratio with strong attraction interaction. Some thermodynamics properties are also investigated here. Average Helmholtz free energy increases fast for elongation ratio lambda<1.15, especially with strong attraction, and increases slowly for lambda>1.15. Similar behaviors are obtained for average energy per bond. Elastic force (f ) and energy contribution to force (f(U)) are also studied, and we find that elastic force decreases abruptly for lambda<1.15, and there is a minimum of elastic force for strong attraction interaction, then increases very slowly with increasing elongation ratio. However, there are different behaviors for weak attraction interaction. For energy contribution to force (f(U)), there is a maximum value for strong attraction interaction in the region of lambda<1.15. Some comparisons with the atomic force microscopy experiments are also made. These investigations may provide some insights into the elastic behaviors of adsorbed polymer chains.     

Translocation of α-helix chains through a nanopore

The translocation of α-helix chains through a nanopore is studied through Langevin dynamics simulations. The α-helix chains exhibit several different characteristics about their average translocation times and the α-helix structures when they transport through the nanopores under the driving forces. First, the relationship between average translocation times τ and the chain length N satisfies the scaling law, τ～N(α), and the scaling exponent α depends on the driving force f for the small forces while it is close to the Flory exponent (ν) in the other force regions. For the chains with given chain lengths, it is observed that the dependence of the average translocation times can be expressed as τ～f(-1/2) for the small forces while can be described as τ～f in the large force regions. Second, for the large driving force, the average number of α-helix structures N(h) decreases first and then increases in the translocation process. The average waiting time of each bead, especially of the first bead, is also dependent on the driving forces. Furthermore, an elasticity spring model is presented to reasonably explain the change of the α-helix number during the translocation and its elasticity can be locally damaged by the large driving forces. Our results demonstrate the unique behaviors of α-helix chains transporting through the pores, which can enrich our insights into and knowledge on biopolymers transporting through membranes.     

Intramolecular Interactions in Anisole,Thioanisole, and Selenoanisole. Application of Natural Bond Orbitals Method

Calculations of molecules PhXMe (X = O, S, Se) in MP2(f)/6-31G(d) approximation were performed. The stationary points on the potential energy surface were determined and identified. The anisole molecule is planar with a barrier to rotation H 7.78 kJ mol^-1. In thioanisole and selenoanisole (H 3.08 and 10.25 kJ mol^-1 respectively) the energy minimum corresponds to an orthogonal form. Analysis of relation between intramolecular interactions and conformational structure of the molecules in question was performed by the method of natural bond orbitals. In X atoms one lone electron pair is a hybrid orbital with the following fraction of s-component: 38-45% (O), 66-68% (S), and 73-74% (Se). The second lone electron pair is virtually pure pz-AO.     

Electrophoresis of Bottle‐Brush Polyelectrolytes in an Attractive Nanochannel

A molecular dynamics study of the electrophoresis of bottle‐brush polyelectrolytes (BPEs) through nanochannels is reported. The BPE molecules consist of a neutral backbone with charged side chains. For strong attractive interactions between the BPE and the wall, the BPE is being trapped on the channel surface. A stretching–shrinking migration of the BPE in a channel of radius 6σ is observed at relatively strong electric fields. The stretching–shrinking transition is periodic for intermediate electric fields but not for stronger electric fields. The BPE also shows a transverse migration toward the wall at weak electric fields, while toward the center with further enhancing the electric field. For a channel with larger radius 12σ, the BPE does not migrate in the stretching–shrinking manner.

     

Interaction between a rodlike inclusion and a supported bilayer membrane

The interactions between a rodlike inclusion and a supported copolymer bilayer membrane are investigated by using the self-consistent field theory. For different system parameters, physical observables, such as the interaction free energy, entropy, and translocation energy barrier, are obtained. Particular emphasis is put on the closely energetic and entropic analyses of the interaction. It shows that the interfacial energy provides a qualitative trend and dominates the basic shape of the interaction free energy curve; the combination of chemical potential energy and total entropy contribution is responsible for the translocation energy barrier and the weak attraction in the vicinity of upper monolayer surface. We also specify the nature, height, and shape of the energy barrier to translocation. Particularly, the height is roughly proportional to the rod radius.     

Elastic Behaviors of Adsorbed Protein-like Chains

Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond.On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.     

C−X Bond Activation by Palladium: Steric Shielding versus Steric Attraction

The C−X bond activation (X = H, C) of a series of substituted C(n°)−H and C(n°)−C(m°) bonds with C(n°) and C(m°) = H₃C− (methyl, 0°), CH₃H₂C− (primary, 1°), (CH₃)₂HC− (secondary, 2°), (CH₃)₃C− (tertiary, 3°) by palladium were investigated using relativistic dispersion-corrected density functional theory at ZORA-BLYP-D3(BJ)/TZ2P. The effect of the stepwise introduction of substituents was pinpointed at the C−X bond on the bond activation process. The C(n°)−X bonds become substantially weaker going from C(0°)−X, to C(1°)−X, to C(2°)−X, to C(3°)−X because of the increasing steric repulsion between the C(n°)- and X-group. Interestingly, this often does not lead to a lower barrier for the C(n°)−X bond activation. The C−H activation barrier, for example, decreases from C(0°)−X, to C(1°)−X, to C(2°)−X and then increases again for the very crowded C(3°)−X bond. For the more congested C−C bond, in contrast, the activation barrier always increases as the degree of substitution is increased. Our activation strain and matching energy decomposition analyses reveal that these differences in C−H and C−C bond activation can be traced back to the opposing interplay between steric repulsion across the C−X bond versus that between the catalyst and substrate.     

Schwingungsspektren der Bis(mercuriojodonium)-hexafluorometallate (HgJ)2MF6 (M = Ti,Zr, Sn) und verwandter Verbindungen

Vibrational Spectra of Bis (mercurioiodonium)-hexafluorometallates (HgI)₂ MF₆(M = Ti, Zr, Sn) and Similar Compounds For the isotypic bis(mercurioiodonium)-hexafluorometallates (HgI)₂MF₆ (M = Ti, Zr and Sn; space group D–Cmcm) with chain structure of the cations [(IHg_2/2)₂]²⁺ the complete vibrational spectra have been discussed on the basis of a factor group analysis. A simple model yields an average force constant f ? 1.37 N · cm^?1 for the Hg? I bonds of the chains and bond angles at the iodine atoms which agree satisfactorily with the data obtained by X-ray structure analysis. Spectra of (HgI)X (X = NO₃ and BF₄; benzene sulphonate and p-toluene sulphonate) also indicate cationic chains in these compounds.     

Translocation of a protein-like chain through an interacting channel

The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations.The interior behavior of chain conformation under different interactions was investigated,such as the number of monomers outside of channel n_out,monomers inside of channel n_m,mean-square radius of gyration〈S²〉and the average energy〈U〉.It shows that with strong attractive interaction,the translocation is more difficult than moderate interaction.At the same time,the dependence of translocation time with different interactions shows that moderate repulsive interaction(ε_cp= 0.5) accelerates the translocation.Although the waiting time for successful translocation ofε_cp = 1.0 is the longest,the average translocation time is not very large.It is far smaller than that ofε_cp=-1.0.The probability distributions of translocation time p（t’） and the probability distributions of three duration times p（t₁’）,p（t₂’） and p（t₃’） were all discussed.Log-normal distributions are found.All these findings will strengthen the understanding of protein translocation.     

The Sphingosine and Acyl Chains of Ceramide [NS] Show Very Different Structure and Dynamics That Challenge Our Understanding of the Skin Barrier

The lipid phase of the uppermost human skin layer is thought to comprise highly rigid lipids in an orthorhombic phase state to protect the body against the environment. By synthesizing sphingosine‐d₂₈ deuterated N‐lignoceroyl‐d ‐erythro‐sphingosine (ceramide [NS]), we compare the structure and dynamics of both chains of that lipid in biologically relevant mixtures using X‐ray diffraction, ²H NMR analysis, and infrared spectroscopy. Our results reveal a substantial fraction of sphingosine chains in a fluid and dynamic phase state at physiological temperature. These findings prompt revision of our current understanding of the skin lipid barrier, where an extended ceramide [NS] conformation is preferred and a possible domain structure is proposed. Mobile lipid chains may be crucial for skin elasticity and the translocation of physiologically important molecules.     

Elastic behavior of short compact chains confined in double parallel boundaries

Adsorption of short two-dimensional compact chains confined in the double attractive parallel planar boundaries is investigated by using enumeration calculation method in this paper. First, we calculate the chain size and shape of adsorbed compact chains, such as mean-square end-to-end distance per bond R²/N, mean-square radii of gyration per bond S²_x/N and S²_y/N, shape factor δ and fraction of adsorbed segments f_a to illuminate that how the size and shape of adsorbed compact chains changes during the process of tensile elongation. There are some special behaviors in the chain size and shape for strong attraction interaction. In the meantime, compact chains can reach to the stable state with large distance between two parallel boundaries D. On the other hand, some thermodynamic properties, such as average energy per bond, Helmholtz free energy per bond, elastic force f and energy contribution to elastic f_U are also investigated in order to study the elastic behavior of compact chains adsorbed on the double attractive parallel planar boundaries. These investigations may provide some insights into the thermodynamic behaviors of adsorbed compact chains.     

Dissociation dynamics of thiolactic acid at 193 nm: detection of the nascent OH product by laser-induced fluorescence

Electronically excited thiolactic acid (2-mercaptopropionic acid), H(3)C-CH(SH)-COOH, undergoes the C-OH bond cleavage on excitation to the S(2) state at 193 nm, generating the primary product OH (v,J), which is detected by laser-induced fluorescence technique in a collisionless condition of flow system. The partitioning of the available energy between vibrational, rotational, and translational degrees of freedom of nascent photofragments is obtained from relative intensities of ro-vibronic lines in laser-induced fluorescence spectrum of OH, and their Doppler profiles. The rotational population of OH (v(")=0) is characterized by rotational temperature of 408+/-25 K. OH is produced in a vibrationally cold state, i.e., mostly in v(")=0. The average translational energy of OH (v(")=0,J(")) is found to be 21.5+/-2.0 kcal/mol, which implies 25.6 kcal/mol of energy in relative translation of photoproducts corresponding to the f(t) value of approximately 0.6. The observed high translational energy is due to the presence of a barrier in the exit channel, implying that the C-OH bond scission takes place on an electronically excited potential energy surface. The observed partitioning of the available energy between various degrees of the photofragments is theoretically modeled, and the hybrid model, with 26.0 kcal/mol of barrier in the exit channel, is found to explain the measured data quite well. The experimental results are also supported with ab initio molecular orbital calculations for both the ground and the excited electronic states. Time-dependent density functional theory is used to understand the nature of various electronic transitions connecting the lower excited states. Potential energy curves as a function of the C-OH bond length of thiolactic acid suggest distinct exit barriers in the S(1), T(1), and T(2) states. But, we could locate the transition state structure for OH formation in the S(1) state alone. Thus, although thiolactic acid is excited to the S(2) state at 193 nm, it undergoes internal conversion to S(1) where it dissociates to yield OH. In addition to the OH channel from excited electronic states, we studied theoretically all probable dissociation channels occurring on the ground electronic state of thiolactic acid.     

Translocation of Polymer Chains Through a Channel with Complex Geometries

The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels (left channel, middle channel, and right channel, respectively) is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f(f>0) versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observedwith the elastic force f<0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the translocation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the componenttranslocation time is not the same for different channels can be presented.