Local relaxation of polymers in dense media: Cooperative kinematics theory and applications

Cooperative kinematics (CK) theory and its recent applications are presented. CK theory has been developed as an efficient approach for predicting the mechanism of segmental relaxation processes in bulk polymers. The theory aims at determining the most probable changes in atomic coordinates, occurring collectively in response to a given, external or localized, structural perturbation. The basic postulate is the minimization of the energy change involved in the overall conformational motion, which naturally yields the optimal pathway of cooperative relaxation. Attention has been confined here to the collective motions accompanying the rotational transitions of backbone bonds in polyethylene (PE) and polybutadiene (PB). The strong dependence of the mechanism of motions on the geometry of the repeat unit and on chain connectivity is emphasized. The differences in the types of correlated transitions operating in different structures, the effective conformational energy changes triggered by bond rotational jumps, and the correlation lengths for particular bond isomerizations are analyzed. The reorientations of C H bond vectors in cis- and trans-PB are also examined to explain the shorter correlation time of cis units, compared to trans, detected by NMR. A good agreement between various CK predictions and results from molecular dynamics (MD) simulations is obtained. The fact that CK calculations are at least two orders of magnitude faster than MD simulations invites attention to the utility of the CK method as an efficient tool for elucidating the pathway of motion in complex systems.     

Analysis of the structural and dynamic properties of human N-terminal domain of apolipoprotein E by molecular dynamics simulations

Whereas the lipid-free N-terminal domain of apolipoprotein E (apoE-NT) adopts a four-helix bundle, the lipid-bound form is believed to undergo a large conformational change likely to be characterized by the opening of the bundle. ApoE-NT in a water/alcohol mixture was also shown to experience conformational changes exhibiting similarities with those induced upon lipid binding. The structure and dynamics of apoE-NT have been here investigated by analyzing 40 ns and 60 ns molecular dynamics simulations performed in water and in a water/propanol mixture, respectively. The overall structural properties show alterations of the tertiary structure of apoE-NT in the water/alcohol system in agreement with those observed experimentally. In contrast, in the water simulation, the sampled conformations remain closer to the crystal structure that served as a starting point for both simulations. Interestingly, several propanol molecules are seen to penetrate two hydrophobic regions of the bundle interior. One of these regions is enclosed in part by the short helix (H1') connecting helices 1 and 2 of the bundle which has been experimentally shown to be important for modulating lipid binding activity of apoE-NT. Principal component analysis of the water/propanol trajectory confirms that the region including H1' is the locus of the largest motion. Another region involves the loop connecting helix 2 and helix 3 which has been hypothesized to play the role of a hinge in the opening of the bundle.     

Conformational transition pathway in the allosteric process of calcium-induced recoverin: molecular dynamics simulations

Recoverin is an important neuronal calcium sensor (NCS) protein, which have been implicated in a wide range of Ca(2+) signaling events in neurons and photoreceptors. To characterize the conformational transition of recoverin from the myristoyl sequestered state to the extrusion state, a series of conventional molecular dynamics (CMD) and targeted molecular dynamics (TMD) simulations were performed. The 36.8 ns long CMD and TMD simulations on recoverin revealed a reliably conformational transition pathway, which can be viewed as a sequential two-stage process. A very important mechanistic conclusion from the present TMD simulations is that the hydrophobic and hydrophilic interactions modulate the allostery cooperatively in the conformational transition pathway. In the first stage, three salt-bridges broken between Lys-84 and Gly-124, between Lys-5 and Glu-103 and between Gly-16 and Lys-97 are major components to destabilize the structure of state T and trigger the swivel of the N- and C-terminal domains. In the second stage, the rupture of H-bond Phe-56-O(...)H(O)-Thr-21 leads to the two helices of EF-1 apart from each other, destabilizing the hydrophobic interactions of the myristoyl group with its environment, whereas the making of H-bond Leu-108-O(...)H(O)-Ser-72 helps the interfacial domain maintain its structural integrity during the course of the myristoyl extrusion. The molecular dynamics simulations results are beneficial to understanding the mechanism of how and why NCS proteins make progress in the photo-signal transduction processes. Further experimental and theoretical studies are still very desirable.     

Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.     

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".     

Three-dimensional structure-activity relationship analysis between motilin and motilide using conformational analysis and a novel molecular superposing method

Motilide, an erythromycin derivative, has been shown to equal activity to that of motilin as an agonist at the motilin receptor. However, there is little information on the three-dimensional (3D) structure-activity relationship between these two molecules, largely because they have quite different structures. In this study, we applied a rational computational procedure consisting of conformational analysis and a novel superposing method to investigate the 3D structure-activity relationship between motilide and motilin. We propose common 3D structural features between these molecules, which may be important for their similar activity.     

Temperature‐shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins

Parallel cascade selection molecular dynamics (PaCS‐MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature‐aided PaCS‐MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS‐MD. In the present study, temperature‐shuffled PaCS‐MD is proposed as a further extension of temperature‐aided PaCS‐MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. To evaluate their conformational sampling efficiencies, the original, temperature‐aided, and temperature‐shuffled PaCS‐MD were applied to a protein‐folding process of Trp‐cage, and their minimum computational costs to identify the native state were addressed. Through the evaluation, it was confirmed that temperature‐shuffled PaCS‐MD remarkably accelerated the protein‐folding process of Trp‐cage compared with the other methods. © 2017 Wiley Periodicals, Inc.     

Investigation of the dynamics of the conformational transitions of dimeric isoquinoline alkaloids by nmr spectroscopy and molecular mechanics

The conformational dynamics of the dimeric isoquinoline alkaloid turconidine has been investigated by the methods of NMR spectroscopy and molecular mechanics. The main conformational states and the trajectories of their mutual transitions have been established. A high lability of the molecule and the predominant state of the dimer in three of the eight possible conformations with respect to the ether bond have been shown.Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 285–289, March-April, 1995. Original article submitted November 28, 1994.     

Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide

Recently a new non-coded amino acid was designed as a replacement for Arg, to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This constrained Arg analog, denoted c(5)Arg, was engineered to also promote the stability of the CREKA bioactive conformation. The conformational profile of the CREKA analog obtained by replacing Arg by c(5)Arg has been extensively investigated in this work. Two molecular dynamics simulations-based strategies have been employed: a modified simulated annealing and replica exchange. Results obtained using both techniques show that the conformational features of the new analog fulfill the purpose of its design. The new CREKA analog not only preserves the main structural attributes found for the bioactive conformation of the parent peptide but also shows lower flexibility. Moreover, the conformational profile of the mutated peptide narrows towards the most stable structures previously observed for the parent CREKA peptide.     

Site-specific solvation determined by intermolecular nuclear Overhauser effect--measurements and molecular dynamics

Site-specific solvation has been determined by intermolecular NOE measurements between solvent and solute. The experimental effect is shown on the four compounds 2-butanol, L-alanyl-L-tryptophan (Ala-Trp), adenosine and the disodium salt of adenosine 5'-monophosphate (5'-AMP) in the two solvents water and dimethyl sulfoxide (DMSO). The strength of NOE transfer correlates with the average distribution of solvent molecules around the corresponding solvation sites represented by the number of solvent molecules in a first solvation sphere, which can be obtained from molecular dynamics simulations in water. Saturation transfer between exchanging protons explains some deviations from this correlation. The NOE transfer measurements provide information on specific solute-solvent interactions and contribute to a better understanding of solvation phenomena. On the basis of a distinct relationship between steric solvation hindrance and the strength of NOE transfer, the application of such measurements for conformational analysis has been demonstrated for the first time.     

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.     

Intermediate state during the crystal transition in aspartame, studied with thermal analysis, solid-state NMR, and molecular dynamics simulation

Aspartame (L-alpha-aspartyl-L-phenylalanine methyl ester) is a dipeptide sweetener about 200 times as sweet as sugar. It exists in crystal forms such as IA, IB, IIA, and IIB, which differ in crystal structure and in the degree of hydration. Among these, IIA is the most stable crystal form, and its crystal structure has been well determined (Hatada et al., J. Am. Chem. Soc., 107, 4279-4282 (1985)). To elucidate the structural factors of thermal stability in the IIA form of aspartame and to examine the physical process in the crystal transformation between the IIA and IIB forms, we performed a thermal analysis and solid-state NMR measurements. We found that a quasi-stable intermediate state exists in the transformation, and it has the same crystal lattice as the usual IIA form, despite the dehydration from 1/2 mol to 1/3 mol per 1 mol of aspartame. The results of the energy component analysis and the molecular dynamics simulation suggest that the entropic effect promotes the generation of the intermediate state, which is presumably caused by the evaporation of the water of crystallization and the increase of molecular motion in aspartame. Thus, the thermal stability of the IIA form is attributable to a structural property, i.e., the crystal lattice itself is retained during the above dehydration. Moreover, the molecular dynamics simulations suggest that the aspartame molecules have two kinds of conformational flexibility in the intermediate state.     

Conformational analysis of a tetrasaccharide based on NMR spectroscopy and molecular dynamics simulations

The conformational preference of the human milk oligosaccharide lacto-N-neotetraose, beta-d-Galp-(1 --> 4)-beta-d-GlcpNAc-(1 --> 3)-beta-d-Galp-(1 --> 4)-d-Glcp, has been analyzed using (1)H,(1)H T-ROESY and (1)H,(13)C trans-glycosidic J coupling experiments in isotropic solution and (1)H,(13)C residual dipolar couplings (RDCs) obtained in lyotropic liquid crystalline media. Molecular dynamics simulations of the tetrasaccharide with explicit water as the solvent revealed that two conformational states are significantly populated at the psi glycosidic torsion angle, defined by C(anomeric)-O-C-H, of the (1 --> 3)-linkage. Calculation of order parameters, related to the molecular shape, were based on the inertia tensor and fitting of experimental RDCs to different conformational states showed that psi(+) > 0 degrees is the major and psi(-) < 0 degrees is the minor conformation in solution, in complete agreement with a two-state analysis based on the T-ROESY data. Attention was also given to the effect of salt (200 mM NaCl) in the anisotropic medium, which was a ternary mixture of n-octyl-penta(ethylene glycol), n-octanol, and D(2)O.     

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.     

Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions

DNA methyltransferases (DNMTs) including DNMT1 are a conserved family of cytosine methylases that play crucial roles in epigenetic regulation. The versatile functions of DNMT1 rely on allosteric networks between its different interacting partners, emerging as novel therapeutic targets. In this work, based on the modeling structures of DNMT1-ubiquitylated H3 (H3Ub)/ubiquitin specific peptidase 7 (USP7) complexes, we have used a combination of elastic network models, molecular dynamics simulations, structural residue perturbation, network modeling, and pocket pathway analysis to examine their molecular mechanisms of allosteric regulation. The comparative intrinsic and conformational dynamics analysis of three DNMT1 systems has highlighted the pivotal role of the RFTS domain as the dynamics hub in both intra- and inter-molecular interactions. The site perturbation and network modeling approaches have revealed the different and more complex allosteric interaction landscape in both DNMT1 complexes, involving the events caused by mutational hotspots and post-translation modification sites through protein-protein interactions (PPIs). Furthermore, communication pathway analysis and pocket detection have provided new mechanistic insights into molecular mechanisms underlying quaternary structures of DNMT1 complexes, suggesting potential targeting pockets for PPI-based allosteric drug design.     

Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides

The fluctuating elastic boundary (FEB) model for molecular dynamics has recently been developed and validated through simulations of liquid argon. In the FEB model, a flexible boundary which consists of particles connected by springs is used to confine the solvated system, thereby eliminating the need for periodic boundary conditions. In this study, we extend this model to the simulation of bulk water and solvated alanine dipeptide. Both the confining potential and boundary particle interaction functions are modified to preserve the structural integrity of the boundary and prevent the leakage of the solute-solvent system through the boundary. A broad spectrum of structural and dynamic properties of liquid water are computed and compared with those obtained from conventional periodic boundary condition simulations. The applicability of the model to biomolecular simulations is investigated through the analysis of conformational population distribution of solvated alanine dipeptide. In most cases we find remarkable agreement between the two simulation approaches.     

Sequence-specific and nonspecific mobilities of single-stranded oligonucleotides observed by changing the borate buffer concentration

The suitability of gel electrophoresis to structural analysis of nucleic acids has been examined, using from borate buffer concentrations (in the range from 4.5 to 450 mM. The gel electrophoretic mobility of single-stranded oligonucleotides was shown to be sequence-dependent at higher concentrations than 27 mM of borate buffer and nondependent at lower one (less than 9 mM). As a result, each dodecamer had a sequence-specific critical concentration of Tris-borate-EDTA (TBE) buffer at which each seems to change its structural state. At the lower concentration than the critical one, all the dodecamers turned to the state of a finite mobility and migrated in a sharp band. This finding is discussed and rationalized by the assumption that the difference in conformational dynamics of oligonucleotides, due to the difference in their sequence, is mainly responsible for the observed difference in their mobility.     

Three-dimensional structure of HIV-1 VIF constructed by comparative modeling and the function characterization analyzed by molecular dynamics simulation

VIF is one of the six accessory proteins of HIV-1. It has been shown to be necessary for the survival of HIV-1 in the human body and for the retention of viral infectivity. It is strongly expected that a new therapeutic strategy against HIV-1 infection could be realized by blocking the biological pathway to VIF. In this paper, a three-dimensional model of VIF was constructed by comparative modeling based on two templates, VHL and NarL, which were used to construct the C-terminal domain and N-terminal domain of VIF, respectively. A model of the VIF-ElonginB-ElonginC complex was constructed, and molecular dynamics simulations were used to investigate the interactions between VIF and ElonginB-ElonginC. Mutagenesis was used to identify the function of some conserved residues in the putative SOCS-box. The results showed that the mutations of the critical residues led to the disruption of the interactions between VIF and ElonginB-ElonginC, consistent with experimental observations. These novel models of VIF and its complex has therefore provided structural information for investigating the function of VIF at the molecular level.     

Dihedral angle principal component analysis of molecular dynamics simulations

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.     

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.