1
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Tulika T, Pedersen RW, Rimbault C, Ahmadi S, Rivera‐de‐Torre E, Fernández‐Quintero ML, Loeffler JR, Bohn M, Ljungars A, Ledsgaard L, Voldborg BG, Ruso‐Julve F, Andersen JT, Laustsen AH. Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library. Protein Sci 2023; 32:e4821. [PMID: 37897425 PMCID: PMC10659949 DOI: 10.1002/pro.4821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Recycling IgG antibodies bind to their target antigen at physiological pH in the blood stream and release them upon endocytosis when pH levels drop, allowing the IgG antibodies to be recycled into circulation via FcRn-mediated cellular pathways, while the antigens undergo lysosomal degradation. This enables recycling antibodies to achieve comparable therapeutic effect at lower doses than their non-recycling counterparts. The development of such antibodies is typically achieved by histidine doping of their variable regions or by performing in vitro antibody selection campaigns utilizing histidine doped libraries. Both are strategies that may introduce sequence liabilities. Here, we present a methodology that employs a naïve antibody phage display library, consisting of natural variable domains, to discover antibodies that bind α-cobratoxin from the venom of Naja kaouthia in a pH-dependent manner. As a result, an antibody was discovered that exhibits a 7-fold higher off-rate at pH 5.5 than pH 7.4 in bio-layer interferometry experiments. Interestingly, no histidine residues were found in its variable domains, and in addition, the antibody showed pH-dependent binding to a histidine-devoid antigen mutant. As such, the results demonstrate that pH-dependent antigen-antibody binding may not always be driven by histidine residues. By employing molecular dynamics simulations, different protonation states of titratable residues were found, which potentially could be responsible for the observed pH-dependent antigen binding properties of the antibody. Finally, given the typically high diversity of naïve antibody libraries, the methodology presented here can likely be applied to discover recycling antibodies against different targets ab initio without the need for histidine doping.
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Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Rasmus W. Pedersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Charlotte Rimbault
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Shirin Ahmadi
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | - Monica L. Fernández‐Quintero
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Markus‐Frederik Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Anne Ljungars
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Line Ledsgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Bjørn G. Voldborg
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Fulgencio Ruso‐Julve
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Jan Terje Andersen
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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2
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Borodina O, Ovchinnikova I, Fedorova O, Makarov G, Bartashevich E. Effect of 4-Hydroxy- -proline-containing podands on the stereoselectivity of Biginelli reaction according to molecular dynamics. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Berselli A, Alberini G, Benfenati F, Maragliano L. Computational study of ion permeation through claudin-4 paracellular channels. Ann N Y Acad Sci 2022; 1516:162-174. [PMID: 35811406 PMCID: PMC9796105 DOI: 10.1111/nyas.14856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Claudins (Cldns) form a large family of protein homologs that are essential for the assembly of paracellular tight junctions (TJs), where they form channels or barriers with tissue-specific selectivity for permeants. In contrast to several family members whose physiological role has been identified, the function of claudin 4 (Cldn4) remains elusive, despite experimental evidence suggesting that it can form anion-selective TJ channels in the renal epithelium. Computational approaches have recently been employed to elucidate the molecular basis of Cldns' function, and hence could help in clarifying the role of Cldn4. In this work, we use structural modeling and all-atom molecular dynamics simulations to transfer two previously introduced structural models of Cldn-based paracellular complexes to Cldn4 to reproduce a paracellular anion channel. Free energy calculations for ionic transport through the pores allow us to establish the thermodynamic properties driving the ion-selectivity of the structures. While one model shows a cavity permeable to chloride and repulsive to cations, the other forms barrier to the passage of all the major physiological ions. Furthermore, our results confirm the charge selectivity role of the residue Lys65 in the first extracellular loop of the protein, rationalizing Cldn4 control of paracellular permeability.
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Affiliation(s)
- Alessandro Berselli
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly,Department of Experimental MedicineUniversità degli Studi di GenovaGenovaItaly
| | - Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly,IRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly,IRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe)Istituto Italiano di TecnologiaGenovaItaly,Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
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4
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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5
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Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR. Int J Mol Sci 2022; 23:ijms23105419. [PMID: 35628231 PMCID: PMC9141556 DOI: 10.3390/ijms23105419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Variable domains of camelid antibodies (so-called nanobodies or VHH) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding nanobody by using molecular dynamics simulations in combination with experimentally derived data from nuclear magnetic resonance (NMR) spectroscopy. The NMR data contain both structural and dynamic information resolved at various timescales, which allows an assessment of the quality of protein MD simulations. Thus, in this study, we compared the ensembles for the anti-GFP-binding nanobody obtained from MD simulations with results from NMR. We find excellent agreement of the NOE-derived distance maps obtained from NMR and MD simulations and observe similar conformational spaces for the simulations with and without NOE time-averaged restraints. We also compare the measured and calculated order parameters and find generally good agreement for the motions observed in the ps–ns timescale, in particular for the CDR3 loop. Understanding of the CDR3 loop dynamics is especially critical for nanobodies, as this loop is typically critical for antigen recognition.
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6
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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7
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Borodina O, Ovchinnikova I, Makarov G, Yeltsov O, Titova Y, Fedorova O, Masunov AE, Bartashevich E. Pseudocyclic Form of 4-Hydroxypyrrolidine-2-carboxanilide Podands with Trioxyethylene Chain: Modeling, Conformational Search, and NMR Analysis. J Phys Chem A 2021; 125:6029-6041. [PMID: 34232648 DOI: 10.1021/acs.jpca.1c02613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 4-hydroxypyrrolidine-2-carboxanilide podand salt demonstrates catalytic activity in asymmetric Biginelli reaction. The systematic search for prevalent conformational state of the cation was carried out by computer simulations in combination with one- and two-dimensional NMR experiments. For that purpose, we proposed a novel algorithm for the generation and selection of conformers based on molecular dynamics and clustering in the space of principal components. The search had found an important trend of the podand to form a pseudocyclic structure with a horseshoe-shaped conformation of the oligooxyethylene fragment. This conformation is stabilized by different types of intramolecular hydrogen bonds between the acidic and basic centers of the two 4-hydroxypyrrolidine-2-carboxanilide residuals (branches). The proposed approach had made it possible to identify the major structural factors, providing a correlation between the calculated and experimental chemical shifts of hydrogen atoms in the 1H NMR spectra of the protonated podand.
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Affiliation(s)
- Olga Borodina
- South Ural State University,76 Lenina Avenue, Chelyabinsk 454080, Russia
| | - Irina Ovchinnikova
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskoy/20 Akademicheskaya Street, Yekaterinburg 620108, Russia
| | - Gennady Makarov
- South Ural State University,76 Lenina Avenue, Chelyabinsk 454080, Russia
| | - Oleg Yeltsov
- Ural Federal University named after the first President of Russia B. N. Yeltsin, Mira Street, 19, Yekaterinburg, 620002, Russia
| | - Yulia Titova
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskoy/20 Akademicheskaya Street, Yekaterinburg 620108, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Mira Street, 19, Yekaterinburg, 620002, Russia
| | - Olga Fedorova
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskoy/20 Akademicheskaya Street, Yekaterinburg 620108, Russia
| | - Artëm E Masunov
- South Ural State University,76 Lenina Avenue, Chelyabinsk 454080, Russia.,NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States.,School of Modeling, Simulation, and Training, University of Central Florida, 3100 Technology Parkway, Orlando, Florida 32816, United States
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8
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Chen AY, Brooks BR, Damjanovic A. Determinants of conductance of a bacterial voltage-gated sodium channel. Biophys J 2021; 120:3050-3069. [PMID: 34214541 DOI: 10.1016/j.bpj.2021.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/22/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022] Open
Abstract
Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel NavMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Nav channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na+ in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.
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Affiliation(s)
- Ada Y Chen
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ana Damjanovic
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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9
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Wegrzyn K, Zabrocka E, Bury K, Tomiczek B, Wieczor M, Czub J, Uciechowska U, Moreno-Del Alamo M, Walkow U, Grochowina I, Dutkiewicz R, Bujnicki JM, Giraldo R, Konieczny I. Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA. Nucleic Acids Res 2021; 49:3394-3408. [PMID: 33660784 PMCID: PMC8034659 DOI: 10.1093/nar/gkab113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/24/2022] Open
Abstract
An essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the broad host range plasmid RK2, in addition to two winged helix domains, contains a third DNA-binding domain. The phylogenetic analysis revealed that the composition of this unique domain is typical within the described TrfA-like protein family. Both in vitro and in vivo experiments involving the constructed TrfA mutant proteins showed that the newly identified domain is essential for the formation of the protein complex with DNA, contributes to the avidity for interaction with DNA, and the replication activity of the initiator. The analysis of mutant proteins, each containing a single substitution, showed that each of the three domains composing TrfA is essential for the formation of the protein complex with DNA. Furthermore, the new domain, along with the winged helix domains, contributes to the sequence specificity of replication initiator interaction within the plasmid replication origin.
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Affiliation(s)
- Katarzyna Wegrzyn
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Elzbieta Zabrocka
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Katarzyna Bury
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Milosz Wieczor
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Urszula Uciechowska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - María Moreno-Del Alamo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas - CSIC, E28040 Madrid, Spain
| | - Urszula Walkow
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Igor Grochowina
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.,Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Rafael Giraldo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas - CSIC, E28040 Madrid, Spain
| | - Igor Konieczny
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
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10
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Golla VK, Prajapati JD, Joshi M, Kleinekathöfer U. Exploration of Free Energy Surfaces Across a Membrane Channel Using Metadynamics and Umbrella Sampling. J Chem Theory Comput 2020; 16:2751-2765. [PMID: 32167296 DOI: 10.1021/acs.jctc.9b00992] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these translocations at an atomic level. To this end, calculations of free energy surfaces for these permeation processes are of key importance. Herein, we investigate the translocation of a variety of anionic solutes through the outer membrane pore OprO of the Gram-negative bacterium Pseudomonas aeruginosa using the metadynamics and umbrella sampling techniques at the all-atom level. Free energy calculations have been performed employing these two distinct methods in order to illustrate the difference in computed free energies, if any. The investigated solutes range from a single atomic chloride ion over a multiatomic monophosphate ion to a more bulky fosmidomycin antibiotic. The role of complexity of the permeating solutes in estimating accurate free energy profiles is demonstrated by performing extensive convergence analysis. For simple monatomic ions, good agreement between the well-tempered metadynamics and the umbrella sampling approaches is achieved, while for the permeation of the monophosphate ion differences start to appear. In the case of larger molecules such as fosmidomycin it is a tough challenge to achieve converged free energy profiles. This issue is mainly due to neglecting orthogonal degrees of freedom during the free energy calculations. Nevertheless, the freely driven metadynamics approach leads to clearly advantageous results. Additionally, atomistic insights of the translocation mechanisms of all three solutes are discussed.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Manas Joshi
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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11
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A noncanonical binding site of linezolid revealed via molecular dynamics simulations. J Comput Aided Mol Des 2019; 34:281-291. [DOI: 10.1007/s10822-019-00269-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/02/2019] [Indexed: 01/29/2023]
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12
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Strong SE, Hestand NJ, Kananenka AA, Zanni MT, Skinner JL. IR Spectroscopy Can Reveal the Mechanism of K + Transport in Ion Channels. Biophys J 2019; 118:254-261. [PMID: 31812356 DOI: 10.1016/j.bpj.2019.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023] Open
Abstract
Ion channels like KcsA enable ions to move across cell membranes at near diffusion-limited rates and with very high selectivity. Various mechanisms have been proposed to explain this phenomenon. Broadly, there is disagreement among the proposed mechanisms about whether ions occupy adjacent sites in the channel during the transport process. Here, using a mixed quantum-classical approach to calculate theoretical infrared spectra, we propose a set of infrared spectroscopy experiments that can discriminate between mechanisms with and without adjacent ions. These experiments differ from previous ones in that they independently probe specific ion binding sites within the selectivity filter. When ions occupy adjacent sites in the selectivity filter, the predicted spectra are significantly redshifted relative to when ions do not occupy adjacent sites. Comparisons between theoretical and experimental peak frequencies will therefore discriminate the mechanisms.
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Affiliation(s)
- Steven E Strong
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Nicholas J Hestand
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Natural and Applied Sciences, Evangel University, Springfield, Missouri
| | - Alexei A Kananenka
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - J L Skinner
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.
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13
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Theoretical conformational studies of podands containing (2S,4R)-4-hydroxyproline moieties. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02531-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Makarov GI, Bartashevich EV, Khnykina KA, Podgornov FV. Molecular dynamics simulation and experimental investigation of material and structural parameters of multicomponent ferroelectric liquid crystal mixture. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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Weiser LJ, Santiso EE. A CGenFF‐based force field for simulations of peptoids with both
cis
and
trans
peptide bonds. J Comput Chem 2019; 40:1946-1956. [DOI: 10.1002/jcc.25850] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/27/2019] [Accepted: 04/14/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Laura J. Weiser
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Campus Box 7905, Raleigh North Carolina 27695–7905
| | - Erik E. Santiso
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Campus Box 7905, Raleigh North Carolina 27695–7905
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16
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Sahoo A, Matysiak S. Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration. Phys Chem Chem Phys 2019; 21:22679-22694. [DOI: 10.1039/c9cp02765c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An overview of recent advances in computational investigation of peptide–lipid interactions in neurodegeneration – Alzheimer's, Parkinson's and Huntington's disease.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program
- Institute of Physical Science and Technology
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Biophysics Program
- Institute of Physical Science and Technology
- University of Maryland
- College Park
- USA
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17
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Makarov G, Makarova T. A noncanonical binding site of chloramphenicol revealed via molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2018; 1862:2940-2947. [DOI: 10.1016/j.bbagen.2018.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 01/13/2023]
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18
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Awasthi S, Nair NN. Exploring high‐dimensional free energy landscapes of chemical reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
| | - Nisanth N. Nair
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
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19
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Callahan KM, Roux B. Molecular Dynamics of Ion Conduction through the Selectivity Filter of the Na VAb Sodium Channel. J Phys Chem B 2018; 122:10126-10142. [PMID: 30351118 DOI: 10.1021/acs.jpcb.8b09678] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The determination of the atomic structures of voltage-gated bacterial sodium channels using X-ray crystallography has provided a first view of this family of membrane proteins. Molecular dynamics simulations offer one approach to clarify the underlying mechanism of permeation and selectivity in these channels. However, it appears that the intracellular gate of the pore domain is either closed or only open partially in the available X-ray structures. The lack of structure with a fully open intracellular gate poses a special challenge to computational studies aimed at simulating ion conduction. To circumvent this problem, we simulated a model of the NaVAb channel in which the transmembrane S5 and S6 helices of the pore domain have been truncated to provide direct open access to the intracellular entryway to the pore. Molecular dynamics simulations were carried out over a range of membrane potential and ion concentration of sodium and potassium. The simulations show that the NaVAb selectivity filter is essentially a cationic pore supporting the conduction of ions at a rate comparable to aqueous diffusion with no significant selectivity for sodium. Conductance and selectivity vary as a function of ion concentration for both cations. Permeation occurs primarily via a knock-on mechanism for both sodium and potassium, although the ion ordering in single file along the pore is not strictly maintained. The character of the outward current appears quite different from the inward current, with a buildup on ions in the selectivity filter prior to escape toward the extracellular side, indicating the presence of a rectification effect that is overcome by nonphysiological applied voltages.
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Affiliation(s)
- Karen M Callahan
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science , The University of Chicago , Chicago , Illinois 60637 , United States
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20
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Alberini G, Benfenati F, Maragliano L. Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel. J Phys Chem B 2018; 122:10783-10792. [DOI: 10.1021/acs.jpcb.8b06484] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
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21
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Prakash A, Fu CD, Bonomi M, Pfaendtner J. Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics. J Chem Theory Comput 2018; 14:4985-4990. [DOI: 10.1021/acs.jctc.8b00448] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Arushi Prakash
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher D. Fu
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Senior Scientist, Pacific Northwest National Laboratory, Richland, Washington, United States
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22
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Rudakov BV, Stash AI, Makarov GI, Matveychuk YV, Zherebtsov DA, Bartashevich EV. Why are reactions of 2- and 8-thioquinoline derivatives with iodine different? ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:974-980. [DOI: 10.1107/s2053229618009385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022]
Abstract
The crystal structures of 1,2-dihydro-1,1′-bi[thiazolo[3,2-a]quinoline]-10a,10a′-diium diiodide hemihydrate, C22H16N2S2
2+·2I−·0.5H2O, and 1,2-dihydro-1,1′-bi[thiazolo[3,2-a]quinoline]-10a,10a′-diium iodide triiodide, C22H16N2S2
2+·I−·I3
−, obtained during the reaction of 1,4-bis(quinolin-2-ylsulfanyl)but-2-yne (2TQB) with iodine, have been determined at 120 K. The crystalline products contain the dication as a result of the reaction proceeding along the iodocyclization pathway. This is fundamentally different from the previously observed reaction of 1,4-bis(quinolin-8-ylsulfanyl)but-2-yne (8TQB) with iodine under similar conditions. A comparative analysis of the possible conformational states indicates differences in the relative stabilities and free rotation for the 2- and 8-thioquinoline derivatives which lead to a disparity in the convergence of the potential reaction centres for 2TQB and 8TQB.
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23
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Abstract
Since the availability of the first crystal structure of a bacterial Na+ channel in 2011, understanding selectivity across this family of membrane proteins has been the subject of intense research efforts. Initially, free energy calculations based on molecular dynamics simulations revealed that although sodium ions can easily permeate the channel with their first hydration shell almost intact, the selectivity filter is too narrow for efficient conduction of hydrated potassium ions. This steric view of selectivity was subsequently questioned by microsecond atomic trajectories, which proved that the selectivity filter appears to the permeating ions as a highly degenerate, liquid-like environment. Although this liquid-like environment looks optimal for rapid conduction of Na+, it seems incompatible with efficient discrimination between similar ion species, such as Na+ and K+, through steric effects. Here extensive molecular dynamics simulations, combined with Markov state model analyses, reveal that at positive membrane potentials, potassium ions trigger a conformational change of the selectivity toward a nonconductive metastable state. It is this transition of the selectivity filter, and not steric effects, that prevents the outward flux of K+ at positive membrane potentials. This description of selectivity, triggered by the nature of the permeating ions, might have implications on the current understanding of how ion channels, and in particular bacterial Na+ channels, operate at the atomic scale.
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24
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Sakipov S, Sobolevsky AI, Kurnikova MG. Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6. Sci Rep 2018; 8:5715. [PMID: 29632318 PMCID: PMC5890290 DOI: 10.1038/s41598-018-23972-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/20/2018] [Indexed: 12/14/2022] Open
Abstract
Calcium is the most abundant metal in the human body that plays vital roles as a cellular electrolyte as well as the smallest and most frequently used signaling molecule. Calcium uptake in epithelial tissues is mediated by tetrameric calcium-selective transient receptor potential (TRP) channels TRPV6 that are implicated in a variety of human diseases, including numerous forms of cancer. We used TRPV6 crystal structures as templates for molecular dynamics simulations to identify ion binding sites and to study the permeation mechanism of calcium and other ions through TRPV6 channels. We found that at low Ca2+ concentrations, a single calcium ion binds at the selectivity filter narrow constriction formed by aspartates D541 and allows Na+ permeation. In the presence of ions, no water binds to or crosses the pore constriction. At high Ca2+ concentrations, calcium permeates the pore according to the knock-off mechanism that includes formation of a short-lived transition state with three calcium ions bound near D541. For Ba2+, the transition state lives longer and the knock-off permeation occurs slower. Gd3+ binds at D541 tightly, blocks the channel and prevents Na+ from permeating the pore. Our results provide structural foundations for understanding permeation and block in tetrameric calcium-selective ion channels.
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Affiliation(s)
- Serzhan Sakipov
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th St., New York, NY, 10032, USA
| | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA.
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25
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Fu CD, Pfaendtner J. Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics. J Chem Theory Comput 2018; 14:2516-2525. [DOI: 10.1021/acs.jctc.7b01289] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher D. Fu
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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26
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Jorgensen C, Furini S, Domene C. Energetics of Ion Permeation in an Open-Activated TRPV1 Channel. Biophys J 2017; 111:1214-1222. [PMID: 27653480 DOI: 10.1016/j.bpj.2016.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/11/2023] Open
Abstract
Ion channels enable diffusion of ions down physiological electrochemical gradients. Modulation of ion permeation is crucial for the physiological functioning of cells, and misregulation of ion channels is linked to a myriad of channelopathies. The ion permeation mechanism in the transient receptor potential (TRP) ion channel family is currently not understood at an atomistic level. In this work, we employed a simulation strategy for ion permeation (molecular-dynamics simulations with bias-exchange metadynamics) to study and compare monovalent (Na(+), K(+)) ion permeation in the open-activated TRP vanniloid-1 (TRPV1) ion channel. Using ∼3.6 μs of simulation trajectories, we obtained atomistic evidence for the nonselective nature of TRPV1. Our analysis shows that solvated monovalent ions permeate through the selectivity filter with comparable energetic barriers via a two-site mechanism. Finally, we confirmed that an intracellular binding site is located between the intracellular gate residues I679 and E684.
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Affiliation(s)
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Carmen Domene
- Department of Chemistry, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom.
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27
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Li Y, Sun R, Liu H, Gong H. Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:879-887. [DOI: 10.1016/j.bbamem.2017.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/12/2017] [Accepted: 02/05/2017] [Indexed: 12/30/2022]
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28
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Fu CD, Oliveira LFL, Pfaendtner J. Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations. J Chem Theory Comput 2017; 13:968-973. [PMID: 28212010 DOI: 10.1021/acs.jctc.7b00038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A persistent challenge in using the metadynamics method is deciding which degrees of freedom, or collective variables, should be biased because these selections are not obvious and require intuition about the system being studied. There are, however, collective variables, which can be constructed with only basic knowledge about the system studied, that provide an opportunity to alleviate this issue. We simulated two different reacting systems where two types of such collective variables (SPRINT coordinates and the collective variable-driven hyperdynamics method) were biased following the infrequent metadynamics method in order to recover the rates of reactions. We demonstrate that both generic collective variables are capable of reproducing the reaction rates of both systems and can enhance the efficiency of the simulation when compared to typical collective variables.
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Affiliation(s)
- Christopher D Fu
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Luiz F L Oliveira
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
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29
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Mollica L, Bessa LM, Hanoulle X, Jensen MR, Blackledge M, Schneider R. Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment. Front Mol Biosci 2016; 3:52. [PMID: 27668217 PMCID: PMC5016563 DOI: 10.3389/fmolb.2016.00052] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context.
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Affiliation(s)
- Luca Mollica
- CompuNet, Drug Discovery and Development, Istituto Italiano di Tecnologia Genova, Italy
| | - Luiza M Bessa
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | - Xavier Hanoulle
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | | | - Martin Blackledge
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes Grenoble, France
| | - Robert Schneider
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
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30
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Oakes V, Furini S, Domene C. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations. CURRENT TOPICS IN MEMBRANES 2016; 78:183-214. [PMID: 27586285 DOI: 10.1016/bs.ctm.2015.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs.
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Affiliation(s)
- V Oakes
- King's College London, London, United Kingdom
| | - S Furini
- University of Siena, Siena, Italy
| | - C Domene
- King's College London, London, United Kingdom; University of Oxford, Oxford, United Kingdom
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31
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Furini S, Domene C. Computational studies of transport in ion channels using metadynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1733-40. [PMID: 26891818 DOI: 10.1016/j.bbamem.2016.02.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/01/2016] [Accepted: 02/11/2016] [Indexed: 01/26/2023]
Abstract
Molecular dynamics simulations have played a fundamental role in numerous fields of science by providing insights into the structure and dynamics of complex systems at the atomistic level. However, exhaustive sampling by standard molecular dynamics is in most cases computationally prohibitive, and the time scales accessible remain significantly shorter than many biological processes of interest. In particular, in the study of ion channels, realistic models to describe permeation and gating require accounting for large numbers of particles and accurate interaction potentials, which severely limits the length of the simulations. To overcome such limitations, several advanced methods have been proposed among which is metadynamics. In this algorithm, an external bias potential to accelerate sampling along selected collective variables is introduced. This bias potential discourages visiting regions of the configurational space already explored. In addition, the bias potential provides an estimate of the free energy as a function of the collective variables chosen once the simulation has converged. In this review, recent contributions of metadynamics to the field of ion channels are discussed, including how metadynamics has been used to search for transition states, predict permeation pathways, treat conformational flexibility that underlies the coupling between gating and permeation, or compute free energy of permeation profiles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Simone Furini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci 16, I-53100 Siena, Italy
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, UK.
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32
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Ing C, Pomès R. Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016; 78:215-60. [DOI: 10.1016/bs.ctm.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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