Prediction of protein–protein complexes using replica exchange with repulsive scaling

The realistic prediction of protein–protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein–protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica-exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)-REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS-REMD technique allowed the sampling of near-native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex structures only for one case. The method showed also improved results for the refinement of docked structures in the vicinity of the native binding geometry compared to regular MD refinement.     

A molecular mechanics model for imatinib and imatinib:kinase binding

Imatinib is an important anticancer drug, which binds specifically to the Abl kinase and blocks its signalling activity. To model imatinib:protein interactions, we have developed a molecular mechanics force field for imatinib and four close analogues, which is consistent with the CHARMM force field for proteins and nucleic acids. Atomic charges and Lennard‐Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with imatinib fragments at 32 different positions. We considered both a neutral and a protonated imatinib. The final RMS deviation between the ab initio and force field energies, averaged over both forms, was 0.2 kcal/mol. The model also reproduces the ab initio geometry and flexibility of imatinib. To apply the force field to imatinib:Abl simulations, it is also necessary to determine the most likely imatinib protonation state when it binds to Abl. This was done using molecular dynamics free energy simulations, where imatinib is reversibly protonated during a series of MD simulations, both in solution and in complex with Abl. The simulations indicate that imatinib binds to Abl in its protonated, positively‐charged form. To help test the force field and the protonation prediction, we did MD free energy simulations that compare the Abl binding affinities of two imatinib analogs, obtaining good agreement with experiment. Finally, two new imatinib variants were considered, one of which is predicted to have improved Abl binding. This variant could be of interest as a potential drug. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A computational study of regioselectivity in a cyclodextrin-mediated Diels-Alder reaction: revelation of site selectivity and the importance of shallow binding and multiple binding modes

The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.     

Understanding interactions between poly(styrene-co-sodium styrene sulfonate) and single-walled carbon nanotubes

Understanding formation mechanisms of hybrids of carbon nanotubes (CNTs) wrapped by polymers and their interactions is critical in modifying solubility of CNTs in aqueous solution and developing new nanotube-based polymer materials. In the present work, we investigate the structural details of poly(styrene-co-sodium styrene sulfonate) (PSS) wrapping around the CNT and the interactions between the PSS chain and the CNT using molecular dynamics (MD) simulations. The fraction of sulfonated groups significantly influences the wrapping conformations of the PSS chain. Due to limited time scale in the MD simulations, two different initial conformations of the chains are introduced to explore the effect of the initial state on the wrapping behavior. When the chains initially wrap around the CNT in a perfect helix manner, more compact pseudo-helical conformations are obtained. For initial straight line arrangement of the chain monomers, the chains adopt looser wrapping conformations. The free-energy analysis and binding interaction of the PSS chain on the CNT surface take a glance on the relationship between the conformational transition of the chain and the energy evolution.     

MMP-2和Hydroxamate类抑制剂绝对自由能的计算

采用基于线性响应近似的自由能计算方法计算了一类hydroxamate抑制剂和MMP-2的绝对结合自由能。计算中,催化锌离子和MMP-2以及配体之间采用了非键模型。分子动力学模拟结果显示,采用非键模型时,催化Zn离子采用五配位的形式,但配位键的形式和初始结构比较有很大的差别。通过拟合,分别得到了单参数、双参数以及三参数的自由能预测模型,其中,含有常数校正项的三参数模型具有最佳的预测能力,预测自由能和实际自由能之间平均绝对误差仅为2.38kJ/mol。     

端羟基聚丁二烯/增塑剂共混物相容性的分子动力学模拟和介观模拟

应用分子动力学(MD)和介观动力学(MesoDyn)模拟方法对固体推进剂中端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性进行了研究. 采用MD模拟方法在COMPASS力场下, 对纯物质、HTPB/增塑剂共混物的密度、内聚能密度、溶度参数和共混物分子间的Flory-Huggins作用参数及结合能等进行了模拟计算, 通过比较溶度参数差值(Δδ)的大小、模拟前后体系密度变化情况均可以预测HTPB与增塑剂的相容性, 结合能的分析揭示了HTPB/增塑剂共混物组分间的相互作用及本质. 将Flory-Huggins作用参数转化为MesoDyn模拟的输入参数, 采用MesoDyn模拟方法对HTPB/增塑剂共混体系的介观形貌与动力学演变过程进行了研究, 通过模拟得到的等密度图、自由能密度和有序度参数等可以判断共混体系的相容性. MD和MesoDyn模拟结果均表明: HTPB/DOS属于相容体系, 而HTPB/NG属于不相容体系, 其结论与实验结果一致.     

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes

The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1-PHD) binds specifically to phosphatidylinositol (3,4,5)-triphosphate (PIP₃), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1-PHD in the presence of membranes containing PC, PS, and PIP₃ lipids in varying compositions. While GRP1-PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane-bound configurations. We report the first observation of two distinct PIP₃ binding modes on GRP1-PHD, involving PIP₃ interactions at a “canonical” and at an “alternate” site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1-PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1-PHD to the membrane, we demonstrate that along with the bound PIP₃, surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1-PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1-PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学(MD)模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物(分别记为M1、M2和M3)与ACh E的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用(vd W)。用MM-PBSA方法计算的3种抑制剂与ACh E之间的结合自由能与抑制剂的实验生物活性数据(IC50值)相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与ACh E之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与ACh E之间的结合自由能有较大的贡献,在区分抑制剂M1(或M2)和M3的生物活性上发挥着重要的作用。     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学（MD）模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物（分别记为M1、M2和M3）与AChE的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用（vdW）。用MM-PBSA方法计算的3种抑制剂与AChE之间的结合自由能与抑制剂的实验生物活性数据（IC₅₀值）相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与AChE之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与AChE之间的结合自由能有较大的贡献,在区分抑制剂M1（或M2）和M3的生物活性上发挥着重要的作用。     

A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes

The monotopic proteins COX-1 and -2 in dimeric form bound to lipid bilayer membranes are studied using molecular dynamics simulations within an aqueous environment. The 25-ns simulations are performed for both isozymes with arachidonic acid bound in the cyclooxygenase sites. The interactions between the enzymes and the lipids are analyzed, providing insight into the attachment mechanism of monotopic proteins to membranes. Our study reveals some key differences between the two isozymes that include the orientations at which they sit on the surface of the membranes and the depths to which they embed within the membranes. The differences in membrane association of the isozymes indicate that they may integrate distinctively with the same membrane, and/or with different membranes or their lipid components. Our results indicate that arachidonic acid can be bound in the cyclooxygenase active site in distinct catalytically competent conformations that lead to certain hydroperoxy acids; and the arachidonic acid and/or cyclooxygenase sites undergo a conformational change which makes only one subunit of each homodimer catalytically active.     

Oxoanion binding by guanidiniocarbonylpyrrole cations in water: a combined DFT and MD investigation

Structures and properties of nonbonding interactions involving guanidinium-functionalized hosts and carboxylate substrates were investigated by a combination of ab initio and molecular dynamics approaches. The systems under study are on one hand intended to be a model of the arginine-anion bond, so often observed in proteins and nucleic acids, and on the other to provide an opportunity to investigate the influence of molecular structure on the formation of supramolecular complexes in detail. Use of DFT calculations, including extended basis sets and implicit water treatment, allowed us to determine minimum-energy structures and binding enthalpies that compared well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions through three hydrogen bonds, one of which is bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting of a rotation of about 180 degrees around the guanidiniocarbonylpyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed in the presence of explicit water molecules by use of the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM-PBSA) and linear interaction energy (LIE) approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes cannot be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible for several low-energy metastable structures.     

Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT     

Structure and thermodynamics of alpha-, beta-, and gamma-cyclodextrin dimers. Molecular dynamics studies of the solvent effect and free binding energies

The alpha-, beta-, and gamma-cyclodextrin (CyDs) dimers were studied by molecular dynamics (MD) simulations in water as an explicit solvent. The relative stability of dimers and the involved molecular interactions were determined. Three possible starting orientations were considered for the dimers: head-to-head, head-to-tail, and tail-to-tail. MD simulations were performed over a period of 5 ns to ensure the stability of the system for both the CyD dimers and monomers. The MM-PBSA methodology was used to obtain the free binding energy of the dimers and to determine the most stable arrangement for each solvated CyD. In a vacuum, MD simulations provided the head-to-head orientation as the most stable orientation for the three CyDs, while in aqueous solution the, the head-to-tail orientation was found to be the most stable for the alpha-CyD dimer and the tail-to-tail orientation the most stable for the beta- and gamma-CyD dimers.     

Atomistic simulations to compute surface properties of poly(N-vinyl-2-pyrrolidone) (PVP) and blends of PVP/chitosan

Atomistic simulations were performed on poly(N-vinyl-2-pyrrolidone) (PVP) and its blends with chitosan (CS) in different ratios using molecular mechanics (MM) and molecular dynamics (MD) simulations in three-dimensionally periodic and effective two-dimensionally periodic condensed phases. Four independent microstructures were generated to analyze their surface properties. The calculated surface-energy values for PVP compared quite well with the experimental data reported in the literature. The density profile was analyzed, and the structure of the films showed an interior region of the bulk density. Various components of the energetic interactions (torsional, van der Waals, etc.) were examined to gain deeper insight into the nature of regular and anomalous interactions between the bulk and the surface films. Surface energies of PVP/CS blends were computed by MD simulations using the bulk pressure-volume-temperature (PVT) parameters. Bulk properties such as the cohesive energy density (CED) and solubility parameter (delta) were calculated using MM and MD simulations in the NVT ensemble under periodic boundary conditions. The Flory equation of state was used to compute the thermal expansion coefficient as well as PVT parameters. These surface-energy values agreed well with the surface-energy data calculated using the Zisman equation, which were also in accordance with the experimental observations. The results from this study suggest that computer simulations would provide valuable information on polymers and polymer-blend surfaces.     

Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight

Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

Acrylonitrile-acrylic acid copolymer membrane imprinted with uric acid for clinical uses

The preparation of new polymeric membranes using molecular imprinting technology for application in blood filtration devices is described. Membranes, based on an acrylic acid-acrylonitrile copolymer, produced through phase inversion, were modified by introducing specific binding sites for uric acid into their structure. The materials prepared are intended for use to selectively remove uric acid from the blood in the case of increased serum uric acid values associated with different pathologies. The interactions at a molecular level between the membrane forming copolymer and the template were investigated by means of calorimetry, infrared spectroscopy and morphological analysis. The presence of interactions between the template and the copolymer, and a good thermal stability of the imprinted membranes were observed. In addition, the results of rebinding tests on the imprinted membranes indicated a good capacity of molecular recognition for the template and satisfactory selectivity properties towards compounds of similar structure such as theophylline. Membrane permeability values suggest their application as (ultra) haemofiltration devices. Poly(acrylonitrile-co-acrylic acid) membrane.     

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

This article addresses calculations of the standard free energy of binding from molecular simulations in which a bound ligand is extracted from its binding site by steered molecular dynamics (MD) simulations or equilibrium umbrella sampling (US). Host–guest systems are used as test beds to examine the requirements for obtaining the reversible work of ligand extraction. We find that, for both steered MD and US, marked irreversibilities can occur when the guest molecule crosses an energy barrier and suddenly jumps to a new position, causing dissipation of energy stored in the stretched molecule(s). For flexible molecules, this occurs even when a stiff pulling spring is used, and it is difficult to suppress in calculations where the spring is attached to the molecules by single, fixed attachment points. We, therefore, introduce and test a method, fluctuation‐guided pulling, which adaptively adjusts the spring's attachment points based on the guest's atomic fluctuations relative to the host. This adaptive approach is found to substantially improve the reversibility of both steered MD and US calculations for the present systems. The results are then used to estimate standard binding free energies within a comprehensive framework, termed attach‐pull‐release, which recognizes that the standard free energy of binding must include not only the pulling work itself, but also the work of attaching and then releasing the spring, where the release work includes an accounting of the standard concentration to which the ligand is discharged. © 2013 Wiley Periodicals, Inc.     

In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between alpha-helix and beta-sheet structures was significantly improved by the modification of charge parameters.