Internal Protein Motions Research Articles

Robust Prediction of B-Factor Profile from Sequence Using Two-Stage SVR Based on Random Forest Feature Selection

B-factor is highly correlated with protein internal motion, which is used to measure the uncertainty in the position of an atom within a crystal structure. Although the rapid progress of structural biology in recent years makes more accurate protein structures available than ever, with the avalanche of new protein sequences emerging during the post-genomic Era, the gap between the known protein sequences and the known protein structures becomes wider and wider. It is urgent to develop automated methods to predict B-factor profile from the amino acid sequences directly, so as to be able to timely utilize them for basic research. In this article, we propose a novel approach, called PredBF, to predict the real value of B-factor. We firstly extract both global and local features from the protein sequences as well as their evolution information, then the random forests feature selection is applied to rank their importance and the most important features are inputted to a two-stage support vector regression (SVR) for prediction, where the initial predicted outputs from the 1(st) SVR are further inputted to the 2nd layer SVR for final refinement. Our results have revealed that a systematic analysis of the importance of different features makes us have deep insights into the different contributions of features and is very necessary for developing effective B-factor prediction tools. The two-layer SVR prediction model designed in this study further enhanced the robustness of predicting the B-factor profile. As a web server, PredBF is freely available at: http://www.csbio.sjtu.edu.cn/bioinf/PredBF for academic use.

Influence of methanol on catalytic activity, stability and internal dynamics of myoglobin

The influence of methanol on the activity, stability and internal dynamics of myoglobin (Mb) has been investigated to obtain information about the effect of alcohol on protein behaviour. Spectroscopic investigations show that there are no significant changes in conformational structures of the protein within the range of alcohol concentrations where the catalytic activity ( k cat) and thermal stability ( T m) of Mb decrease. Neutron scattering measurements indicate that the characteristic times related to protein internal fluctuations increase when the methanol molar fraction in the mixtures increases. This suggests a direct relationship between the protein internal motion rate and the catalytic activity.

From Powder to Solution: Hydration Dependence of Human Hemoglobin Dynamics Correlated to Body Temperature

A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.

Temperature dependence on structure and dynamics of Bovine Pancreatic Trypsin Inhibitor (BPTI): A neutron scattering study

We have studied the influence of temperature on the structure of BPTI in solution by small angle neutron scattering. We have investigated the variation of the radius of gyration and the modification of the shape of BPTI between ambient temperature and 368 K. Results have shown an increase of the radius of gyration from 10.9 Å at ambient temperature up to 13.3 Å at 368 K. Global and internal dynamics of BPTI in solution were studied by quasielastic neutron scattering. The analysis of neutron data in terms of intermediate scattering function reveals two relaxation times τ 1 and τ 2 related respectively to global translational diffusive motions and to internal motions of protein. Motions of protons belonging to lateral chains of residues located at the surface of the protein have been detected. The results are compared to the recently published results concerning the influence of pressure on structure and dynamics of BPTI in solution [Appavou MS et al. Biochimica et Biophysica Acta, 1764, 2006, pp 414–423].

A unified model of protein dynamics

Protein functions require conformational motions. We show here that the dominant conformational motions are slaved by the hydration shell and the bulk solvent. The protein contributes the structure necessary for function. We formulate a model that is based on experiments, insights from the physics of glass-forming liquids, and the concepts of a hierarchically organized energy landscape. To explore the effect of external fluctuations on protein dynamics, we measure the fluctuations in the bulk solvent and the hydration shell with broadband dielectric spectroscopy and compare them with internal fluctuations measured with the Mössbauer effect and neutron scattering. The result is clear. Large-scale protein motions are slaved to the fluctuations in the bulk solvent. They are controlled by the solvent viscosity, and are absent in a solid environment. Internal protein motions are slaved to the beta fluctuations of the hydration shell, are controlled by hydration, and are absent in a dehydrated protein. The model quantitatively predicts the rapid increase of the mean-square displacement above approximately 200 K, shows that the external beta fluctuations determine the temperature- and time-dependence of the passage of carbon monoxide through myoglobin, and explains the nonexponential time dependence of the protein relaxation after photodissociation.

REACH: A program for coarse-grained biomolecular simulation

REACH ( Realistic Extension Algorithm via Covariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance–covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. The method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence. Program summary Program title: REACH Catalogue identifier: AEDA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 42 244 No. of bytes in distributed program, including test data, etc.: 3 682 118 Distribution format: tar.gz Programming language: FORTRAN 77 Computer: x86 PC Operating system: GNU/Linux, SUSE and Red Hat RAM: Depends on the system size to be calculated Word size: 32 or 64 bits Classification: 3 External routines: LAPACK, BLAS Nature of problem: A direct calculation of force field for residue-scale coarse-grained biomolecular simulation derived from atomistic molecular dynamics trajectory. Solution method: A variance–covariance matrix and the associated Hessian (second-derivative) matrix are calculated from an atomistic molecular dynamics trajectory of single-domain protein internal motion and the off-diagonal Hessian matrix is fitted to that of a residue-scale elastic network model. The resulting force constants for the residue pair interactions are expressed as model functions as a function of pairwise distance. Running time: Depends on the system size and the number of MD trajectory frames used. The test run provided with the distribution takes only a few seconds to execute.

Hemoglobin Dynamics in Red Blood Cells: Correlation to Body Temperature

A transition in hemoglobin behavior at close to body temperature has been discovered recently by micropipette aspiration experiments on single red blood cells (RBCs) and circular dichroism spectroscopy on hemoglobin solutions. The transition temperature was directly correlated to the body temperatures of a variety of species. In an exploration of the molecular basis for the transition, we present neutron scattering measurements of the temperature dependence of hemoglobin dynamics in whole human RBCs in vivo. The data reveal a change in the geometry of internal protein motions at 36.9°C, at human body temperature. Above that temperature, amino acid side-chain motions occupy larger volumes than expected from normal temperature dependence, indicating partial unfolding of the protein. Global protein diffusion in RBCs was also measured and the findings compared favorably with theoretical predictions for short-time self-diffusion of noncharged hard-sphere colloids. The results demonstrated that changes in molecular dynamics in the picosecond time range and angstrom length scale might well be connected to a macroscopic effect on whole RBCs that occurs at body temperature.

Protein fluctuations explored by inelastic neutron scattering and dielectric relaxation spectroscopy

Glasses, supercooled liquids and proteins share common properties, in particular the existence of an energy landscape and the presence of two types of fluctuations, α and β. While the effect of α fluctuations on proteins has been known for a few years, the effect of β fluctuations has not been fully understood. By comparing neutron-scattering data on the protein myoglobin with β fluctuations in the hydration shell measured by dielectric relaxation spectroscopy, we show that the internal protein motions are slaved to these fluctuations. We also show that there is no ‘dynamical transition’ in proteins near 200 K. The rapid increase in the mean-square displacement with temperature in many neutron-scattering experiments can be quantitatively predicted by β fluctuations in the hydration shell.

Re-Evaluation of the Model-Free Analysis of Fast Internal Motion in Proteins Using NMR Relaxation

NMR spin relaxation retains a central role in the characterization of the fast internal motion of proteins and their complexes. Knowledge of the distribution and amplitude of the motion of amino acid side chains is critical for the interpretation of the dynamical proxy for the residual conformational entropy of proteins, which can potentially significantly contribute to the entropy of protein function. A popular treatment of NMR relaxation phenomena in macromolecules dissolved in liquids is the so-called model-free approach of Lipari and Szabo. The robustness of the mode-free approach has recently been strongly criticized and the remarkable range and structural context of the internal motion of proteins, characterized by such NMR relaxation techniques, attributed to artifacts arising from the model-free treatment, particularly with respect to the symmetry of the underlying motion. We develop an objective quantification of both spatial and temporal asymmetry of motion and re-examine the foundation of the model-free treatment. Concerns regarding the robustness of the model-free approach to asymmetric motion appear to be generally unwarranted. The generalized order parameter is robustly recovered. The sensitivity of the model-free treatment to asymmetric motion is restricted to the effective correlation time, which is by definition a normalized quantity and not a true time constant and therefore of much less interest in this context. With renewed confidence in the model-free approach, we then examine the microscopic distribution of side chain motion in the complex between calcium-saturated calmodulin and the calmodulin-binding domain of the endothelial nitric oxide synthase. Deuterium relaxation is used to characterize the motion of methyl groups in the complex. A remarkable range of Lipari-Szabo model-free generalized order parameters are seen with little correlation with basic structural parameters such as the depth of burial. These results are contrasted with the homologous complex with the neuronal nitric oxide synthase calmodulin-binding domain, which has distinctly different thermodynamic origins for high affinity binding.

Analysis of the C12A-p8MTCP1 protein internal motions using fast spectral density mapping at multiple magnetic fields

La cartographie des densites spectrales a differentes valeurs d'induction magnetique est certainement la meilleure methode pour decrire le comportement dynamique d'une proteine en solution, a travers l'analyse des parametres de relaxation heteronucleaire 15 N. Cependant, de telles analyses ne sont que rarement reportees dans la litterature, probablement parce que cette methode est excessivement consommatrice de temps machine. En effet, si l'on utilise n valeurs differentes de champs magnetiques, l'echantillonnage discret de la fonction de densite spectrale par 2n + 1 points demande la mesure de 3n parametres de relaxation (n R 1 , n R 2 et n 15 N{ 1 H}NOEs), dans l'hypothese de validite de l'approximation des hautes frequences. Nous avons propose une nouvelle strategie qui permet de decrire la fonction densite spectrale par n + 2 points en ne mesurant qu'un total de n +2 parametres de relaxation heteronucleaire, moyennant quelques approximations dont nous avons verifie la validite par simulation. Appliquee a l'analyse de la proteine C12A-pB MTCP1 a cinq inductions differentes de champ magnetique, cette approche permet de diviser au minimum par deux le temps de mesure experimentale, sans alterer l'interpretation dynamique des fonctions de densite spectrale par le modele de Lipari-Szabo.

Asymmetric doublets in MAS NMR: coherent and incoherent mechanisms

It has been long noted that J-resolved doublets observed in solid-state MAS experiments are asymmetric. The asymmetry has been attributed to a coherent interference effect involving dipolar and CSA interactions. Recently, Bernd Reif and co-workers suggested that under fast MAS conditions the coherent portion of the effect is suppressed and it becomes possible to observe an incoherent mechanism reminiscent of TROSY. The researchers were able to observe the characteristic TROSY-type patterns in (15)N-(1)H(N) spectra of heavily deuterated protein samples (Chevlekov, Diehl, and Reif, previous article in this issue). In the present computer simulation study, we seek to obtain a unified picture of this phenomenon, including both coherent and incoherent aspects. The chosen model focuses on the (15)N-(1)H(N) pair from a polycrystalline sample subject to magic angle spinning. To mimic local dynamics, we assume that the corresponding peptide plane jumps between two orientations. The simulations demonstrate that this simple model reproduces both coherent and incoherent behavior, depending on the MAS speed and the time scale of local dynamics. Furthermore, semianalytical expressions can be derived for both coherent and incoherent (Redfield) limits. Of particular interest is the possibility to use solution-style Redfield results to probe internal protein motions, especially slower motions on the nanosecond time scale. Our simulations show that the differential relaxation measurement permits accurate determination of (15)N dipolar-CSA cross correlations already at moderately high MAS speed (ca 15 kHz).

How to Turn the Reaction Coordinate into Time

What are the internal motions of an ion channel protein when it “gates” between closed and open-channel conformations? In 2005, Zhou, Pearson, and Auerbach (ZPA) ( Biophys. J . 89:3680–3685) showed that Φ, a parameter derived from the forward and backward rate constants of a chemical reaction

Nonequilibrium Dynamic Mechanism for Allosteric Effect

Allosteric regulation is often viewed as thermodynamic in nature. However, protein internal motions during an enzymatic reaction cycle can slow the hoping processes over numerous potential barriers. We propose that regulating molecules may function by modifying the nonequilibrium protein dynamics. The theory predicts that an enzyme under the new mechanism has a different temperature dependence, waiting time distribution of the turnover cycle, and dynamic fluctuation patterns with and without an effector. Experimental tests of the theory are proposed.

A diverse view of protein dynamics from NMR studies of HIV‐1 protease flaps

Internal motion in proteins fulfills a multitude of roles in biological processes. NMR spectroscopy has been applied to elucidate protein dynamics at the atomic level, albeit at a low resolution, and is often complemented by molecular dynamics simulation. However, it is critical to justify the consistency between simulation results and conclusions often drawn from multiple experiments in which uncertainties arising from assumed motional models may not be explicitly evaluated. To understand the role of the flaps of HIV-1 protease dimer in substrate recognition and protease function, many molecular dynamics simulations have been performed. The simulations have resulted in various proposed models of the flap dynamics, some of which are more consistent than others with our working model previously derived from experiments. However, using the working model to discriminate among the simulation results is not straightforward because the working model was derived from a combination of NMR experiments and crystal structure data. In this study, we use the NMR chemical shifts and relaxation data of the protease "monomer" rather than structural data to narrow down the possible conformations of the flaps of the "dimer". For the first time, we show that the tips of the flaps in the unliganded protease dimer interact with each other in solution. Accordingly, we discuss the consistency of the simulations with the model derived from all experimental data.

Binding Pathways of Ligands to HIV‐1 Protease: Coarse‐grained and Atomistic Simulations

Multiscale simulations (coarse-grained Brownian dynamics simulations and all-atom molecular dynamics simulations in implicit solvent) were applied to reveal the binding processes of ligands as they enter the binding site of the HIV-1 protease. The initial structures used for the molecular dynamics simulations were generated based on the Brownian dynamics trajectories, and this is the first molecular dynamics simulation of modeling the association of a ligand with the protease. We found that a protease substrate successfully binds to the protein when the flaps are fully open. Surprisingly, a smaller cyclic urea inhibitor (XK263) can reach the binding site when the flaps are not fully open. However, if the flaps are nearly closed, the inhibitor must rearrange or binding can fail because the inhibitor cannot attain proper conformations to enter the binding site. Both the peptide substrate and XK263 can also affect the protein's internal motion, which may help the flaps to open. Simulations allow us to efficiently study the ligand binding processes and may help those who study drug discovery to find optimal association pathways and to design those ligands with the best binding kinetics.

Have enzyme folds evolved due to the role of protein dynamics in catalysis?

An integrated view of protein structure, dynamics and function is emerging, where proteins are considered as dynamically active assemblies and internal motions are closely linked to function such as enzyme catalysis. In the past, enzymes have been viewed as static entities and their high catalytic power has been explained on the basis of direct structural interactions between the enzyme and the substrate. More recently there is wide interest, both from experimental and computational groups, in investigating internal protein motions. Protein motions have been linked to the rate-enhancement achieved by enzymes. Protein residues far away from the active-site and playing dynamical role, in addition to the active-site residues, are conserved across species ranging from bacteria to human for several enzymes including cyclophilin A, dihydrofolate reductase and ribonuclease A.

High-Affinity Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type Cytochrome OmcA

The purified outer membrane bacterial protein OmcA binds densely to the surface of hematite (Fe2O3), permitting direct electron transfer to this solid mineral to reduce Fe (III) with an electron flux of about 1013 electrons /cm2/s. In the presence of hematite, there is a substantial increase in the amplitude of internal protein motions that correlate with metal reduction. Binding is highly favorable, with a partition coefficient of approximately 2 x 105 (DeltaGo' = -28 kJ/mol), where approximately 1014 OmcA proteins bind per cm2 to the solid metal surface, indicating the utility of using purified OmcA in the construction of a biofuel cell.

Internal diffusive and collective motions in proteins studied by neutron scattering

It is well known that water plays a major role in the stability and catalytic function of proteins. Both the effect of hydration water on the dynamics of proteins and the effect of proteins on the dynamics of water have been studied using inelastic neutron scattering. Dynamic neutron scattering is the most direct probe of diffusive and collective protein dynamics on the picosecond–nanosecond timescale. We present here results for C-phycocyanin, which is a globular protein important for photosynthesis. It can be obtained in protonated and deuterated forms. Diffusive motions have been studied using the protonated C-phycocyanin protein. The collective dynamics has been investigated using the fully deuterated C-phycocyanin protein. Comparison is made with results of molecular dynamics simulation.

Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model

The internal motions of proteins may serve as a “gate” in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to study the gated association rate constants of HIV-1 proteases and drugs. The computed gated association rate constants of three protease mutants, G48V/V82A/I84V/L90M, G48V, and L90M with three drugs, amprenavir, indinavir, and saquinavir, yield good agreements with experiments. The work shows that the flap dynamics leads to “slow gating”. The simulations suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a lower gated rate constant. The developed methodology is fast and provides an efficient way to predict the gated association rate constants for various protease mutants and ligands.

Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution.

The physical basis of protein structure, dynamics and function has been intensely studied for several decades. Indeed since the new millennium there has been a tremendous expansion in the number of unique topological folds that have been characterized at high resolution by crystallographic and nuclear magnetic resonance (NMR) based methods. In the midst of this rush towards a grand scale structural genomics effort, a quieter effort dedicated to the experimental characterization of protein conformational heterogeneity has also emerged. The influence of atomic scale structure on molecular recognition and catalysis by proteins is often the focus of attention while the role of dynamics is largely unknown and frequently ignored. Nevertheless, it has long been recognized that proteins are indeed dynamic systems. Early insights into the time scale and character of protein internal motion largely employed local optical probes, unresolved hydrogen exchange, and one dimensional NMR techniques that, though limited, revealed a startling complexity and richness in the internal motion of proteins.1–5 These initial views contributed significantly to the development of current treatments of protein dynamics and thermodynamics.6 The connection to biological function rather than just biological form is more recent. Internal protein dynamics can potentially affect protein function through a variety of mechanisms, some of which are tautological or obvious in nature while others are subtle and remain to be fully explored and appreciated. There are now several examples of protein-protein and protein-ligand interactions that illustrate that dynamics may be fundamentally linked to function in several ways. Nuclear magnetic resonance (NMR) spectroscopy is very much at the center of current efforts to illuminate the nature of protein dynamics and their role in biological function. Here we will focus on the use of solution NMR methods to provide fast subnanosecond dynamics of protein side chains. The interested reader is referred to separate reviews in this issue by Goehlert and Stone,7 Tolman8 and Palmer and Massi9 discussing dynamics of the polypeptide backbone. The emerging success of NMR spectroscopy in the arena of protein dynamics rests on four general areas of development over the past two decades. First and perhaps foremost, triple resonance NMR spectroscopy now provides an efficient and robust set of tools for the comprehensive resonance assignment of proteins of significant size.10,11 These methods, in turn, derive much of their power from companion isotopic enrichment strategies,12,13 which have been subsequently refined to allow for isotopic labeling patterns that are optimized for NMR relaxation studies (vide infra). Two-dimensional sampling of relaxation has allowed for comprehensive studies to be efficiently undertaken, albeit with great instrumental cost.14–16 A variety of technical issues such as the effects of macromolecular tumbling and the influence of competing relaxation mechanisms have also been largely resolved (vide infra). These advances have positioned solution NMR spectroscopy to efficiently and comprehensively characterize the fast internal dynamics of proteins of significant size. This review seeks to provide a compact but reasonably complete description of the theoretical and technical foundation for solution NMR relaxation methods that are currently being brought to bear on fast sub-nanosecond protein side chain dynamics and to present a summary of current findings and their possible significance. A survey of basic observations about side chain dynamics derived from NMR-relaxation studies is presented along with several analyses meant to dispel commonly held but apparently inaccurate correlations between dynamics, structure and function. How dynamics can enter into fundamental thermodynamic and kinetic aspects of protein function is also reviewed and illustrated with intriguing results from several systems that point to a promising future for this area of inquiry.