@article {2022|2156, title = {Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies}, journal = {Frontiers in Molecular Biosciences}, volume = {9}, year = {2022}, pages = {826136}, abstract = {

Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2022.826136}, url = {https://www.frontiersin.org/article/10.3389/fmolb.2022.826136}, author = {Molza, Anne-Elisabeth and Westermaier, Yvonne and Moutte, Magali and Ducrot, Pierre and Danilowicz, Claudia and Godoy-Carter, Veronica and Prentiss, Mara and Robert, Charles H. and Marc Baaden and Pr{\'e}vost, Chantal} } @article {2022|2158, title = {Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {90}, year = {2022}, pages = {858-868}, abstract = {

Abstract Tripeptide loop closure (TLC) is a standard procedure to reconstruct protein backbone conformations, by solving a zero-dimensional polynomial system yielding up to 16 solutions. In this work, we first show that multiprecision is required in a TLC solver to guarantee the existence and the accuracy of solutions. We then compare solutions yielded by the TLC solver against tripeptides from the Protein Data Bank. We show that these solutions are geometrically diverse (up to Root mean square deviation with respect to the data) and sound in terms of potential energy. Finally, we compare Ramachandran distributions of data and reconstructions for the three amino acids. The distribution of reconstructions in the second angular space stands out, with a rather uniform distribution leaving a central void. We anticipate that these insights, coupled to our robust implementation in the Structural Bioinformatics Library ( https://sbl.inria.fr/doc/Tripeptide_loop_closure-user-manual.html), will help understanding the properties of TLC reconstructions, with potential applications to the generation of conformations of flexible loops in particular.

}, keywords = {protein loop conformations, Ramachandran diagrams, robust numerics, tripeptide loop closure, tripeptides}, doi = {https://doi.org/10.1002/prot.26281}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.26281}, author = {O{\textquoteright}Donnell, Timoth{\'e}e and Robert, Charles H. and Cazals, Fr{\'e}d{\'e}ric} } @article {2021|2155, title = {Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom}, journal = {Bio-protocol}, volume = {11}, year = {2021}, pages = {e4097}, abstract = {

Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA nucleofilaments and their consequences on the filament-DNA and bound DNA-DNA interactions at different stages of the homologous recombination process can be modeled using the PTools/Heligeom software and subsequent molecular dynamics simulation with NAMD. Modeling methods dealing with helical macromolecular objects typically rely on symmetric assemblies and take advantage of known symmetry descriptors. Other methods dealing with single objects, such as MMTK or VMD, do not integrate the specificities of regular assemblies. By basing the model building on binding geometries at the protomer-protomer level, PTools/Heligeom frees the building process from a priori knowledge of the system topology and enables irregular architectures and symmetry disruption to be accounted for. doi: 10.21769/BioProtoc.4097

}, doi = {10.21769/BioProtoc.4097}, url = {www.bioprotocol.org/e4097}, author = {Boyer, B. and Laurent, B. and Robert, C. H. and Prevost, C.} } @article {2020|2077, title = {Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.}, journal = {Protein Sci}, volume = {29}, year = {2020}, month = {2020 Jan}, pages = {237-246}, abstract = {

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson-Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.

}, issn = {1469-896X}, doi = {10.1002/pro.3773}, author = {Laureanti, Joseph and Brandi, Juan and Offor, Elvis and Engel, David and Rallo, Robert and Ginovska, Bojana and Martinez, Xavier and Marc Baaden and Baker, Nathan A} } @article {2019|2079, title = {Molecular Graphics: Bridging Structural Biologists and Computer Scientists.}, journal = {Structure}, volume = {27}, year = {2019}, month = {2019 11 05}, pages = {1617-1623}, abstract = {

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

}, issn = {1878-4186}, doi = {10.1016/j.str.2019.09.001}, author = {Martinez, Xavier and Krone, Michael and Alharbi, Naif and Rose, Alexander S and Laramee, Robert S and O{\textquoteright}Donoghue, Sean and Marc Baaden and Chavent, Matthieu} } @inbook {2018|2085, title = {Applications to water transport systems: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {389-414}, issn = {1364-5498}, doi = {10.1039/c8fd90022a}, author = {Marc Baaden and Barboiu, Mihail and Borthakur, Manash Pratim and Chen, Chun-Long and Coalson, Rob and Davis, Jeffery and Freger, Viatcheslav and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hirunpinyopas, Wisit and Horner, Andreas and Hou, Jun-Li and Hummer, Gerhard and Iamprasertkun, Pawin and Kazushi, Kinbara and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Mitra, Sushanta and Murail, Samuel and Noy, Aleksandr and Nunes, Suzana and Pohl, Peter and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish} } @inbook {2018|2082, title = {Biomimetic water channels: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {205-229}, issn = {1364-5498}, doi = {10.1039/c8fd90020e}, author = {Marc Baaden and Barboiu, Mihail and Bill, Roslyn M and Chen, Chun-Long and Davis, Jeffery and Di Vincenzo, Maria and Freger, Viatcheslav and Fr{\"o}ba, Michael and Gale, Philip A and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hou, Jun-Li and Hummer, Gerhard and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Murail, Samuel and Pohl, Peter and Sansom, Mark and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish and V{\"o}gele, Martin} } @article {2017, title = {Mobility and core-protein binding patterns of disordered C-terminal tails in β-tubulin isotypes.}, journal = {Biochemistry}, volume = { 56}, year = {2017}, pages = {1746{\textendash}1756}, chapter = {1746}, abstract = {

Although they play a significant part in the regulation of microtubule structure, dynamics and function, the disordered C-terminal tails of tubulin remain invisible to experimental structural methods and do not appear in the crystallographic structures that are currently available in the Protein Data Bank. Interestingly, these tails concentrate most of the sequence variability between tubulin isotypes, and are the sites of the principal post-translational modifications undergone by this protein. Using homology modeling, we developed two complete models for the human αI/βI and αI/βIII tubulin isotypes that include their C-terminal tails. We then investigated the conformational variability of the two β-tails using long time-scale classical Molecular Dynamics (MD) simulations that revealed similar features, notably the unexpected presence of common anchoring regions on the surface of the tubulin dimer, but also distinctive mobility or interaction patterns, some of which could be related to the tail lengths and charge distributions. We also observed in our simulations that the C-terminal tail from the βI isotype, but not the βIII, formed contacts in the putative binding site of a recently discovered peptide that disrupts microtubule formation in glioma cells. Hindering the binding site in the βI isotype would be consistent with this peptide\’s preferential disruption of microtubule formation in glioma, whose cells overexpress βIII, compared to normal glial cells. While these observations need to be confirmed with more intensive sampling, our study opens up new perspectives for the development of isotype-specific chemotherapy drugs.

}, doi = {10.1021/acs.biochem.6b00988}, author = {Laurin, Yoann and Eyer, Joel and Charles H. Robert and Chantal Pr{\'e}vost and S Sacquin-Mora} } @conference {2017|2101, title = {Molecular Visualization of Computational Biology Data: A Survey of Surveys}, booktitle = {EuroVis 2017 - Short Papers}, year = {2017}, publisher = {The Eurographics Association}, organization = {The Eurographics Association}, isbn = {978-3-03868-043-7}, doi = {10.2312/eurovisshort.20171146}, author = {Alharbi, Naif and Alharbi, Mohammad and Martinez, Xavier and Krone, Michael and Rose, Alexander S. and Marc Baaden and Laramee, Robert S. and Chavent, Matthieu}, editor = {Barbora Kozlikova and Tobias Schreck and Thomas Wischgoll} } @article {2016|1661, title = {Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes}, journal = {J. Comput. Chem.}, volume = {37}, year = {2016}, month = {mar}, pages = {752}, chapter = {739}, abstract = {

The number of local minima of the potential energy landscape (PEL) of molecular systems generally grows exponentially with the number of degrees of freedom, so that a crucial property of PEL exploration algorithms is their ability to identify local minima, which are low lying and diverse. In this work, we pres- ent a new exploration algorithm, retaining the ability of basin hopping (BH) to identify local minima, and that of transition based rapidly exploring random trees (T-RRT) to foster the exploration of yet unexplored regions. This ability is obtained by interleaving calls to the extension procedures of BH and T- RRT, and we show tuning the balance between these two types of calls allows the algorithm to focus on low lying regions. Computational efficiency is obtained using state-of- the art data structures, in particular for searching approximate nearest neighbors in metric spaces. We present results for the BLN69, a protein model whose conformational space has dimension 207 and whose PEL has been studied exhaustively. On this system, we show that the propensity of our algorithm to explore low lying regions of the landscape significantly out- performs those of BH and T-RRT.

}, doi = {10.1002/jcc.24256}, author = {Christine A. Roth and Tom Dreyfus and Charles H. Robert and Fr{\'e}d{\'e}ric Cazals} } @article {2015|1657, title = {Changes in protein structure at the interface accompanying complex formation.}, journal = {Iucrj}, volume = {2}, number = {Pt 6}, year = {2015}, month = {nov}, pages = {643{\textendash}652}, publisher = {Department of Biochemistry, Bose Institute , P-1/12 CIT Scheme VIIM, Kolkata 700 054, India.}, abstract = {Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69\%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16\% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.}, doi = {10.1107/S2052252515015250}, author = {Chakravarty, Devlina and Janin, Jo{\"e}l and Charles H. Robert and Chakrabarti, Pinak} } @article {2015|1679, title = {Conformational ensembles and sampled landscapes: analysis and comparison}, journal = {J. Comp. Chem.}, volume = {36}, year = {2015}, pages = {1213{\textendash}31}, author = {Fr{\'e}d{\'e}ric Cazals and A Roth and T Dreyfus and D Mazauric and Charles H. Robert} } @article {2015|1965, title = {An integrative approach to the study of filamentous oligomeric assemblies, with application to {R}ec{A}}, journal = {Plos One}, volume = {in press}, year = {2015}, pages = {e0116414}, abstract = {

Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called \"extended\" and \"compressed\" forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.

}, doi = {10.1371/journal.pone.0116414}, author = {Benjamin Boyer and Johann Ezelin and Pierre Poulain and A Saladin and Martin Zacharias and Charles H. Robert and Chantal Pr{\'e}vost} } @article {2015|1586, title = {Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin}, journal = {Biochemistry}, volume = {54}, number = {23}, year = {2015}, month = {jun}, pages = {3660{\textendash}3669}, doi = {10.1021/acs.biochem5b00146}, author = {Laurin, Y. and Savarin, P. and Charles H. Robert and M. Takahashi and Eyer, J. and Chantal Pr{\'e}vost and S Sacquin-Mora} } @article {2014|1412, title = {{E}xa{V}iz: a flexible framework to analyse, steer and interact with molecular dynamics simulations}, journal = {Faraday Discuss.}, volume = {169}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1039/c3fd00142c}{10.1039/c3fd00142c}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25340956}{25340956}]}, pages = {119{\textendash}142}, author = {Dreher, M and Prevoteau-Jonquet, J and Trellet, M and Piuzzi, M and Marc Baaden and Raffin, B and Nicolas F{\'e}rey and Robert, S and Limet, S.} } @article {2014|1772, title = {INRIA Tech Report: Conformational ensembles and sampled landscapes: analysis and comparison.}, year = {2014}, author = {Fr{\'e}d{\'e}ric Cazals and T. Dreyfus and D. Mazauric and A. Roth and Charles H. Robert} } @article {2013|1531, title = {Interactive Molecular Dynamics: Scaling up to Large Systems.}, journal = {Procedia Comput. Sci.}, volume = {18}, year = {2013}, pages = {20{\textendash}29}, doi = {10.1016/j.procs.2013.05.165}, author = {M. Dreher and M. Piuzzi and A. Turki and Matthieu Chavent and Marc Baaden and Nicolas F{\'e}rey and S. Limet and B. Raffin and S. Robert} } @inbook {2013|1499, title = {Modeling macromolecular complexes: a journey across scales}, booktitle = {Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor}, year = {2013}, note = {(in press)}, publisher = {Springer-Verlag Berlin Heidelberg}, organization = {Springer-Verlag Berlin Heidelberg}, author = {Fr{\'e}d{\'e}ric Cazals and Tom Dreyfus and Charles H. Robert} } @article {2013|1976, title = {Reassessing buried surface areas in protein-protein complexes.}, journal = {Protein Sci.}, volume = {22}, year = {2013}, month = {aug}, pages = {1453{\textendash}57}, abstract = {

The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20\%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3\% greater than in their unbound state, and the BSA, 7\% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.

}, keywords = {binding free energy, conformation changes, protein-protein interaction, solvent accessible surface}, doi = {10.1002/pro.2330}, author = {Chakravarty, Devlina and Guharoy, Mainak and Robert, Charles H. and Chakrabarti, Pinak and Janin, Jo{\"e}l} } @article {2013|1814, title = {Towards Morse theory for point cloud data.}, journal = {Inria Tech Reports}, number = {8331}, year = {2013}, publisher = {Inria}, url = {http://hal.inria.fr/hal-00848753}, author = {F. Cazals and C. Mueller and C. Robert and A. Roth} } @article {2011|1665, title = {Community-wide assessment of protein-interface modeling suggests improvements to design methodology.}, journal = {J. Mol. Biol.}, volume = {414}, year = {2011}, month = {nov}, pages = {289{\textendash}302}, abstract = {

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.

}, keywords = {Binding Sites, Models, Molecular, Protein Binding, Proteins}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.031}, author = {Fleishman, Sarel J and Whitehead, Timothy A and Strauch, Eva-Maria and Corn, Jacob E and Qin, Sanbo and Zhou, Huan-Xiang and Mitchell, Julie C and Demerdash, Omar N A and Takeda-Shitaka, Mayuko and Terashi, Genki and Moal, Iain H and Li, Xiaofan and Bates, Paul A and Martin Zacharias and Park, Hahnbeom and Ko, Jun-su and Lee, Hasup and Seok, Chaok and Bourquard, Thomas and Bernauer, Julie and Poupon, Anne and Az{\'e}, J{\'e}r{\^o}me and Soner, Seren and Ovali, Sefik Kerem and Ozbek, Pemra and Tal, Nir Ben and Haliloglu, T{\"u}rkan and Hwang, Howook and Vreven, Thom and Pierce, Brian G and Weng, Zhiping and P{\'e}rez-Cano, Laura and Pons, Carles and Fern{\'a}ndez-Recio, Juan and Jiang, Fan and Yang, Feng and Gong, Xinqi and Cao, Libin and Xu, Xianjin and Liu, Bin and Wang, Panwen and Li, Chunhua and Wang, Cunxin and Charles H. Robert and Guharoy, Mainak and Liu, Shiyong and Huang, Yangyu and Li, Lin and Guo, Dachuan and Chen, Ying and Xiao, Yi and London, Nir and Itzhaki, Zohar and Schueler-Furman, Ora and Inbar, Yuval and Potapov, Vladimir and Cohen, Mati and Schreiber, Gideon and Tsuchiya, Yuko and Kanamori, Eiji and Standley, Daron M and Nakamura, Haruki and Kinoshita, Kengo and Driggers, Camden M and Hall, Robert G and Morgan, Jessica L and Hsu, Victor L and Zhan, Jian and Yang, Yuedong and Zhou, Yaoqi and Kastritis, Panagiotis L and Bonvin, Alexandre M J J and Zhang, Weiyi and Camacho, Carlos J and Kilambi, Krishna P and Sircar, Aroop and Gray, Jeffrey J and Ohue, Masahito and Uchikoga, Nobuyuki and Matsuzaki, Yuri and Ishida, Takashi and Akiyama, Yutaka and Khashan, Raed and Bush, Stephen and Fouches, Denis and Tropsha, Alexander and Esquivel-Rodr{\'\i}guez, Juan and Kihara, Daisuke and Stranges, P Benjamin and Jacak, Ron and Kuhlman, Brian and Huang, Sheng-You and Zou, Xiaoqin and Wodak, Shoshana J and Janin, Jo{\"e}l and Baker, David} } @article {2011|1848, title = {Free energy profiles along consensus normal modes provide insight into {HIV}-1 protease flap opening}, journal = {J. Chem. Theor. Comput.}, volume = {7}, year = {2011}, pages = {2348{\textendash}52}, author = {Paulo R. Batista and Gaurav Pandey and Paulo M. Bisch and Paulo G. Pascutti and David Perahia and Charles H. Robert} } @article {2011|1437, title = {GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids}, journal = {J. Comput. Chem.}, volume = {32}, number = {13}, year = {2011}, month = {oct}, pages = {2924{\textendash}2935}, doi = {10.1002/jcc.21861/abstract}, author = {Matthieu Chavent and A. Vanel and A. Tek and B. L{\'e}vy and S. Robert and B. Raffin and Marc Baaden} } @inbook {2011|1417, title = {Receptor Flexibility in Ligand Docking and Virtual Screening.}, booktitle = {In-silico lead discovery}, year = {2011}, publisher = {Bentham Science Publishers}, organization = {Bentham Science Publishers}, author = {Maria A. Miteva and Charles H. Robert and J. D. Marechal and David Perahia} } @article {2010|1749, title = {A computational study of a recreated {G} protein-{GEF} reaction intermediate competent for nucleotide exchange: fate of the {M}g ion}, journal = {Plos One}, volume = {5}, number = {2}, year = {2010}, month = {feb}, pages = {e9142}, publisher = {Public Library of Science}, abstract = {

Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchange-competent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg2+ associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity.

}, doi = {10.1371/journal.pone.0009142}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0009142}, author = {M{\'e}riam Ben Hamida{\textendash}Reba\"{\i} and Charles H. Robert} } @article {2010|1736, title = {Consensus {M}odes, a robust description of protein collective motions from multiple-minima normal mode analysis{\textendash}application to the {HIV}-1 protease.}, journal = {Phys. Chem. Chem. Phys.}, volume = {12}, year = {2010}, month = {mar}, pages = {2850{\textendash}2859}, abstract = {

Protein flexibility is essential for enzymatic function, ligand binding, and protein-protein or protein-nucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining \"consensus\" normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap opening and closing that can be used in interpreting structural changes accompanying the binding of widely differing inhibitors.

}, doi = {10.1039/b919148h}, author = {Paulo R. Batista and Charles H. Robert and Jean-Didier Mar{\'e}chal and M{\'e}riam Ben Hamida{\textendash}Reba\"{\i} and Paulo Pascutti and Paulo M. Bisch and David P. Perahia} } @article {2010|1788, title = {How does heparin prevent the p{H} inactivation of cathepsin {B}? Allosteric mechanism elucidated by docking and molecular dynamics.}, journal = {Bmc Genomics}, volume = {11, S5}, year = {2010}, author = {Mauricio G.S. Costa and Paulo R. Batista and Cl{\`a}udio S Shida and Charles H. Robert and Paulo M. Bisch and Pedro G. Pascutti} } @article {2010|1977, title = {Side-chain rotamer transitions at protein-protein interfaces}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {78}, year = {2010}, pages = {3219{\textendash}25}, author = {Mainak Guharoy and Jo\�el Janin and Charles H. Robert} } @article {2009|1394, title = {Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.}, journal = {Chembiochem}, volume = {10}, year = {2009}, pages = {1349{\textendash}1359}, author = {Antoine Drevelle and Agathe Urvoas and M{\'e}riam Ben Hamida-Rebai and G{\'e}rard Van Vooren and Magali Nicaise and Marie Valerio-Lepiniec and Michel Desmadril and Charles H. Robert and Philippe Minard} } @article {2009|1779, title = {Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.}, journal = {Biochemistry}, volume = {48}, number = {2}, year = {2009}, month = {jan}, pages = {276{\textendash}288}, publisher = {Department of Biological Sciences and Cell Differentiation and Development Center, Marshall University, Huntington, West Virginia 25755, USA.}, abstract = {

Recent studies of the mechanisms involved in the regulation of gene expression in eukaryotic organisms depict a highly complex process requiring a coordinated rearrangement of numerous molecules to mediate DNA accessibility. Silencing in Saccharomyces cerevisiae involves the Sir family of proteins. Sir3p, originally described as repressing key areas of the yeast genome through interactions with the tails of histones H3 and H4, appears to have additional roles in that process, including involvement with a DNA binding component. Our in vitro studies focused on the characterization of Sir3p-nucleic acid interactions and their biological functions in Sir3p-mediated silencing using binding assays, EM imaging, and theoretical modeling. Our results suggest that the initial Sir3p recruitment is partially DNA-driven, highly cooperative, and dependent on nucleosomal features other than histone tails. The initial step appears to be rapidly followed by the spreading of silencing using linker DNA as a track.

}, doi = {10.1021/bi801705g}, author = {Nicholas L Adkins and Steve J McBryant and Cotteka N Johnson and Jennifer M Leidy and Christopher L Woodcock and Charles H Robert and Jeffrey C Hansen and Philippe T Georgel} } @article {2006|1810, title = {Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors}, journal = {Febs Lett.}, volume = {580}, number = {22}, year = {2006}, month = {oct}, pages = {5130{\textendash}5136}, abstract = {We demonstrate the utility of normal mode analysis in correctly predicting the binding modes of inhibitors in the active sites of matrix metalloproteinases (MMPs). We show the accuracy in predicting the positions of MMP-3 inhibitors is strongly dependent on which structure is used as the target, especially when it has been energy minimized. This dependency can be overcome by using intermediate structures generated along one of the normal modes previously calculated for a given target. These results may be of prime importance for further in silico drug discovery.}, doi = {10.1016/j.febslet.2006.08.037}, author = {Nicolas Floquet and Jean-Didier Mar{\'e}chal and Marie-Ange Badet-Denisot and Charles H Robert and Manuel Dauchez and David Perahia} } @article {2006|1658, title = {Odorant Binding and Conformational Dynamics in the Odorant-binding Protein}, journal = {J. Biol. Chem.}, volume = {281}, number = {40}, year = {2006}, month = {oct}, pages = {29929{\textendash}29937}, abstract = {In mammals, the olfactory epithelium secretes odorant-binding proteins (OBPs), which are lipocalins found freely dissolved in the mucus layer protecting the olfactory neurons. OBPs may act as passive transporters of predominantly hydrophobic odorant molecules across the aqueous mucus layer, or they may play a more active role in which the olfactory neuronal receptor recognizes the OBP-ligand complex. To better understand the molecular events accompanying the initial steps in the olfaction process, we have performed molecular dynamics studies of rat and pig OBPs with the odorant molecule thymol. These calculations provide an atomic level description of conformational changes and pathway intermediates that remain difficult to study directly. A series of eight independent molecular dynamics trajectories of rat OBP permitted the observation of a consensus pathway for ligand unbinding and the calculation of the potential of mean force (PMF) along this path. Titration microcalorimetry confirmed the specific binding of thymol to this protein with a strong hydrophobic component. In both rat and pig OBPs we observed lipocalin strand pair opening in the presence of ligand, consistent with potential roles of these proteins in olfactive receptor recognition.}, doi = {10.1074/jbc.M604869200}, author = {Eric Hajjar and David Perahia and Helene D{\'e}bat and Claude Nespoulous and Charles H. Robert} } @article {2004|1824, title = {Integrating three views of Arf1 activation dynamics}, journal = {J. Mol. Biol.}, volume = {337}, number = {4}, year = {2004}, month = {apr}, pages = {969{\textendash}983}, author = {Robert, Charles H and Cherfils, Jacqueline and Mouawad, Liliane and Perahia, David} } @article {2002|1790, title = {Differential core histone binding behavior: {R}{N}{A} polymerase {I} promoter region vs 5{S} r{D}{N}{A} positioning {D}{N}{A} sequences}, journal = {Cell Biochem. Biophys.}, volume = {37}, number = {1}, year = {2002}, pages = {1{\textendash}13}, author = {Georgel, Philippe T and Robert, Charles H} } @article {2002|1599, title = {New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations}, journal = {Biophys. J.}, volume = {82}, number = {6}, year = {2002}, month = {jun}, pages = {3224{\textendash}3245}, author = {Mouawad, Liliane and Perahia, David and Charles H. Robert and Guilbert, Christophe} } @article {1998|1822, title = {A soft, mean{\textendash}field potential derived from crystal contacts for predicting protein{\textendash}protein interactions}, journal = {J. Mol. Biol.}, volume = {283}, number = {5}, year = {1998}, month = {nov}, pages = {1037{\textendash}1047}, author = {Robert, C H and Janin, J} } @article {1997|1680, title = {Collective-variable Monte Carlo simulation of DNA}, journal = {J. Comp. Chem.}, volume = {18}, year = {1997}, pages = {2001{\textendash}2011}, author = {H. Gabb and Chantal Pr{\'e}vost and G. Bertucat and Charles H. Robert and Richard Lavery} } @article {1996|1666, title = {Finding and visualizing nucleic acid base stacking}, journal = {J Mol Graph}, volume = {14}, number = {1}, year = {1996}, month = {feb}, pages = {6{\textendash}11}, author = {Gabb, H A and Sanghani, S R and Charles H. Robert and Chantal Pr{\'e}vost} } @article {1995|1601, title = {Estimating friction coefficients of mixed globular/chain molecules, such as protein/{DNA} complexes}, journal = {Biophys. J.}, volume = {69}, number = {3}, year = {1995}, month = {sep}, pages = {840{\textendash}848}, author = {Charles H. Robert} } @article {1995|1969, title = {Significance of bound water to local chain conformations in protein crystals}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {92}, number = {16}, year = {1995}, month = {aug}, pages = {7600{\textendash}7604}, author = {Robert, C H and Ho, P S} } @article {1994|1968, title = {Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {91}, number = {24}, year = {1994}, month = {nov}, pages = {11621{\textendash}11625}, abstract = {Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a scanning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a three-dimensional organization of the fibers. The planar "zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histones H1 and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeling studies, suggest that chromatin fibers may exist as irregular three-dimensional arrays of nucleosomes even at low ionic strength.}, keywords = {Animals, Atomic Force, Biological, Chickens, Chromatin, Fixatives, Histones, Microscopy, Models, Non-P.H.S., Non-U.S. Gov{\textquoteright}t, Osmolar Concentration, P.H.S., Research Support, Sodium Chloride, U.S. Gov{\textquoteright}t}, author = {S. H. Leuba and G. Yang and C. Robert and B. Samori and K. van Holde and J. Zlatanova and C. Bustamante} } @article {1992|1596, title = {Kinetics of pore-mediated release of marker molecules from liposomes or cells}, journal = {Biophys. Chem.}, volume = {42}, number = {3}, year = {1992}, month = {apr}, pages = {291{\textendash}296}, author = {Schwarz, G and Charles H. Robert} } @article {1991|1593, title = {A combined study of aggregation, membrane affinity and pore activity of natural and modified melittin}, journal = {Biochim. Biophys. Acta}, volume = {1069}, number = {1}, year = {1991}, month = {oct}, pages = {77{\textendash}86}, author = {Stankowski, S and Pawlak, M and Kaisheva, E and Charles H. Robert and Schwarz, G} } @article {1990|1786, title = {A hierarchical {\textquoteleft}nesting{\textquoteright} approach to describe the stability of alpha helices with side-chain interactions}, journal = {Biopolymers}, volume = {30}, number = {3-4}, year = {1990}, pages = {335{\textendash}347}, author = {Robert, C H} } @article {1990, title = {Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells}, journal = {Biophys. J.}, volume = {58}, year = {1990}, pages = {577{\textendash}583}, author = {Schwarz, Gerhard and Charles H. Robert} } @article {1989|1785, title = {Allosteric formulation of thermal transitions in macromolecules, including effects of ligand binding and oligomerization}, journal = {Biopolymers}, volume = {28}, number = {10}, year = {1989}, month = {oct}, pages = {1705{\textendash}1729}, author = {Robert, C H and Colosimo, A and Gill, S J} } @article {1989|1821, title = {Binding of oxygen and carbon monoxide to the hemocyanin from the spiny lobster}, journal = {J. Mol. Biol.}, volume = {207}, number = {4}, year = {1989}, month = {jun}, pages = {829{\textendash}832}, author = {Connelly, P R and Johnson, C R and Robert, C H and Bak, H J and Gill, S J} } @article {1988|1597, title = {Analysis and parameter resolution in highly cooperative systems}, journal = {Biophys. Chem.}, volume = {30}, number = {2}, year = {1988}, month = {jun}, pages = {133{\textendash}141}, author = {Gill, S J and Connelly, P R and Di Cera, E and Charles H. Robert} } @inbook {1988, title = {Analysis of allosteric systems}, booktitle = {Biochemical Thermodynamics}, year = {1988}, publisher = {Elsevier}, organization = {Elsevier}, edition = {2nd}, address = {Holland}, author = {Gill, S. J. and Robert, C. H. and Wyman, J.} } @article {1988|1858, title = {Enthalpy of dimerization of benzene in water}, journal = {J. Phys. Chem.}, volume = {92}, year = {1988}, pages = {3623{\textendash}3625}, author = {D. Hallen and I. Wadso and D. J. Wasserman and C. H. Robert and S. J. Gill} } @article {1988|1589, title = {Linkage of organic phosphates to oxygen binding in human hemoglobin at high concentrations}, journal = {Biochemistry}, volume = {27}, number = {18}, year = {1988}, month = {sep}, pages = {6835{\textendash}6843}, author = {Charles H. Robert and Fall, L and Gill, S J} } @article {1988|1590, title = {Nested allosteric interaction in tarantula hemocyanin revealed through the binding of oxygen and carbon monoxide}, journal = {Biochemistry}, volume = {27}, number = {18}, year = {1988}, month = {sep}, pages = {6901{\textendash}6908}, author = {Decker, H and Connelly, P R and Charles H. Robert and Gill, S J} } @article {1988|1591, title = {Quantitative analysis of linkage in macromolecules when one ligand is present in limited total quantity}, journal = {Biochemistry}, volume = {27}, number = {18}, year = {1988}, month = {sep}, pages = {6829{\textendash}6835}, author = {Charles H. Robert and Gill, S J and Wyman, J} } @article {1987|1777, title = {Allosteric interpretation of the oxygen-binding reaction of human hemoglobin tetramers}, journal = {Biochemistry}, volume = {26}, number = {13}, year = {1987}, month = {jun}, pages = {4003{\textendash}4008}, author = {Di Cera, E and Robert, C H and Gill, S J} } @inbook {1987, title = {Calorimetric analysis of oxygen binding to lobster hemocyanin}, booktitle = {Invertebrate Oxygen Carriers}, year = {1987}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin}, author = {Parody-Morreale, A. and Robert, C. H. and Gill, S. J.} } @article {1987|1818, title = {Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen}, journal = {J. Biol. Chem.}, volume = {262}, number = {23}, year = {1987}, month = {aug}, pages = {10994{\textendash}10999}, author = {Parody-Morreale, A and Robert, C H and Bishop, G A and Gill, S J} } @article {1987|1820, title = {Carbon dioxide and oxygen linkage in human hemoglobin tetramers}, journal = {J. Mol. Biol.}, volume = {196}, number = {4}, year = {1987}, month = {aug}, pages = {927{\textendash}934}, author = {Doyle, M L and Di Cera, E and Robert, C H and Gill, S J} } @article {1987|1991, title = {Gas-solution microcalorimeter for determining heat binding curves}, journal = {Rev. Sci. Instr.}, volume = {58}, year = {1987}, pages = {632{\textendash}638}, author = {Bishop, G. A. and Parody-Morreale, A. and Robert, C. and and Gill, S. J.} } @inbook {1987|1429, title = {Nesting- An extension of the MWC model and its application to tarantula hemocyanin}, booktitle = {Invertebrate Oxygen Carriers}, year = {1987}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin}, author = {Decker, H. and Robert, C. H. and Gill, S. J.} } @article {1987|1967, title = {Nesting: hierarchies of allosteric interactions}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {84}, number = {7}, year = {1987}, month = {apr}, pages = {1891{\textendash}1895}, author = {Robert, C H and Decker, H and Richey, B and Gill, S J and Wyman, J} } @article {1987|1592, title = {Oxygen binding constants for human hemoglobin tetramers}, journal = {Biochemistry}, volume = {26}, number = {13}, year = {1987}, month = {jun}, pages = {3995{\textendash}4002}, author = {Gill, S J and Di Cera, E and Doyle, M L and Bishop, G A and Charles H. Robert} } @article {1986|1781, title = {Analysis of zeros of binding polynomials for tetrameric hemoglobins}, journal = {Biophys. Chem.}, volume = {24}, number = {3}, year = {1986}, month = {aug}, pages = {295{\textendash}309}, author = {Connelly, P R and Charles H. Robert and Briggs, W E and Gill, S J} } @article {1986|1602, title = {Cooperative free energies for nested allosteric models as applied to human hemoglobin}, journal = {Biophys. J.}, volume = {50}, number = {4}, year = {1986}, month = {oct}, pages = {747{\textendash}752}, author = {Gill, S J and Charles H. Robert and Coletta, M and Di Cera, E and Brunori, M} } @article {1985|1855, title = {Dry deposition of nitric acid to grass}, journal = {J. Geophys. Res.}, volume = {90}, year = {1985}, pages = {2085{\textendash}2090}, author = {B. A. Huebert and C. H. Robert} }