1
|
Kienlein M, Zacharias M. How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations. Protein Sci 2024; 33:e5077. [PMID: 38888275 PMCID: PMC11184577 DOI: 10.1002/pro.5077] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
The substrate-binding domain 2 (SBD2) is an important part of the bacterial glutamine (GLN) transporter and mediates binding and delivery of GLN to the transporter translocation subunit. The SBD2 consists of two domains, D1 and D2, that bind GLN in the space between domains in a closed structure. In the absence of ligand, the SBD2 adopts an open conformation with larger space between domains. The GLN binding and closing are essential for the subsequent transport into the cell. Arginine (ARG) can also bind to SBD2 but does not induce closing and inhibits GLN transport. We use atomistic molecular dynamics (MD) simulations in explicit solvent to study ARG binding in the presence of the open SBD2 structure and observed reversible binding to the native GLN binding site with similar contacts but no transition to a closed SBD2 state. Absolute binding free energy simulations predict a considerable binding affinity of ARG and GLN to the binding site on the D1 domain. Free energy simulations to induce subsequent closing revealed a strong free energy penalty in case of ARG binding in contrast to GLN binding that favors the closed SBD2 state but still retains a free energy barrier for closing. The simulations allowed the identification of the molecular origin of the closing penalty in case of bound ARG and suggested a mutation of lysine at position 373 to alanine that strongly reduced the penalty and allowed closing even in the presence of bound ARG. The study offers an explanation of the molecular mechanism of how ARG competitively inhibits GLN from binding to SBD2 and from triggering the transition to a closed conformation. The proposed Lys373Ala mutation shows promise as a potential tool to validate whether a conformational mismatch between open SBD2 and the translocator is responsible for preventing ARG uptake to the cell.
Collapse
Affiliation(s)
- Maximilian Kienlein
- Center for Functional Protein Assemblies (CPA)Technical University of MunichGarchingGermany
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA)Technical University of MunichGarchingGermany
| |
Collapse
|
2
|
Rudani BA, Jakubowski A, Kriegs H, Wiegand S. Deciphering the guanidinium cation: Insights into thermal diffusion. J Chem Phys 2024; 160:214502. [PMID: 38828819 DOI: 10.1063/5.0215843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Thermophoresis, or thermodiffusion, is becoming a more popular method for investigating the interactions between proteins and ligands due to its high sensitivity to the interactions between solutes and water. Despite its growing use, the intricate mechanisms behind thermodiffusion remain unclear. This gap in knowledge stems from the complexities of thermodiffusion in solvents that have specific interactions as well as the intricate nature of systems that include many components with both non-ionic and ionic groups. To deepen our understanding, we reduce complexity by conducting systematic studies on aqueous salt solutions. In this work, we focused on how guanidinium salt solutions behave in a temperature gradient, using thermal diffusion forced Rayleigh scattering experiments at temperatures ranging from 15 to 35 °C. We looked at the thermodiffusive behavior of four guanidinium salts (thiocyanate, iodide, chloride, and carbonate) in solutions with concentrations ranging from 1 to 3 mol/kg. The guanidinium cation is disk-shaped and is characterized by flat hydrophobic surfaces and three amine groups, which enable directional hydrogen bonding along the edges. We compare our results to the behavior of salts with spherical cations, such as sodium, potassium, and lithium. Our discussions are framed around how different salts are solvated, specifically in the context of the Hofmeister series, which ranks ions based on their effects on the solvation of proteins.
Collapse
Affiliation(s)
- Binny A Rudani
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Andre Jakubowski
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Hartmut Kriegs
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Simone Wiegand
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| |
Collapse
|
3
|
Kim YS. Hydrocarbon Ionomeric Binders for Fuel Cells and Electrolyzers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303914. [PMID: 37814366 DOI: 10.1002/advs.202303914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/08/2023] [Indexed: 10/11/2023]
Abstract
Ionomeric binders in catalyst layers, abbreviated as ionomers, play an essential role in the performance of polymer-electrolyte membrane fuel cells and electrolyzers. Due to environmental issues associated with perfluoroalkyl substances, alternative hydrocarbon ionomers have drawn substantial attention over the past few years. This review surveys literature to discuss ionomer requirements for the electrodes of fuel cells and electrolyzers, highlighting design principles of hydrocarbon ionomers to guide the development of advanced hydrocarbon ionomers.
Collapse
Affiliation(s)
- Yu Seung Kim
- MPA-11: Materials Synthesis and Integrated Devices, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| |
Collapse
|
4
|
Masella M, Crudu A, Léonforté F. Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation. J Chem Phys 2021; 155:114903. [PMID: 34551548 DOI: 10.1063/5.0056508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid modeling approaches based on all-atom force fields to handle a solute and coarse-grained models to account for the solvent are promising numerical tools that can be used to understand the properties of large and multi-components solutions and thus to speed up the development of new industrial products that obey the standard of green and sustainable chemistry. Here, we discuss the ability of a full polarizable hybrid approach coupled to a standard molecular dynamics scheme to model the behavior in the aqueous phase and at infinite dilution conditions of a standard hydrophobic polyelectrolyte polymer whose charge is neutralized by explicit counterions. Beyond the standard picture of a polyelectrolyte behavior governed by an interplay between opposite intra-polyelectrolyte and inter-polyelectrolyte/counterion Coulombic effects, our simulations show the key role played by both intra-solute polarization effects and long range solute/solvent electrostatics to stabilize compact globular conformations of that polyelectrolyte. Our full polarizable hybrid modeling approach is thus a new theoretical tool well suited to be used in digital strategies for accelerating innovation for green science, for instance.
Collapse
Affiliation(s)
- Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Alina Crudu
- L'Oréal Research and Innovation, Aulnay-Sous-Bois, France
| | | |
Collapse
|
5
|
Yu L, Deng Z, Zhang W, Liu S, Zhang F, Zhou J, Ma C, Wang C. Opposite Regulatory Effects of Immobilized Cations on the Folding Vs. Assembly of Melittin. Front Chem 2021; 9:685947. [PMID: 34178946 PMCID: PMC8225954 DOI: 10.3389/fchem.2021.685947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Ions are crucial in modulating the protein structure. For the free ions in bulk solution, ammonium is kosmotropic (structure forming) and guanidinium is chaotropic (structure breaking) to the protein structure within the Hofmeister series. However, the effect of immobilized ions on a protein surface is less explored. Herein, we explored the influence of two immobilized cations (ammonium in the side chain of lysine and guanidinium in the side chain of arginine) on the folding and assembly of melittin. Melittin adopts an α-helix structure and is driven by hydrophobic interactions to associate into a helical bundle. To test the influence of immobilized cations on the peptide structure, we designed the homozygous mutants exclusively containing ammonium (melittin-K) or guanidinium (melittin-R) and compared the differences of melittin-K vs. melittin-R in their folding, assembly, and molecular functions. The side chains of lysine and arginine differ in their influences on the folding and assembly of melittin. Specifically, the side chain of R increases the α-helical propensity of melittin relative to that of K, following an inverse Hofmeister series. In contrast, the side chain of K favors the assembly of melittin relative to the side chain of R in line with a direct Hofmeister series. The opposite regulatory effects of immobilized cations on the folding and assembly of melittin highlight the complexity of the noncovalent interactions that govern protein intermolecular architecture.
Collapse
Affiliation(s)
- Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Zhun Deng
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Shuli Liu
- Department of Clinical Laboratory, Peking University Civil Aviation School of Clinical Medicine, Beijing, China
| | - Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, China
| | | | | | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| |
Collapse
|
6
|
Neal JF, Saha A, Zerkle MM, Zhao W, Rogers MM, Flood AH, Allen HC. Molecular Recognition and Hydration Energy Mismatch Combine To Inform Ion Binding Selectivity at Aqueous Interfaces. J Phys Chem A 2020; 124:10171-10180. [DOI: 10.1021/acs.jpca.0c09568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jennifer F. Neal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ankur Saha
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mia M. Zerkle
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Mickey M. Rogers
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amar H. Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Heather C. Allen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
7
|
Mahanti M, Pal KB, Sundin AP, Leffler H, Nilsson UJ. Epimers Switch Galectin-9 Domain Selectivity: 3 N-Aryl Galactosides Bind the C-Terminal and Gulosides Bind the N-Terminal. ACS Med Chem Lett 2020; 11:34-39. [PMID: 31938460 DOI: 10.1021/acsmedchemlett.9b00396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
A series of 3-deoxy-3-N-arylated-β-d-galactoside and -guloside derivatives have been synthesized by cesium fluoride/trimetylsilylaryl triflate-mediated benzyne generation and N-arylation of 3-deoxy-3-amino-β-d-galactosides and -gulosides, respectively. Evaluation as ligands to galectin-1, 2, 3, 4N (N-terminal domain), 4C (C-terminal domain), 7, 8N, 8C, 9C, and 9N revealed that the galactosides selectively bound galectin-9C, whereas the gulosides selectively bound galectin-9N. Hence, the N-aryl group induces galectin-9 selectivity and the ligand 3C-configuration acts as an epimeric selectivity switch between the two domains of galectin-9. Furthermore, MD simulations revealed that galacto derivatives in galectin-9C and gulo derivatives in galectin-9N find stable poses with specific interactions, which proposes a possible explanation to the gal/gulo 9C/9N selectivity.
Collapse
Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Kumar Bhaskar Pal
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Anders P. Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84 Lund, Sweden
| | - Ulf J. Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
8
|
Houriez C, Réal F, Vallet V, Mautner M, Masella M. Ion hydration free energies and water surface potential in water nano drops: The cluster pair approximation and the proton hydration Gibbs free energy in solution. J Chem Phys 2019; 151:174504. [PMID: 31703526 DOI: 10.1063/1.5109777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We estimate both single ion hydration Gibbs free energies in water droplets, comprising from 50 to 1000 molecules, and water/vacuum surface potentials in pure water droplets comprising up to 10 000 molecules. We consider four ions, namely, Li+, NH4 +, F-, and Cl-, and we model their hydration process and water/water interactions using polarizable force fields based on an induced point dipole approach. We show both ion hydration Gibbs free energies and water surface potentials to obey linear functions of the droplet radius as soon as droplets comprising a few hundred water molecules. Moreover, we also show that the differences in anion/cation hydration Gibbs free energies in droplets obey a different regime in large droplets than in small clusters comprising no more than six water molecules, in line with the earlier results computed from standard additive point charge force fields. Hence, both point charge and more sophisticated induced point dipole molecular modeling approaches suggest that methods considering only the thermodynamical properties of small ion/water clusters to estimate the absolute proton hydration Gibbs free energy in solution are questionable. In particular, taking into account the data of large ion/water droplets may yield a proton hydration Gibbs free energy in solution value to be shifted by several kBT units compared to small clusters-based approaches.
Collapse
Affiliation(s)
- Céline Houriez
- MINES ParisTech, PSL Research University, CTP - Centre Thermodynamique des Procédés, 35 rue Saint-Honoré, 77300 Fontainebleau, France
| | - Florent Réal
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Valérie Vallet
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Michael Mautner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA and Department of Chemistry, University of Canterbury, Christchurch 8001, New Zealand
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
| |
Collapse
|
9
|
Réal F, Vallet V, Masella M. Improving the description of solvent pairwise interactions using local solute/solvent three-body functions. The case of halides and carboxylates in aqueous environment. J Comput Chem 2019; 40:1209-1218. [PMID: 30702761 DOI: 10.1002/jcc.25779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 11/07/2022]
Abstract
We propose a general strategy to remediate force-field artifacts in describing pairwise interactions among similar molecules M in the vicinity of another chemical species, C, like water molecules interacting at short distance from a monoatomic ion. This strategy is based on introducing a three-body potential energy term that alters the pairwise interactions among M-type molecules when they lie at short range from the species C. In other words the species C is the center of a space domain where the pairwise interactions among the molecules M is altered. Here, we apply it to improve the description of the water interactions provided by the polarizable water model TCPE/2013 in the vicinity of halides, from F- to At- , and of the prototypical carboxylate anion CH3 COO- . We show the accuracy and the transferability of such an approach to investigate not only the hydration process of single anions but also of a salt solution NH 4 + / Cl - in aqueous phase. This strategy can be used to remediate the drawbacks of any kind of force fields. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Florent Réal
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, Université de Lille, F-59000 Lille, France
| | - Valérie Vallet
- CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, Université de Lille, F-59000 Lille, France
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
| |
Collapse
|