Coarse-grained UNited RESidue Force Field Research Articles

On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field

During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation).The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.

Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment

The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES-contact group), and (iii) template-assisted (the UNRES-template group). For most of the targets, the contact restraints were derived from the server models top-ranked by the DeepQA method, while the DNCON2 method was used for 11 targets. Our consensus-fragment procedure was used to run template-assisted predictions. Each group also processed the Nuclear Magnetic Resonance (NMR)- and Small Angle X-Ray Scattering (SAXS)-data assisted targets. The average Global Distance Test Total Score (GDT_TS) of the ‘Model 1’ predictions were 29.17, 39.32, and 56.37 for the UNRES, UNRES-contact, and UNRES-template predictions, respectively, increasing by 0.53, 2.24, and 3.76, respectively, compared to CASP13. It was also found that the GDT_TS of the UNRES models obtained in ab initio mode and in the contact-assisted mode decreases with the square root of chain length, while the exponent in this relationship is 0.20 for the UNRES-template group models and 0.11 for the best performing AlphaFold2 models, which suggests that incorporation of database information, which stems from protein evolution, brings in long-range correlations, thus enabling the correction of force-field inaccuracies.

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.

Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218-62.

Extension of coarse-grained UNRES force field to treat carbon nanotubes

Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3–4 order of magnitude larger timescale than using regular all-atom force fields.Graphical abstractBovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ

Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.

Fibrils formed by the β-amyloid (Aβ) peptide play a central role in the development of Alzheimer's disease. In this study, the principles governing their growth and stability are investigated by analyzing canonical and replica-exchange molecular dynamics trajectories of Aβ(9-40) fibrils. In particular, an unstructured monomer was allowed to interact freely with an Aβ fibril template. Trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue and principal components, respectively, were analyzed. Also, thermal unbinding (unfolding) of an Aβ peptide from the fibril template was investigated. These analyses enable us to illustrate the entire process of Aβ fibril elongation and to elucidate the key residues involved in it. Several different pathways were identified during the search for the fibril conformation by the monomer, which finally follows a dock-lock mechanism with two distinct locking stages. However, it was found that the correct binding, with native hydrogen bonds, of the free monomer to the fibril template at both stages is crucial for fibril elongation. In other words, if the monomer is incorrectly bound (with nonnative hydrogen bonds) to the fibril template during the first "docking" stage, it can remain attached to it for a long time before it dissociates and either attempts a different binding or allows another monomer to bind. This finding is consistent with an experimentally observed "stop-and-go" mechanism of fibril growth.

Local vs Global Motions in Protein Folding

It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respectively, were analyzed. The key residues involved in the folding of the FBP28 WW domain are elucidated by this analysis. The correlations between local and global motions are found. It is shown that most of the residues in the folding trajectories of the system studied here move in a concerted fashion, following the dynamics of the whole system. This demonstrates how the choice of a pathway has to involve concerted movements in order for this protein to fold. This finding also sheds light on the effectiveness of principal component analysis (PCA) for the description of the folding dynamics of the system studied. It is demonstrated that the FEL along the PCs, computed by considering only several critically-placed residues, can correctly describe the folding dynamics.

Hidden Protein Folding Pathways in Free-Energy Landscapes Uncovered by Network Analysis

A network analysis is used to uncover hidden folding pathways in free-energy landscapes usually defined in terms of such arbitrary order parameters as root-mean-square deviation from the native structure, radius of gyration, etc. The analysis has been applied to molecular dynamics (MD) trajectories of the B-domain of staphylococcal protein A, generated with the coarse-grained united-residue (UNRES) force field in a broad range of temperatures (270K ≤ T ≤ 325K). Thousands of folding pathways have been identified at each temperature. Out of these many folding pathways, several most probable ones were selected for investigation of the conformational transitions during protein folding. Unlike other conformational space network (CSN) methods, a node in the CSN variant implemented in this work is defined according to the nativelikeness class of the structure, which defines the similarity of segments of the compared structures in terms of secondary-structure, contact-pattern, and local geometry, as well as the overall geometric similarity of the conformation under consideration to that of the reference (experimental) structure. Our previous findings, regarding the folding model and conformations found at the folding-transition temperature for protein A (Maisuradze et al., J. Am. Chem. Soc. 132, 9444, 2010), were confirmed by the conformational space network analysis. In the methodology and in the analysis of the results, the shortest path identified by using the shortest-path algorithm corresponds to the most probable folding pathway in the conformational space network.

Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ 1–40 fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding modes during their search for the fibril conformation. Although different assembly pathways were seen, they all follow a dock-lock mechanism with two distinct locking stages, consistent with experimental data on fibril elongation. Whereas these experiments have not been able to characterize the conformations populating the different stages, we have been able to describe these different stages explicitly by following free monomers as they dock onto a fibril template and to adopt the fibril conformation (i.e., we describe fibril elongation step by step at the molecular level). During the first stage of the assembly (“docking”), the monomer tries different conformations. After docking, the monomer is locked into the fibril through two different locking stages. In the first stage, the monomer forms hydrogen bonds with the fibril template along one of the strands in a two-stranded β-hairpin; in the second stage, hydrogen bonds are formed along the second strand, locking the monomer into the fibril structure. The data reveal a free-energy barrier separating the two locking stages. The importance of hydrophobic interactions and hydrogen bonds in the stability of the Aβ fibril structure was examined by carrying out additional canonical MD simulations of oligomers with different numbers of chains (4–16 chains), with the fibril structure as the initial conformation. The data confirm that the structures are stabilized largely by hydrophobic interactions and show that intermolecular hydrogen bonds are highly stable and contribute to the stability of the oligomers as well.

Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field

Three algorithms, namely a Replica Exchange method (REM), a Replica Exchange Multicanonical method (REMUCA), and Replica Exchange Multicanonical with Replica Exchange (REMUCAREM), were implemented with the coarse-grained united-residue force field (UNRES) in both Monte Carlo and Molecular Dynamics versions. The MD algorithms use the constant-temperature Berendsen thermostat, with the velocity Verlet algorithm and variable time step. The algorithms were applied to one peptide (20 residues of Alanine with free ends; ala(20)) and two small proteins, namely an α-helical protein of 46 residues (the B-domain of the staphylococal protein A; 1BDD), and an α+β-protein of 48 residues (the E. Coli Mltd Lysm Domain; 1E0G). Calculated thermodynamic averages, such as canonical average energy and heat capacity, are in good agreement among all simulations for poly-L-alanine, showing that the algorithms were implemented correctly, and that all three algorithms are equally effective for small systems. For protein A, all algorithms performed reasonably well, although some variability in the calculated results was observed whereas, for a more complicated α+β-protein (1E0G), only Replica Exchange was capable of producing reliable statistics for calculating thermodynamic quantities. Finally, from the Replica Exchange molecular dynamics results, we calculated free energy maps as functions of RMSD and radius of gyration for different temperatures. The free energy calculations show correct folding behavior for poly-L-alanine and protein A while, for 1E0G, the native structure had the lowest free energy only at very low temperatures. Hence, the entropy contribution for 1E0G is larger than that for protein A at the same temperature. A larger contribution from entropy means that there are more accessible conformations at a given temperature, making it more difficult to obtain an efficient coverage of conformational space to obtain reliable thermodynamic properties. At the same temperature, ala(20) has the smallest entropy contribution, followed by protein A, and then by 1E0G.