Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.

Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies.

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-BP2) 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 Cs of selected pairs of residues.

Dynamic and conformational switching in proteins.

Using bioinformatic methods for treating protein dynamics, developed in earlier work, we study the relationship between sequence mobility and dynamics in proteins. It is shown that sequence mobility drives a transition between two dynamic regimes in proteins, and that the specific details of this transition differ qualitatively between α-helical proteins and those in other structural classes. We examine the possibility that conformational switching is related to dynamic switching, by considering a specific system of sequences which exhibit the switching phenomenon.

The structure of protein dynamic space.

We use a bioinformatic description of amino acid dynamic properties, based on residue-specific average B factors, to construct a dynamics-based, large-scale description of a space of protein sequences. We examine the relationship between that space and an independently constructed, structure-based space comprising the same sequences. It is demonstrated that structure and dynamics are only moderately correlated.

Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding.

Thermal protein unfolding resembles a global (two-state) phase transition. At the local scale, protein unfolding is, however, heterogeneous and probe dependent. Here, we consider local order parameters defined by the local curvature and torsion of the protein main chain.

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.

Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain.

PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking.

The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF.

Assessing the One-Bond C-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches.

In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed SSCC values.

Outline of an experimental design aimed to detect a protein A mirror image in solution.

There is abundant theoretical evidence indicating that a mirror image of may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of in solution.

Sequence-specific dynamic information in proteins.

We examine the local and global properties of the average B-factor, 〈B〉, as a residue-specific indicator of protein dynamic characteristics. It has been shown that values of 〈B〉 for the 20 amino acids differ in a statistically significant manner, and that, while strongly determined by the static physical properties of amino acids, they also encode averaged information about the influence of global fold on single-residue dynamics. Therefore, complete sequences of amino acids also encode fold-related global dynamic information, in addition to the local information that arises from static physical properties.

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.

Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein-nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al., J.

Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ.

One of the hallmarks of Alzheimer's disease is the formation of aggregates of the tau protein, a process that can be facilitated by the presence of fibrils formed by the amyloid β peptide (Aβ). However, the mechanism that triggers tau aggregation is still a matter of debate. The effect of Aβ fibrils on the aggregation of the repeat domain of tau (TauRD) is investigated here by employing coarse-grained molecular dynamics simulations.

From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.

α-Synuclein (αS) is a major constituent of Lewy bodies, the insoluble aggregates that are the hallmark of one of the most prevalent neurodegenerative disorders, Parkinson's disease (PD). The vast majority of experiments in vitro and in vivo provide extensive evidence that a disordered monomeric form is the predominant state of αS in water solution, and it undergoes a large-scale disorder-to-helix transition upon binding to vesicles of different types. Recently, another form, tetrameric, of αS with a stable helical structure was identified experimentally.

Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale.

Protein folding/unfolding can be analyzed experimentally at a local scale by monitoring the physical properties of local probes as a function of the temperature, for example, the distance between fluorophores or the values of chemical shifts of backbone atoms. Here, the analytical Lifson-Roig model for the helix-coil transition is modified to analyze local thermal unfolding of the fast-folder W protein of bacteriophage lambda (gpW) simulated by all-atom molecular dynamics (MD) simulations in explicit solvent at 15 different temperatures. The protein structure is described by the coarse-grained dihedral angles (γ) and bond angles (θ) built between successive C-C virtual bonds.

Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain.

Accumulation of amyloid-beta (Aβ), which is associated with Alzheimer's disease, can be caused by excess production or insufficient clearance. Because of its β-sheet structure, fibrillar Aβ is resistant to proteolysis, which would contribute to slow degradation of Aβ plaques in vivo. Fibrillar Aβ can be internalized by microglia, which are the scavenger cells of the brain, but the fibrils are degraded only slowly in microglial lysosomes.

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

Ribonuclease A (RNase A) is the most studied member of ribonucleases - a group of enzymes responsible for catalyzing RNA degradation. RNase A contains four disulfide bonds, which were found to be necessary for the native structure of the protein to form. In this work the kinetics and thermodynamics of RNase unfolding were studied by means of a series of coarse-grained canonical molecular-dynamics simulations, run at various temperatures, and replica-exchange molecular dynamics simulations with the UNRES force field, which is capable of dynamic formation and breaking the disulfide bonds during the course of the simulations.

Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

Assessment of the relative amounts of the forms of the imidazole ring of Histidine (His), namely the protonated (H) and the tautomeric N-H and N-H forms, respectively, is a challenging task in NMR spectroscopy. Indeed, their determination by direct observation of the N and C chemical shifts or the one-bond C-H, , Spin-Spin Coupling Constants (SSCC) requires knowledge of the "canonical" limiting values of these forms in which each one is present to the extent of 100%. In particular, at high-pH, an accurate determination of these "canonical" limiting values, at which the tautomeric forms of His coexist, is an elusive problem in NMR spectroscopy.

A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.

A recently introduced electrostatic-based method to determine the pKa values of ionizable residues and fractions of ionized and tautomeric forms of histidine (His) and acid residues in proteins, at a given fixed pH, is applied here to the analysis of a His-rich protein, namely Loligo vulgaris (pdb id 1E1A), a 314-residue all-β protein. The average tautomeric fractions for the imidazole ring of each of the six histidines in the sequence were computed using an approach that includes, but is not limited to, molecular dynamic simulations coupled with calculations of the ionization states for all 94 ionizable residues of protein 1E1A in water at pH 6.5 and 300 K.

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.

By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the simulated conformational ensembles of selected training proteins and the corresponding ensembles determined experimentally at various temperatures, the physics-based coarse-grained UNRES force field for simulations of protein structure and dynamics was optimized with seven small training proteins exhibiting a variety of secondary and tertiary structures. Four runs of optimization, in which the number of optimized force-field parameters was gradually increased, were carried out, and the resulting force fields were subsequently tested with a set of 22 α-, 12 β-, and 12 α + β-proteins not used in optimization. The variant in which energy-term weights, local, and correlation potentials, side-chain radii, and anisotropies were optimized turned out to be the most transferable and outperformed all previous versions of UNRES on the test set.

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.

We recently introduced a physically based approach to sequence comparison, the property factor method (PFM). In the present work, we apply the PFM approach to the study of a challenging set of sequences-the bacterial chemotaxis protein CheY, the N-terminal receiver domain of the nitrogen regulation protein NT-NtrC, and the sporulation response regulator Spo0F. These are all response regulators involved in signal transduction.

Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.

A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water.

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 fibrils. In particular, an unstructured monomer was allowed to interact freely with an Aβ fibril template.

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.

The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains.