Introduction of steered molecular dynamics into UNRES coarse‐grained simulations package

In this article, an implementation of steered molecular dynamics (SMD) in coarse‐grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all‐atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø‐like force field, all‐atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.     

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

We explored the energy‐parameter space of our coarse‐grained UNRES force field for large‐scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual‐bond‐angle bending and side‐chain‐rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy‐term weights were generated randomly, and good sets were selected by carrying out replica‐exchange molecular dynamics simulations of two peptides with a minimal α‐helical and a minimal β‐hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native‐like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native‐like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native‐like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Molecular simulations restrained to single or multiple templates are commonly used in protein‐structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template‐restrained canonical molecular dynamics (MD), multiplexed replica‐exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse‐grained UNRES force field on nine selected proteins, with pseudo‐harmonic log‐Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non‐ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor‐quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc.     

Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints

Contact-assisted simulations, the contacts being predicted or determined experimentally, have become very important in the determination of the structures of proteins and other biological macromolecules. In this work, the effect of contact-distance restraints on the simulated structures was investigated with the use of multiplexed replica exchange simulations with the coarse-grained UNRES force field. A modified bounded flat-bottom restraint function that does not generate a gradient when a restraint cannot be satisfied was implemented. Calculations were run with (i) a set of four small proteins, with contact restraints derived from experimental structures, and (ii) selected CASP11 and CASP12 targets, with restraints as used at prediction time. The bounded penalty function largely omitted false contacts, which were usually inconsistent. It was found that at least 20% of correct contacts must be present in the restraint set to improve model quality with respect to unrestrained simulations. © 2019 Wiley Periodicals, Inc.     

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

We report the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. We tested the approach on three training proteins separately: 1E0L (beta), 1GAB (alpha), and 1E0G (alpha + beta). Heretofore, the UNRES force field had been designed and parametrized to locate native-like structures of proteins as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES and applied it with success to simulate protein folding pathways. However, the force field turned out to be largely biased toward -helical structures in canonical simulations because the conformational entropy had been neglected in the parametrization. We applied the hierarchical optimization method, developed in our earlier work, to optimize the force field; in this method, the conformational space of a training protein is divided into levels, each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements, and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica-exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential energy function. beta     

Determination of side‐chain‐rotamer and side‐chain and backbone virtual‐bond‐stretching potentials of mean force from AM1 energy surfaces of terminally‐blocked amino‐acid residues,for coarse‐grained simulations of protein structure and folding. I. The method

In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simulations of protein structure and dynamics. In this article, we describe the methodology for determining the corresponding potentials of mean force (PMF's) from the energy surfaces of terminally‐blocked amino‐acid residues calculated with the AM1 quantum‐mechanical semiempirical method. The approach is based on minimization of the AM1 energy for fixed values of the angles λ for rotation of the peptide groups about the C^α ··· C^α virtual bonds, and for fixed values of the side‐chain dihedral angles χ, which formed a multidimensional grid. A harmonic‐approximation approach was developed to extrapolate from the energy at a given grid point to other points of the conformational space to compute the respective contributions to the PMF. To test the applicability of the harmonic approximation, the rotamer PMF's of alanine and valine obtained with this approach have been compared with those obtained by using a Metropolis Monte Carlo method. The PMF surfaces computed with the harmonic approximation are more rugged and have more pronounced minima than the MC‐calculated surfaces but the harmonic‐approximation‐and MC‐calculated PMF values are linearly correlated. The potentials derived with the harmonic approximation are, therefore, appropriate for UNRES for which the weights (scaling factors) of the energy terms are determined by force‐field optimization for foldability. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Preparation of macrodiols and polyols by chopping high‐molecular‐weight aliphatic polycarbonates

High‐molecular‐weight poly(1,4‐butylene carbonate) (PBC) (M_n: 40,000?90,000) was prepared through the condensation polymerization of dimethyl carbonate (DMC) and 1,4‐butanediol (BD) in the presence of 0.05 mol % sodium alkoxide catalyst. The subsequent feeding of 15 mol % HOAOH, such as 1,6‐hexanediol, 1,5‐pentanediol, 1,4‐cyclohexanedimethanol, or 1,4‐benzenedimethanol and stirring at 190–150 °C converted the extremely thick high‐molecular‐weight polymer to low‐molecular‐weight macrodiols with GPC‐measured M_n ～2000. The analysis of the ¹H NMR spectra indicated that the –A– units and 1,4‐butylene units were randomly distributed in the resulting oligomers. The chopping of the high‐molecular‐weight PBC using either triols or tetraols such as glycerol propoxylate, 1,1,1‐tris(hydroxymethyl)ethane, or pentaerythritol also afforded macropolyols containing branched chains with GPC‐measured M_n ～2000. When the chopped polymers were genuine PBCs, the resulting macrodiols or polyols were in a waxy state at room temperature. However, permanently oily compounds were obtained when the chopped polymers were prepared using 0.90 mole fraction of BD admixed with various other diols. The macrodiols and polyols synthesized in this study may have potential applications in the polyurethane industry. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1570–1580     

Protein Folding with a Reduced Model and Inaccurate Short‐Range Restraints

Summary: A reduced high‐coordination lattice protein model and the Replica Exchange Monte Carlo sampling were employed in de novo folding simulations of a set of representative small proteins. Three distinct situations were analyzed. In the first series of simulations, the folding was controlled purely by the generic force field of the model. In the second, a bias was introduced towards the theoretically predicted secondary structure. Finally, we superimposed soft restraints towards the native‐like local conformation of the backbone. The short‐range restraints used in these simulations are based on approximate values of ϕ and ψ dihedral angles, which may simulate restraints derived from inaccurate experimental measurements. Incorporating such data into the reduced model required developing a procedure, which transforms the ϕ and ψ coordinates into coordinates of the protein alpha carbon trace. It has been shown that such limited data are sufficient for de novo determination of three‐dimensional structures of small and topologically not too complex proteins.

Protein folding based on secondary structure prediction and simulated torsion angles data.     

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all‐atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side‐chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met‐enkephalin (CHO‐Tyr‐Gly‐Gly‐Phe‐Met‐NH₂) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard‐Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H‐Gly‐Tyr‐Asp‐Pro‐Glu‐Thr‐Gly‐Thr‐Trp‐Gly‐OH) reasonably reproduced a native‐like β‐hairpin structure in water although the C‐terminal and side‐chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

The implementation of molecular dynamics (MD) with our physics-based protein united-residue (UNRES) force field, described in the accompanying paper, was extended to Langevin dynamics. The equations of motion are integrated by using a simplified stochastic velocity Verlet algorithm. To compare the results to those with all-atom simulations with implicit solvent in which no explicit stochastic and friction forces are present, we alternatively introduced the Berendsen thermostat. Test simulations on the Ala(10) polypeptide demonstrated that the average kinetic energy is stable with about a 5 fs time step. To determine the correspondence between the UNRES time step and the time step of all-atom molecular dynamics, all-atom simulations with the AMBER 99 force field and explicit solvent and also with implicit solvent taken into account within the framework of the generalized Born/surface area (GBSA) model were carried out on the unblocked Ala(10) polypeptide. We found that the UNRES time scale is 4 times longer than that of all-atom MD simulations because the degrees of freedom corresponding to the fastest motions in UNRES are averaged out. When the reduction of the computational cost for evaluation of the UNRES energy function is also taken into account, UNRES (with hydration included implicitly in the side chain-side chain interaction potential) offers about at least a 4000-fold speed up of computations relative to all-atom simulations with explicit solvent and at least a 65-fold speed up relative to all-atom simulations with implicit solvent. To carry out an initial full-blown test of the UNRES/MD approach, we ran Berendsen-bath and Langevin dynamics simulations of the 46-residue B-domain of staphylococcal protein A. We were able to determine the folding temperature at which all trajectories converged to nativelike structures with both approaches. For comparison, we carried out ab initio folding simulations of this protein at the AMBER 99/GBSA level. The average CPU time for folding protein A by UNRES molecular dynamics was 30 min with a single Alpha processor, compared to about 152 h for all-atom simulations with implicit solvent. It can be concluded that the UNRES/MD approach will enable us to carry out microsecond and, possibly, millisecond simulations of protein folding and, consequently, of the folding process of proteins in real time.     

Coarse-grained force field: general folding theory

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described.     

Serological comparative proteomics analysis of mitochondrial autoantibody‐negative and ‐positive primary biliary cirrhosis

Here, we investigated the pathogenesis of primary biliary cirrhosis (PBC) by using 2D‐DIGE to analyze serological differences between anti‐mitochondrial antibody (AMA)‐positive and ‐negative PBC patients. The study comprised 30 patients with PBC; 20 AMA‐positive and ten AMA‐negative patients matched for age, sex , and pathological stage. A screening group (four AMA‐positive and four AMA‐negative patients) was used for 2D‐DIGE. Protein spots that were differently abundant between the two groups were identified via dye intensity and MS. Nine candidate proteins were identified from these spots. Western blotting was used to verify two of the identified proteins, serum amyloid P‐component (SAP) and vitronectin (VN). VN levels were significantly higher in the sera of AMA‐negative PBC patients (p < 0.01), whereas no significant difference was found between the two groups for SAP. To our knowledge, this is the first study to use serological comparative proteomics to explore differences between AMA‐positive and ‐negative PBC patients. VN levels were higher in AMA‐negative PBC patients, and this finding could be related to the more severe bile duct destruction observed in this group.     

Magnetic Field‐Induced Shape Transitions in Multiphase Polymer‐Liquid Crystal Blends

Summary: This paper presents a computational study of phase separation‐phase ordering‐texturing in blends of polymer coils and rod‐like nematic liquid crystals under the presence of magnetic fields, using an extended version of the Matsuyama‐Evans‐Cates model (Phys. Rev. E 2000 , 61, 2977). This work demonstrates that demixing in these blends leads to droplet morphologies with tunable droplet shapes and director textures. In contrast to filled nematics, where solids are suspended in a nematic liquid crystal matrix, demixing in coil‐mesogenic rods blends leads to nematic emulsions, in which the deformable viscoelastic polymer drops are suspended in a nematic matrix. Under strong anchoring conditions, the imposition of a magnetic field leads to a director re‐orientation that due to strong anchoring produces a droplet shape change. Magnetic field‐induced shape transitions in these blends are shown to be second order with a finite critical field threshold that diverges as anchoring strength vanishes. A morphological‐texture diagram summarizes the magnetic field‐anchoring conditions that promote anisotropic shapes. This work presents additional material processing routes to design and control bi‐phasic morphologies in polymer‐liquid crystal blend.

Computed morphology phase diagram in terms of magnetic field strength Λ_M and anchoring strength. Λ_ϕQ.     

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function

A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated with a shorter time step, which is an integral fraction of the basic time step. Based on the split operator formalism, the equations of motion were derived. Separation of the fast- and slow-varying forces leads to stable molecular dynamics with longer time steps. The algorithms were tested with the Ala(10) polypeptide chain and two versions of the UNRES force field: the current one in which the energy components accounting for the energetics of side-chain rotamers (U(rot)) can lead to numerically unstable forces and a modified one in which the the present U(rot) was replaced by a numerically stable expression which, at present, is parametrized only for polyalanine chains. With the modified UNRES potential, stable trajectories were obtained even when extending the basic time step to 15 fs and, with the original UNRES potentials, the basic time step is 1 fs. An adaptive multiple-time-step (A-MTS) algorithm is proposed to handle instabilities in the forces; in this method, the number of substeps in the basic time step varies depending on the change of the magnitude of the acceleration. With this algorithm, the basic time step is 1 fs but the number of substeps and, consequently, the computational cost are reduced with respect to the MTS algorithm. The use of the UNRES mesoscopic energy function and the algorithms derived in this work enables one to increase the simulation time period by several orders of magnitude compared to conventional atomic-resolution molecular dynamics approaches and, consequently, such an approach appears applicable to simulating protein-folding pathways, protein functional dynamics in a real molecular environment, and dynamical molecular recognition processes.     

MCDP: an advanced tool to simulate comb‐like polymers

A strategy to study polymeric systems with ordered structures, and in particular comb‐like polymers, is presented. These are dense systems for which atomistic simulations with conventional methods are difficult or even impracticable. The strategy, which has been incorporated into a computer program named MCDP, is based on a Configuration Bias Monte Carlo algorithm and a method to investigate the structure of crystalline polymers using force‐field calculations. To obtain a maximum efficiency, the MCDP computer program has been optimized and parallelized. The ability of MCDP to investigate ordered polymers have been tested by simulating two complex systems: (1) the crystal structure of poly(4‐methyl‐1‐pentene), and (2) the biphasic structure of poly(α‐octyl‐β‐L‐aspartate), a comb‐like polyamide derived from β‐amino acids. The results obtained from MCDP simulations demonstrates the efficiency and reliability of this method to study both the NVT and NPT behavior of ordered dense polymers. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 162–171, 2001     

Interfacial crosslinking of self‐assembled triblock copolymer nanoparticles via alkoxysilane hydrolysis and condensation

The use of amphiphilic triblock copolymers bearing a reactive alkoxysilane middle block as polymeric stabilizers is reported in this work. A series of poly(ethylene glycol) methyl ether methacrylate‐b‐(3‐trimethoxysilyl)propyl methacrylate‐b‐benzyl methacrylate (PEGMA‐b‐MPS‐b‐BzMA) triblock copolymers were prepared by RAFT solution polymerization and polymerization‐induced self‐assembly (PISA), respectively, where the various block lengths and overall composition were varied. The copolymers prepared by solution polymerization were employed as oil‐in‐water stabilizers where upon application of a catalyst, the 3‐(trimethoxysilyl)propyl methacrylate (MPS) block at the droplet interface was crosslinked to yield capsule‐like structures. The effectiveness of interfacial crosslinking was validated by dynamic light scattering and electron microscopy. In situ self‐assembly by the PISA method resulted in spherical nanoparticles of controllable size that were readily crosslinked by addition of base, with significant enhancement of colloidal stability. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1897–1907     

Vapor‐induced spreading dynamics of adsorbed linear and brush‐like macromolecules as observed by environmental SFM: Polymer chain statistics and scaling exponents

Scaling exponents ν, that describe the correlation between mean square end‐to‐end distances and contour lengths of macromolecules, were determined by statistical analysis of scanning force micrographs of single linear poly(2‐vinylpyridine) and brush‐like poly(butanoate‐ethyl methacrylate)‐graft‐poly(n‐butyl acrylate) macromolecules adsorbed on mica. Using an atmosphere‐controlled scanning force microscope, single adsorbed molecules were collapsed and re‐expanded upon being exposed to alcohol and water vapor, respectively. This manipulated collapse‐unfolding was used to equilibrate the molecular structure/conformation. The in situ and real‐time scanning force microscopy analysis allows the scientist to quantitatively characterize end‐to‐end distances and contour lengths of the molecules directly on the image and to observe differences in the spreading dynamics for the two types of macromolecules. A distinct difference has been observed between the expanded two‐dimensional (2D) conformations of linear and brush‐like polymer chains. Whereas a scaling exponent ν of 0.73 was found for the expanded 2D conformation of the linear molecules, a ν‐value of 0.53 was determined for the expanded 2D conformation of the seemingly stiffer brush‐like molecules. A theoretical explanation of the differences between the 2D conformations of brush‐like and linear macromolecules is proposed here. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2368–2379, 2007     

The role of TEOS‐TIP within a pentablock ionomer: Morphology,physical properties,and ion transport

Inorganic–organic nanocomposites were created using tetraethylorthosilicate (TEOS), titanium isopropoxide (TIP), and poly(t‐butylstyrene‐b‐hydrogenated isoprene‐b‐sulfonated styrene‐b‐hydrogenated isoprene‐b‐t‐butylstyrene) or pentablock copolymer (PBC). A TEOS–TIP–H₂O ternary phase diagram was generated to create homogenous sol solutions with designable condensation reactions that led to controllable materials. An inorganic TEOS–TIP network was synthesized using sol–gel chemistry within the organic PBC domain. All TEOS–TIP–PBC films exhibited higher water sorption than unmodified PBC ionomer that was attributed to a change in morphology. Proton conductivity increased up to 80% due to TEOS–TIP within the nanocomposite film. This can be attributed to ion domain redistribution and partial charge transfer from the titanate's inorganic domains to sulfonate groups that promote acid dissociation. PBC had a microphase‐separated morphology that changed with increasing TIP concentration, which was observed from atomic force microscopy and small‐angle X‐ray scattering results. Finally, thermal gravimetric analysis revealed a decrease in degradation temperature, and dynamic mechanical analysis results demonstrated reduced polymer chain mobility caused by inorganic–organic interactions. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 575–586     

Improved treatment of cyclic β‐amino acids and successful prediction of β‐peptide secondary structure using a modified force field: AMBER*C

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000     

CABS‐NMR—De novo tool for rapid global fold determination from chemical shifts,residual dipolar couplings and sparse methyl‐methyl noes

Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low‐cost global protein fold determination. Here, we present CABS‐NMR, an efficient protein modeling tool, which takes advantage of such structural restraints. The restraints are converted from original NMR data to fit the coarse grained protein representation of the C‐Alpha‐Beta‐Side‐group (CABS) algorithm. CABS is a Monte Carlo search algorithm that uses a knowledge‐based force field. Its versatile structure enables a variety of protein‐modeling protocols, including purely de novo folding, folding guided by restraints derived from template structures or, structure assembly based on experimental data. In particular, CABS‐NMR uses the distance and angular restraints set derived from various NMR experiments. This new modeling technique was successfully tested in structure determination of 10 globular proteins of size up to 216 residues, for which sparse NMR data were available. Additional detailed analysis was performed for a S100A1 protein. Namely, we successfully predicted Nuclear Overhauser Effect signals on the basis of low‐energy structures obtained from chemical shifts by CABS‐NMR. It has been observed that utility of chemical shifts and other types of experimental data (i.e. residual dipolar couplings and methyl‐methyl Nuclear Overhauser Effect signals) in the presented modeling pipeline depends mainly on size of a protein and complexity of its topology. In this work, we have provided tools for either post‐experiment processing of various kinds of NMR data or fast and low‐cost structural analysis in the still challenging field of new fold predictions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011