Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures

Abstract High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. Dynamin-2 is one of such protein forming helical oligomers that catalyze membrane fission. Mutations in this protein, where R465W is the most frequent, cause dominant centronuclear myopathy, but the molecular mechanisms underpinning the functional modifications remain to be investigated. To unveil the structural impact of this mutation in dynamin-2, we used full-atom molecular dynamics simulations and coarse-grained models and built dimers and helices of wild-type (WT) monomers, mutant monomers, or both WT and mutant monomers combined. Our results show that the mutation R465W causes changes in the interactions with neighbor amino acids that propagate through the oligomer. These new interactions perturb the contact between monomers and favor an extended conformation of the bundle signaling element (BSE), a dynamin region that transmits the conformational changes from the GTPase domain to the rest of the protein. This extended configuration of the BSE that is only relevant in the helices illustrates how a small change in the microenvironment surrounding a single residue can propagate through the oligomer structures of dynamin explaining how dominance emerges in large protein complexes.

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Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽

10.1093/glycob/cwab025 ◽

2021 ◽

Author(s):

Margrethe Gaardløs ◽

Sergey A Samsonov ◽

Marit Sletmoen ◽

Maya Hjørnevik ◽

Gerd Inger Sætrom ◽

...

Keyword(s):

Optical Tweezers ◽

Conformational Changes ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

Substrate Binding ◽

Interdisciplinary Approach ◽

Product Formation ◽

Titration Calorimetry ◽

Binding Groove ◽

Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

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Simplified geometric representations of protein structures identify complementary interaction interfaces

10.1101/2019.12.18.880575 ◽

2019 ◽

Cited By ~ 1

Author(s):

Caitlyn L. McCafferty ◽

Edward M. Marcotte ◽

David W. Taylor

Keyword(s):

Conformational Changes ◽

Protein Interaction ◽

Protein Function ◽

Large Scale ◽

Predictive Accuracy ◽

Protein Complexes ◽

Protein Structures ◽

Molecular Properties ◽

3D Structures ◽

Geometric Representations

ABSTRACTProtein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for molecular motions to optimize rigid 3D translations and rotations. However, such approaches can be computationally expensive, and faster, less accurate approximations may prove useful for large-scale prediction and assembly of 3D structures of multi-protein complexes. We asked if a reduced representation of protein geometry retains enough information about molecular properties to predict pairwise protein interaction interfaces that are tolerant of limited structural rearrangements. Here, we describe a cuboid transformation of 3D protein accessible surfaces on which molecular properties such as charge, hydrophobicity, and mutation rate can be easily mapped, implemented in the MorphProt package. Pairs of surfaces are compared to rapidly assess partner-specific potential surface complementarity. On two available benchmarks of 85 overall known protein complexes, we observed F1 scores (a weighted combination of precision and recall) of 19-34% at correctly identifying protein interaction surfaces, comparable to more computationally intensive 3D docking methods in the annual Critical Assessment of PRedicted Interactions. Furthermore, we examined the effect of molecular motion through normal mode simulation on a benchmark receptor-ligand pair and observed no marked loss of predictive accuracy for distortions of up to 6 Å RMSD. Thus, a cuboid transformation of protein surfaces retains considerable information about surface complementarity, offers enhanced speed of comparison relative to more complex geometric representations, and exhibits tolerance to conformational changes.

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Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations

Biochemical Society Transactions ◽

10.1042/bst20140144 ◽

2014 ◽

Vol 42 (5) ◽

pp. 1418-1424 ◽

Cited By ~ 28

Author(s):

Antreas C. Kalli ◽

Mark S. P. Sansom

Keyword(s):

Lipid Bilayers ◽

Molecular Mechanisms ◽

Phospholipid Composition ◽

Md Simulations ◽

Multiscale Simulation ◽

Lipid Binding ◽

Coarse Grained ◽

Peripheral Proteins ◽

Dynamics Simulations ◽

Phosphatidylinositol Phosphates

Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.

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Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314091463 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C853-C853

Author(s):

Driss Mountassif ◽

Lucien Fabre ◽

Kaustuv Basu ◽

Mihnea Bostina ◽

Slavica Jonic ◽

...

Keyword(s):

Atpase Activity ◽

Conformational Changes ◽

Single Particle ◽

Molecular Mechanisms ◽

Protein Complexes ◽

Normal Mode Analysis ◽

Single Amino Acid ◽

Mode Analysis ◽

Conformational Heterogeneity ◽

Aaa Atpase

p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.

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A coarse-grained methodology identifies intrinsic mechanisms that dissociate interacting protein pairs

10.1101/2020.07.10.196717 ◽

2020 ◽

Author(s):

Haleh Abdizadeh ◽

Farzaneh Jalalypour ◽

Ali Rana Atilgan ◽

Canan Atilgan

Keyword(s):

Conformational Changes ◽

Electromechanical Coupling ◽

Protein Complexes ◽

Three Dimensional ◽

Biological Significance ◽

Local Environment ◽

Coarse Grained ◽

Alternative Mode ◽

Interacting Protein ◽

Elastic Network

AbstractWe address the problem of triggering dissociation events between proteins that have formed a complex. We have collected a set of 25 non-redundant, functionally diverse protein complexes having high-resolution three-dimensional structures in both the unbound and bound forms. We unify elastic network models with perturbation response scanning (PRS) methodology as an efficient approach for predicting residues that have the propensity to trigger dissociation of an interacting protein pair, using the three-dimensional structures of the bound and unbound proteins as input. PRS reveals that while for a group of protein pairs, residues involved in the conformational shifts are confined to regions with large motions, there are others where they originate from parts of the protein unaffected structurally by binding. Strikingly, only a few of the complexes have interface residues responsible for dissociation. We find two main modes of response: In one mode, remote control of disassociation in which disruption of the electrostatic potential distribution along protein surfaces play the major role; in the alternative mode, mechanical control of dissociation by remote residues prevail. In the former, dissociation is triggered by changes in the local environment of the protein e.g. pH or ionic strength, while in the latter, specific perturbations arriving at the controlling residues, e.g. via binding to a third interacting partner is required for decomplexation. We resolve the observations by relying on an electromechanical coupling model which reduces to the usual elastic network result in the limit of the lack of coupling. We validate the approach by illustrating the biological significance of top residues selected by PRS on select cases where we show that the residues whose perturbation leads to the observed conformational changes correspond to either functionally important or highly conserved residues in the complex.

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SNP2SIM: A modular workflow for standardizing molecular simulation and functional analysis of protein variants

10.1101/457192 ◽

2018 ◽

Author(s):

Matthew D. McCoy ◽

Vikram Shivakumar ◽

Sridhar Nimmagadda ◽

Mohsin Saleet Jafri ◽

Subha Madhavan

Keyword(s):

Molecular Dynamics ◽

Protein Function ◽

Molecular Mechanisms ◽

Cancer Genomics ◽

Atomic Scale ◽

Protein Variant ◽

Docking Simulations ◽

Small Molecule Ligands ◽

Dynamics Simulations ◽

The Impact

AbstractMolecular simulations are used to provide insight into protein structure and function, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In addition to understanding molecular mechanisms and interactions on the atomic scale, translational applications of those approaches include drug screening, development of novel molecular therapies, and treatment planning when selecting targeted therapies. Supporting the continued development of these applications, we have developed the SNP2SIM workflow generates reproducible molecular dynamics and molecular docking simulations for downstream functional variant analysis. Three modules execute molecular dynamics simulations of solvated protein variant structures, analyze the resulting trajectories for unique structural conformations, and bind small molecule ligands to representative variant scaffolds. In addition to availability as a command line workflow, SNP2SIM modules are also available as individual apps on the Seven Bridges Cancer Genomics Cloud.

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A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

The Journal of General Physiology ◽

10.1085/jgp.201411335 ◽

2015 ◽

Vol 145 (5) ◽

pp. 443-456 ◽

Cited By ~ 25

Author(s):

Wenjun Zheng ◽

Feng Qin

Keyword(s):

Conformational Changes ◽

Md Simulation ◽

Molecular Mechanisms ◽

Transient Receptor Potential ◽

Trp Channels ◽

Normal Mode Analysis ◽

Coarse Grained ◽

Mode Analysis ◽

Structural Dynamic ◽

Heat Activation

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies.

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The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target

Scientific Reports ◽

10.1038/s41598-019-50213-0 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Renata Fioravanti Tarabini ◽

Luís Fernando Saraiva Macedo Timmers ◽

Carlos Eduardo Sequeiros-Borja ◽

Osmar Norberto de Souza

Keyword(s):

Mycobacterium Tuberculosis ◽

Conformational Changes ◽

Protein Function ◽

Environmental Changes ◽

Quaternary Structure ◽

Single Point ◽

Point Mutations ◽

Conformational Ensembles ◽

Dynamics Simulations ◽

Coa Reductase

Abstract Flexibility is a feature intimately related to protein function, since conformational changes can be used to describe environmental changes, chemical modifications, protein-protein and protein-ligand interactions. In this study, we have investigated the influence of the quaternary structure of 2-trans-enoyl-ACP (CoA) reductase or InhA, from Mycobacterium tuberculosis, to its flexibility. We carried out classical molecular dynamics simulations using monomeric and tetrameric forms to elucidate the enzyme’s flexibility. Overall, we observed statistically significant differences between conformational ensembles of tertiary and quaternary structures. In addition, the enzyme’s binding site is the most affected region, reinforcing the importance of the quaternary structure to evaluate the binding affinity of small molecules, as well as the effect of single point mutations to InhA protein dynamics.

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From residue coevolution to protein conformational ensembles and functional dynamics

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1508584112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13567-13572 ◽

Cited By ~ 80

Author(s):

Ludovico Sutto ◽

Simone Marsili ◽

Alfonso Valencia ◽

Francesco Luigi Gervasio

Keyword(s):

Protein Function ◽

Structure Prediction ◽

De Novo ◽

Learning Algorithm ◽

Coarse Grained ◽

Static Structure ◽

Biologically Relevant ◽

Alternative Structures ◽

Functional Dynamics ◽

Dynamics Simulations

The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful use in de novo protein native structure prediction. However, many aspects of protein function, such as substrate binding and product release in enzymatic activity, can be fully understood only in terms of an equilibrium ensemble of alternative structures, rather than a single static structure. In this paper we combine coevolutionary data and molecular dynamics simulations to study protein conformational heterogeneity. To that end, we adapt the Boltzmann-learning algorithm to the analysis of homologous protein sequences and develop a coarse-grained protein model specifically tailored to convert the resulting contact predictions to a protein structural ensemble. By means of exhaustive sampling simulations, we analyze the set of conformations that are consistent with the observed residue correlations for a set of representative protein domains, showing that (i) the most representative structure is consistent with the experimental fold and (ii) the various regions of the sequence display different stability, related to multiple biologically relevant conformations and to the cooperativity of the coevolving pairs. Moreover, we show that the proposed protocol is able to reproduce the essential features of a protein folding mechanism as well as to account for regions involved in conformational transitions through the correct sampling of the involved conformers.

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Differences in Thermal Structural Changes and Melting Between Mesophilic and Thermophilic Dihydrofolate Reductase Enzymes

10.26434/chemrxiv.12369737.v1 ◽

2020 ◽

Author(s):

Irene Maffucci ◽

Damien Laage ◽

Guillaume Stirnemann ◽

Fabio Sterpone

Keyword(s):

Dihydrofolate Reductase ◽

Conformational Changes ◽

Structural Changes ◽

Molecular Mechanisms ◽

Thermotoga Maritima ◽

Conformational Sampling ◽

Detailed Understanding ◽

Wide Range ◽

The Difference ◽

Dynamics Simulations

A key aspect of life's evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological processes. Despite important advances, a comprehensive picture of how thermophilic enzymes succeed in functioning under extreme temperatures remains incomplete. Here, we examine the temperature dependence of stability and of flexibility in the mesophilic monomeric Escherichia coli (Ec) and thermophilic dimeric Thermotoga maritima (Tm) homologs of the paradigm dihydrofolate reductase (DHFR) enzyme. We use all-atom molecular dynamics simulations and a replica-exchange scheme that allows to enhance the conformational sampling while providing at the same time a detailed understanding of the enzymes' behavior at increasing temperatures. We show that this approach reproduces the stability shift between the two homologs, and provides a molecular description of the denaturation mechanism by identifying the sequence of secondary structure elements melting as temperature increases, which is not straightforwardly obtained in the experiments. By repeating our approach on the hypothetical TmDHFR monomer, we further determine the respective effects of sequence and oligomerization in the exceptional stability of TmDFHR. We show that the intuitive expectation that protein flexibility and thermal stability are correlated is not verified. Finally, our simulations reveal that significant conformational fluctuations already take place much below the melting temperature. While the difference between the TmDHFR and EcDHFR catalytic activities is often interpreted via a simplified two-state picture involving the open and closed conformations of the key M20 loop, our simulations suggest that the two homologs' markedly different activity temperature dependences are caused by changes in the ligand-cofactor distance distributions in response to these conformational changes.

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