Measuring and comparing structural fluctuation patterns in large protein datasets

Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of ex- perimental and theoretical work on protein dynamics. Further insight into the dynamics?function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native struc- ture. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. Results: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than struc- tural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evo- lutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites.Fil: Fuglebakk, Edvin. University of Bergen; NoruegaFil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Reuter, Nathalie. University of Bergen; Norueg

TMM@: a web application for the analysis of transmembrane helix mobility

Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. It has been widely used to study transmembrane channels and pumps. It relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. In particular NMA can be used to study dynamics of TM regions, but no tool making this approach available for non-experts, has been available so far. Results: We developed the web-application TMM@ (TransMembrane α-helical Mobility analyzer). It uses NMA to characterize the propensity of transmembrane α-helices to be displaced. Starting from a structure file at the PDB format, the server computes the normal modes of the protein and identifies which helices in the bundle are the most mobile. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to further analyze the output data with their favourite software, raw results can also be downloaded. Conclusion: We built a novel and unique tool, TMM@, to study the mobility of transmembrane α-helices. The tool can be applied to for example membrane transporters and provides biologists studying transmembrane proteins with an approach to investigate which α-helices are likely to undergo the largest displacements, and hence which helices are most likely to be involved in the transportation of molecules in and out of the cell

Peptidomimetic inhibitors targeting the membrane-binding site of the neutrophil proteinase 3

Proteinase 3 (PR3), together with other serine proteases, such as neutrophil elastase (NE) and cathepsin G (CG), regulates inflammatory and immune responses. However, in comparison with NE and CG, there is increasing evidence that PR3 functions significantly differ. In particular, PR3 can bind to cell membranes and such membrane-bound PR3 (mbPR3) might be differently involved in the activation of cytokines, growth factors, cellular receptors, and in the regulation of cell apoptosis. For instance, PR3 membrane binding can block some “eat me” signals, notably, phosphatidylserine membrane lipid, and facilitate non-resolving inflammation. Based on the clear evidence that PR3 membrane binding affects the biological functions of PR3, we designed peptidomimetic inhibitors that can remove mbPR3 from the membrane surface in vitro without influencing PR3 catalytic activity. Such inhibitors, which specifically target PR3 binding to membranes, are still lacking. In particular, we found peptidomimetics that inhibit binding of PR3 to POPC:PS liposomes, which mimic the biological environment of PR3.publishedVersio

WEBnm@: a web application for normal mode analyses of proteins

BACKGROUND: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. RESULTS: We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on . We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. CONCLUSION: We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains

Cation‐π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field

Cation-π interactions between tryptophan and choline or trimethylated lysines are vital for many biological processes. The performance of the additive CHARMM36 force field against target quantum mechanical data is shown to reproduce QM equilibrium geometries but required modified Lennard-Jones potentials to accurately reproduce the QM interaction energies. The modified parameter set allows accurate modeling, including free energies, of cation-π indole-choline and indole-trimethylated lysines interactions relevant for protein–ligand, protein–membrane, and protein–protein interfaces.acceptedVersio

Membrane models for molecular simulations of peripheral membrane proteins

Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature.publishedVersio

Improving the force field description of tyrosine-choline cation-π interactions : QM investigation of phenol-N(Me)₄⁺ interactions

Cation-pi interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)(3)) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARIVIM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/augcc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-pi interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-pi interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants

Molecular Dynamics Simulations

figurasGroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant “opening” of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition.The Norwegian Research Council is acknowledged for CPU resources granted through the NOTUR supercomputing program (http://www.notur.no/) and Bergen Center for Computational Science for providing powerful computer facilities (http://www.bccs.uni.no/). Work at CSIC/UPV/EHU was financed by MICINN (Grant BUF2007-64452). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe