1
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Schneck E, Reed J, Seki T, Nagata Y, Kanduč M. Experimental and simulation-based characterization of surfactant adsorption layers at fluid interfaces. Adv Colloid Interface Sci 2024; 331:103237. [PMID: 38959812 DOI: 10.1016/j.cis.2024.103237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024]
Abstract
Adsorption of surfactants to fluid interfaces occurs in numerous technological and daily-life contexts. The coverage at the interface and other properties of the formed adsorption layers determine the performance of a surfactant with regard to the desired application. Given the importance of these applications, there is a great demand for the comprehensive characterization and understanding of surfactant adsorption layers. In this review, we provide an overview of suitable experimental and simulation-based techniques and review the literature in which they were used for the investigation of surfactant adsorption layers. We come to the conclusion that, while these techniques have been successfully applied to investigate Langmuir monolayers of water-insoluble surfactants, their application to the study of Gibbs adsorption layers of water-soluble surfactants has not been fully exploited. Finally, we emphasize the great potential of these methods in providing a deeper understanding of the behavior of soluble surfactants at interfaces, which is crucial for optimizing their performance in various applications.
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Affiliation(s)
- Emanuel Schneck
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany.
| | - Joshua Reed
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany
| | - Takakazu Seki
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, 036-8561 Aomori, Japan
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Matej Kanduč
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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2
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Wilson CJ, de Groot BL, Gapsys V. Resolving coupled pH titrations using alchemical free energy calculations. J Comput Chem 2024; 45:1444-1455. [PMID: 38471815 DOI: 10.1002/jcc.27318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 03/14/2024]
Abstract
In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured p K a . Here, we derive a formalism based on double free energy differences ( Δ Δ G ) for quantifying the individual site p K a values of coupled residues. As Δ Δ G values can be obtained by means of alchemical free energy calculations, the presented approach allows for a convenient estimation of coupled residue p K a s in practice. We demonstrate that our approach and a previously proposed microscopic p K a formalism, can be combined with alchemical free energy calculations to resolve pH-dependent protein p K a values. Toy models and both, regular and constant-pH molecular dynamics simulations, alongside experimental data, are used to validate this approach. Our results highlight the insights gleaned when coupling and microstate probabilities are analyzed and suggest extensions to more complex enzymatic contexts. Furthermore, we find that naïvely computed p K a values that ignore coupling, can be significantly improved when coupling is accounted for, in some cases reducing the error by half. In short, alchemical free energy methods can resolve the p K a values of both uncoupled and coupled residues.
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Affiliation(s)
- Carter J Wilson
- Department of Mathematics, The University of Western Ontario, London, Ontario, Canada
- Centre for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, London, Ontario, Canada
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Computational Chemistry, Janssen Research & Development, Beerse, Belgium
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3
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Gődény M, Joerg F, Kovar MPP, Schröder C. Updates to Protex for Simulating Proton Transfers in an Ionic Liquid. J Phys Chem B 2024; 128:3416-3426. [PMID: 38557106 PMCID: PMC11017242 DOI: 10.1021/acs.jpcb.3c07356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The Python-based program Protex was initially developed for simulating proton transfers in a pure protic ionic liquid via polarizable molecular dynamics simulations. This method employs a single topology approach wherein deprotonated species retain a dummy atom, which is transformed into a real hydrogen atom during the protonation process. In this work, we extended Protex to include more intricate systems and to facilitate the simulation of the Grotthuss mechanism to enhance alignment with the empirical findings. The handling of proton transfer events within Protex was further refined for increased flexibility. In the original model, each deprotonated molecule contained a single dummy atom connected to the hydrogen acceptor atom. This model posed limitations for molecules with multiple atoms that could undergo protonation. To mitigate this issue, Protex was extended to execute a proton transfer when one of these potential atoms was within a suitable proximity for the transfer event. For the purpose of maintaining simplicity, Protex continues to utilize only a single dummy atom per deprotonated molecule. Another new feature pertains to the determination of the eligibility for a proton transfer event. A range of acceptable distances can now be defined within which the transfer probability is gradually turned off. These modifications allow for a more nuanced approach to simulating proton transfer events, offering greater accuracy and control of the modeling process.
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Affiliation(s)
- Márta Gődény
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- University
of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, Vienna 1090, Austria
| | - Florian Joerg
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- University
of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, Vienna 1090, Austria
| | - Maximilian P.-P. Kovar
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Christian Schröder
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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4
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Thiel A, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2024; 20:2921-2933. [PMID: 38507252 PMCID: PMC11008096 DOI: 10.1021/acs.jctc.3c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Additionally, our implementation in the open-source Force Field X (FFX) software has the unique ability to handle titration state changes for crystalline systems including flexible support for all 230 space groups. The evaluation of constant-pH molecular dynamics (CpHMD) with the AMOEBA force field was performed on 11 crystalline peptide systems that span the titrating amino acids (Asp, Glu, His, Lys, and Cys). Titration states were correctly predicted for 15 out of the 16 amino acids present in the 11 systems, including for the coordination of Zn2+ by cysteines. The lone exception was for a HIS-ALA peptide where CpHMD predicted both neutral histidine tautomers to be equally populated, whereas the experimental model did not consider multiple conformers and diffraction data are unavailable for rerefinement. This work demonstrates the promise polarizable CpHMD simulations for pKa predictions, the study of biochemical mechanisms such as the catalytic triad of proteases, and for improved protein-ligand binding affinity accuracy in the context of pharmaceutical lead optimization.
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Affiliation(s)
- Andrew
C. Thiel
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Matthew J. Speranza
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Sanika Jadhav
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Lewis L. Stevens
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Daniel K. Unruh
- Office
of the Vice President for Research, University
of Iowa, Iowa City, Iowa 52242, United
States
| | - Pengyu Ren
- Department
of Biomedical Engineering, University of
Texas, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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5
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Jansen A, Aho N, Groenhof G, Buslaev P, Hess B. phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. J Chem Inf Model 2024; 64:567-574. [PMID: 38215282 PMCID: PMC10865341 DOI: 10.1021/acs.jcim.3c01313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.
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Affiliation(s)
- Anton Jansen
- Department
of Applied Physics and Swedish e-Science Research Center, Science
for Life Laboratory, KTH Royal Institute
of Technology, 100 44 Stockholm, Sweden
| | - Noora Aho
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Gerrit Groenhof
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, 40014 Jyväskylä, Finland
| | - Berk Hess
- Department
of Applied Physics and Swedish e-Science Research Center, Science
for Life Laboratory, KTH Royal Institute
of Technology, 100 44 Stockholm, Sweden
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6
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Grava M, Ibrahim M, Sudarsan A, Pusterla J, Philipp J, Rädler JO, Schwierz N, Schneck E. Combining molecular dynamics simulations and x-ray scattering techniques for the accurate treatment of protonation degree and packing of ionizable lipids in monolayers. J Chem Phys 2023; 159:154706. [PMID: 37861119 DOI: 10.1063/5.0172552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The pH-dependent change in protonation of ionizable lipids is crucial for the success of lipid-based nanoparticles as mRNA delivery systems. Despite their widespread application in vaccines, the structural changes upon acidification are not well understood. Molecular dynamics simulations support structure prediction but require an a priori knowledge of the lipid packing and protonation degree. The presetting of the protonation degree is a challenging task in the case of ionizable lipids since it depends on pH and on the local lipid environment and often lacks experimental validation. Here, we introduce a methodology of combining all-atom molecular dynamics simulations with experimental total-reflection x-ray fluorescence and scattering measurements for the ionizable lipid Dlin-MC3-DMA (MC3) in POPC monolayers. This joint approach allows us to simultaneously determine the lipid packing and the protonation degree of MC3. The consistent parameterization is expected to be useful for further predictive modeling of the action of MC3-based lipid nanoparticles.
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Affiliation(s)
- Miriam Grava
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Mohd Ibrahim
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Akhil Sudarsan
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Julio Pusterla
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Julian Philipp
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Joachim O Rädler
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
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7
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Hartl SL, Žakelj S, Dolenc MS, Smrkolj V, Mavri J. How Azide Ion/Hydrazoic Acid Passes Through Biological Membranes: An Experimental and Computational Study. Protein J 2023:10.1007/s10930-023-10127-3. [PMID: 37289420 DOI: 10.1007/s10930-023-10127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/09/2023]
Abstract
Hydrazoic acid (HN3) and its deprotonated form azide ion (N3-) (AHA) are toxic because they inhibit the cytochrome c oxidase complex IV (CoX IV) embedded in the inner mitochondrial membrane that forms part of the enzyme complexes involved in cellular respiration. Critical to its toxicity is the inhibition of CoX IV in the central nervous system and cardiovascular system. Hydrazoic acid is an ionizable species and its affinity for membranes, and the associated permeabilities, depend on the pH values of aqueous media on both sides of the membranes. In this article, we address the permeability of AHA through the biological membrane. In order to understand the affinity of the membrane for the neutral and ionized form of azide, we measured the octanol/water partition coefficients at pH values of 2.0 and 8.0, which are 2.01 and 0.00034, respectively. Using a Parallel Artificial Membrane Permeability Assay (PAMPA) experiment, we measured the effective permeability through the membrane, which is logPe - 4.97 and - 5.26 for pH values of 7.4 and pH 8.0, respectively. Experimental permeability was used to validate theoretical permeability, which was estimated by numerically solving a Smoluchowski equation for AHA diffusion through the membrane. We demonstrated that the rate of permeation through the cell membrane of 8.46·104 s-1 is much higher than the rate of the chemical step of CoX IV inhibition by azide of 200 s-1. The results of this study show that transport through the membrane does not represent the rate-limiting step and therefore does not control the rate of CoX IV inhibition in the mitochondria. However, the observed dynamics of azide poisoning is controlled by circulatory transport that takes place on a time scale of minutes.
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Affiliation(s)
- Simona Lojevec Hartl
- National Institute of Chemistry, Center for Validation Technologies and Analytics, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | - Simon Žakelj
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
| | | | - Vladimir Smrkolj
- University of Ljubljana, Faculty of Medicine, Institute of Anatomy, Ljubljana, Slovenia.
| | - Janez Mavri
- National Institute of Chemistry, Laboratory of Computational Biochemistry and Drug Design, Ljubljana, Slovenia.
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8
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Cui L, Shi X, Li H, Wang S, Guo L, Lan Z, Dai Y, Zhang Q, Wu Y, Liu W. Crystal structures and solution conformations of HtrA from Helicobacter pylori reveal pH-dependent oligomeric conversion and conformational rearrangements. Int J Biol Macromol 2023:125274. [PMID: 37301353 DOI: 10.1016/j.ijbiomac.2023.125274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects over 50 % of the world's population, making it a major risk factor for chronic gastritis, ulcer diseases of the stomach and duodenum, MALT lymphoma, and gastric cancer. The clinical consequences of H. pylori infection are closely linked with the expression of virulence factors secreted by the bacterium. One such virulence factor is high temperature requirement A (HtrA), which possesses chaperone and serine protease activity. In the host stomach, HtrA secreted from H. pylori (HpHtrA) disrupts intercellular adhesions by cleaving epithelial adhesion proteins including E-cadherin and desmoglein-2. This disruption causes intercellular junctions to open, allowing the bacterium to pass through the epithelial barrier, access the intercellular space, and colonize the gastric mucosa. HtrA proteases are well known for their structural complexity, reflected in their diverse oligomer forms and multi-tasking activities in both prokaryotes and eukaryotes. In this study, we determined crystal structures and solution conformations of HpHtrA monomer and trimer, which revealed large domain rearrangements between them. Notably, this is the first report of a monomeric structure in the HtrA family. We further found a pH-dependent dynamic trimer-to-monomer conversion and concurrent conformational changes that seem closely linked with a pH-sensing ability through the protonation of certain Asp residues. These results advance our understanding of the functional roles and the related mechanisms of this protease in bacterial infection, which may shed light on the development of HtrA-targeted therapies for H. pylori-associated diseases.
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Affiliation(s)
- Liwei Cui
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China; Department of Tropical Medicine and Infectious Diseases, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572000, China
| | - Xiangrui Shi
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Huiling Li
- Department of Tropical Medicine and Infectious Diseases, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572000, China
| | - Sheng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Ling Guo
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China; Center for drug evaluation and inspection of Chongqing Medical Products Administration, Chongqing 401120, China
| | - Zhu Lan
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China
| | - Yujie Dai
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China.
| | - Wei Liu
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China.
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9
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Joerg F, Wieder M, Schröder C. Protex-A Python utility for proton exchange in molecular dynamics simulations. Front Chem 2023; 11:1140896. [PMID: 36874061 PMCID: PMC9981665 DOI: 10.3389/fchem.2023.1140896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Protex is an open-source program that enables proton exchanges of solvent molecules during molecular dynamics simulations. While conventional molecular dynamics simulations do not allow for bond breaking or formation, protex offers an easy-to-use interface to augment these simulations and define multiple proton sites for (de-)protonation using a single topology approach with two different λ-states. Protex was successfully applied to a protic ionic liquid system, where each molecule is prone to (de-)protonation. Transport properties were calculated and compared to experimental values and simulations without proton exchange.
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Affiliation(s)
- Florian Joerg
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.,Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Marcus Wieder
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Christian Schröder
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
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10
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de Oliveira VM, Liu R, Shen J. Constant pH molecular dynamics simulations: Current status and recent applications. Curr Opin Struct Biol 2022; 77:102498. [PMID: 36410222 PMCID: PMC9933785 DOI: 10.1016/j.sbi.2022.102498] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2022]
Abstract
Many important protein functions are carried out through proton-coupled conformational dynamics. Thus, the ability to accurately model protonation states dynamically has wide-ranging implications. Over the past two decades, two main types of constant pH methods (discrete and continuous) have been developed to enable proton-coupled molecular dynamics (MD) simulations. In this short review, we discuss the current status of the development and highlight recent applications that have advanced our understanding of protein structure-function relationships. We conclude the review by outlining the remaining challenges in the method development and projecting important areas for future applications.
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Affiliation(s)
- Vinicius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, 20201, Maryland, U.S.A
| | - Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, 20201, Maryland, U.S.A
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, 20201, MD, USA.
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11
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Sequeira JN, Rodrigues FEP, Silva TGD, Reis PBPS, Machuqueiro M. Extending the Stochastic Titration CpHMD to CHARMM36m. J Phys Chem B 2022; 126:7870-7882. [PMID: 36190807 PMCID: PMC9776569 DOI: 10.1021/acs.jpcb.2c04529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The impact of pH on proteins is significant but often neglected in molecular dynamics simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology to deal with these effects. However, it still lacks widespread adoption by the scientific community. The stochastic titration CpHMD is one of such methods that, until now, only supported the GROMOS force field family. Here, we extend this method's implementation to include the CHARMM36m force field available in the GROMACS software package. We test this new implementation with a diverse group of proteins, namely, lysozyme, Staphylococcal nuclease, and human and E. coli thioredoxins. All proteins were conformationally stable in the simulations, even at extreme pH values. The RMSE values (pKa prediction vs experimental) obtained were very encouraging, in particular for lysozyme and human thioredoxin. We have also identified a few residues that challenged the CpHMD simulations, highlighting scenarios where the method still needs improvement independently of the force field. The CHARMM36m all-atom implementation was more computationally efficient when compared with the GROMOS 54A7, taking advantage of a shorter nonbonded interaction cutoff and a less frequent neighboring list update. The new extension will allow the study of pH effects in many systems for which this force field is particularly suited, i.e., proteins, membrane proteins, lipid bilayers, and nucleic acids.
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12
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Aho N, Buslaev P, Jansen A, Bauer P, Groenhof G, Hess B. Scalable Constant pH Molecular Dynamics in GROMACS. J Chem Theory Comput 2022; 18:6148-6160. [PMID: 36128977 PMCID: PMC9558312 DOI: 10.1021/acs.jctc.2c00516] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
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13
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Buslaev P, Aho N, Jansen A, Bauer P, Hess B, Groenhof G. Best Practices in Constant pH MD Simulations: Accuracy and Sampling. J Chem Theory Comput 2022; 18:6134-6147. [PMID: 36107791 PMCID: PMC9558372 DOI: 10.1021/acs.jctc.2c00517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Various approaches
have been proposed to include the
effect of
pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed
by Brooks and
co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed
with little computational overhead and hfor each typeence be used
to routinely perform MD simulations at microsecond time scales, as
shown in the accompanying paper [Aho, N. et al. J. Chem. Theory
Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At
such time scales, however, the accuracy of the molecular mechanics
force field and the parametrization becomes critical. Here, we address
these issues and provide the community with guidelines on how to set
up and perform long time scale constant pH MD simulations. We found
that barriers associated with the torsions of side chains in the CHARMM36m
force field are too high for reaching convergence in constant pH MD
simulations on microsecond time scales. To avoid the high computational
cost of extending the sampling, we propose small modifications to
the force field to selectively reduce the torsional barriers. We demonstrate
that with such modifications we obtain converged distributions of
both protonation and torsional degrees of freedom and hence consistent
pKa estimates, while the sampling of the
overall configurational space accessible to proteins is unaffected
as compared to normal MD simulations. We also show that the results
of constant pH MD depend on the accuracy of the correction potentials.
While these potentials are typically obtained by fitting a low-order
polynomial to calculated free energy profiles, we find that higher
order fits are essential to provide accurate and consistent results.
By resolving problems in accuracy and sampling, the work described
in this and the accompanying paper paves the way to the widespread
application of constant pH MD beyond pKa prediction.
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Affiliation(s)
- Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
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14
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Ries B, Rieder S, Rhiner C, Hünenberger PH, Riniker S. RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. J Comput Aided Mol Des 2022; 36:175-192. [PMID: 35314898 PMCID: PMC8994745 DOI: 10.1007/s10822-022-00445-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/23/2022] [Indexed: 11/24/2022]
Abstract
The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed "single topology" or "dual topology". As the terminology is often used ambiguously in the literature, a systematic categorization of the system representations is proposed here. In the dual-topology approach, the molecules are simulated as separate molecules. Such an approach is relatively easy to automate for high-throughput RBFE calculations compared to the single-topology approach. Distance restraints are commonly applied to prevent the molecules from drifting apart, thereby improving the sampling efficiency. In this study, we introduce the program RestraintMaker, which relies on a greedy algorithm to find (locally) optimal distance restraints between pairs of atoms based on geometric measures. The algorithm is further extended for multi-state methods such as enveloping distribution sampling (EDS) or multi-site [Formula: see text]-dynamics. The performance of RestraintMaker is demonstrated for toy models and for the calculation of relative hydration free energies. The Python program can be used in script form or through an interactive GUI within PyMol. The selected distance restraints can be written out in GROMOS or GROMACS file formats. Additionally, the program provides a human-readable JSON format that can easily be parsed and processed further. The code of RestraintMaker is freely available on GitHub https://github.com/rinikerlab/restraintmaker.
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Affiliation(s)
- Benjamin Ries
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland
| | - Salomé Rieder
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland
| | - Clemens Rhiner
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland.
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, 8093, Switzerland.
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15
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Fossat MJ, Posey AE, Pappu RV. Quantifying charge state heterogeneity for proteins with multiple ionizable residues. Biophys J 2021; 120:5438-5453. [PMID: 34826385 PMCID: PMC8715249 DOI: 10.1016/j.bpj.2021.11.2886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023] Open
Abstract
Ionizable residues can release and take up protons and this has an influence on protein structure and function. The extent of protonation is linked to the overall pH of the solution and the local environments of ionizable residues. Binding or unbinding of a single proton generates a distinct charge microstate defined by a specific pattern of charges. Accordingly, the overall partition function is a sum over all charge microstates and Boltzmann weights of all conformations associated with each of the charge microstates. This ensemble-of-ensembles description recast as a q-canonical ensemble allows us to analyze and interpret potentiometric titrations that provide information regarding net charge as a function of pH. In the q-canonical ensemble, charge microstates are grouped into mesostates where each mesostate is a collection of microstates of the same net charge. Here, we show that leveraging the structure of the q-canonical ensemble allows us to decouple contributions of net proton binding and release from proton arrangement and conformational considerations. Through application of the q-canonical formalism to analyze potentiometric measurements of net charge in proteins with repetitive patterns of Lys and Glu residues, we determine the underlying mesostate pKa values and, more importantly, we estimate relative mesostate populations as a function of pH. This is a strength of using the q-canonical approach that cannot be replicated using purely site-specific analyses. Overall, our work shows how measurements of charge equilibria, decoupled from measurements of conformational equilibria, and analyzed using the framework of the q-canonical ensemble, provide protein-specific quantitative descriptions of pH-dependent populations of mesostates. This method is of direct relevance for measuring and understanding how different charge states contribute to conformational, binding, and phase equilibria of proteins.
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Affiliation(s)
- Martin J Fossat
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri
| | - Ammon E Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri.
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16
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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17
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Grünewald F, Souza PCT, Abdizadeh H, Barnoud J, de Vries AH, Marrink SJ. Titratable Martini model for constant pH simulations. J Chem Phys 2020; 153:024118. [PMID: 32668918 DOI: 10.1063/5.0014258] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this work, we deliver a proof of concept for a fast method that introduces pH effects into classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon the latest version of the popular Martini CG model to which explicit proton mimicking particles are added. We verify our approach against experimental data involving several different molecules and different environmental conditions. In particular, we compute titration curves, pH dependent free energies of transfer, and lipid bilayer membrane affinities as a function of pH. Using oleic acid as an example compound, we further illustrate that our method can be used to study passive translocation in lipid bilayers via protonation. Finally, our model reproduces qualitatively the expansion of the macromolecule dendrimer poly(propylene imine) as well as the associated pKa shift of its different generations. This example demonstrates that our model is able to pick up collective interactions between titratable sites in large molecules comprising many titratable functional groups.
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Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
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18
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Batys P, Morga M, Bonarek P, Sammalkorpi M. pH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation. J Phys Chem B 2020; 124:2961-2972. [PMID: 32182068 PMCID: PMC7590956 DOI: 10.1021/acs.jpcb.0c01475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 12/17/2022]
Abstract
Microsecond-long all-atom molecular dynamics (MD) simulations, circular dichroism, laser Doppler velocimetry, and dynamic light-scattering techniques have been used to investigate pH-induced changes in the secondary structure, charge, and conformation of poly l-lysine (PLL) and poly l-glutamic acid (PGA). The employed combination of the experimental methods reveals for both PLL and PGA a narrow pH range at which they are charged enough to form stable colloidal suspensions, maintaining their α-helix content above 60%; an elevated charge state of the peptides required for colloidal stability promotes the peptide solvation as a random coil. To obtain a more microscopic view on the conformations and to verify the modeling performance, peptide secondary structure and conformations rising in MD simulations are also examined using three different force fields, i.e., OPLS-AA, CHARMM27, and AMBER99SB*-ILDNP. Ramachandran plots reveal that in the examined setup the α-helix content is systematically overestimated in CHARMM27, while OPLS-AA overestimates the β-sheet fraction at lower ionization degrees. At high ionization degrees, the OPLS-AA force-field-predicted secondary structure fractions match the experimentally measured distribution most closely. However, the pH-induced changes in PLL and PGA secondary structure are reasonably captured only by the AMBER99SB*-ILDNP force field, with the exception of the fully charged PGA in which the α-helix content is overestimated. The comparison to simulations results shows that the examined force fields involve significant deviations in their predictions for charged homopolypeptides. The detailed mapping of secondary structure dependency on pH for the polypeptides, especially finding the stable colloidal α-helical regime for both examined peptides, has significant potential for practical applications of the charged homopolypeptides. The findings raise attention especially to the pH fine tuning as an underappreciated control factor in surface modification and self-assembly.
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Affiliation(s)
- Piotr Batys
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Maria Morga
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Piotr Bonarek
- Department
of Physical Biochemistry, Faculty of Biochemistry, Biophysics and
Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science and Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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19
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Dobrev P, Vemulapalli SPB, Nath N, Griesinger C, Grubmüller H. Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides. J Chem Theory Comput 2020; 16:2561-2569. [PMID: 32192342 DOI: 10.1021/acs.jctc.9b01232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protonation states of titratable amino acids play a key role in many biomolecular processes. Knowledge of protonatable residue charges at a given pH is essential for a correct understanding of protein catalysis, inter- and intramolecular interactions, substrate binding, and protein dynamics for instance. However, acquiring experimental values for individual amino acid protonation states of complex systems is not straightforward; therefore, several in silico approaches have been developed to tackle this issue. In this work, we assess the accuracy of our previously developed constant pH MD approach by comparing our theoretically obtained pKa values for titratable residues with experimental values from an equivalent NMR study. We selected a set of four pentapeptides, of adequately small size to ensure comprehensive sampling, but concurrently, due to their charge composition, posing a challenge for protonation state calculation. The comparison of the pKa values shows good agreement of the experimental and the theoretical approach with a largest difference of 0.25 pKa units. Further, the corresponding titration curves are in fair agreement, although the shift of the Hill coefficient from a value of 1 was not always reproduced in simulations. The phase space overlap in Cartesian space between trajectories generated in constant pH and standard MD simulations is fair and suggests that our constant pH MD approach reasonably well preserves the dynamics of the system, allowing dynamic protonation MD simulations without introducing structural artifacts.
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Affiliation(s)
- Plamen Dobrev
- Max-Planck-Institut fur Biophysikalische Chemie, Theoretical and computational biophysics, Gottingen 37077, Germany
| | | | - Nilamoni Nath
- Max Planck Institute for Biophysical Chemistry, NMR-based Structural Biology, Gottingen 37077, Germany.,Gauhati University, Department of Chemistry, Guwahati, 781014 Assam, India
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, NMR-based Structural Biology, Gottingen 37077, Germany
| | - Helmut Grubmüller
- Max-Planck-Institut fur Biophysikalische Chemie, Theoretical and computational biophysics, Gottingen 37077, Germany
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20
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Barroso da Silva FL, Carloni P, Cheung D, Cottone G, Donnini S, Foegeding EA, Gulzar M, Jacquier JC, Lobaskin V, MacKernan D, Mohammad Hosseini Naveh Z, Radhakrishnan R, Santiso EE. Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations. Annu Rev Food Sci Technol 2020; 11:365-387. [PMID: 31951485 DOI: 10.1146/annurev-food-032519-051640] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The structure and interactions of proteins play a critical role in determining the quality attributes of many foods, beverages, and pharmaceutical products. Incorporating a multiscale understanding of the structure-function relationships of proteins can provide greater insight into, and control of, the relevant processes at play. Combining data from experimental measurements, human sensory panels, and computer simulations through machine learning allows the construction of statistical models relating nanoscale properties of proteins to the physicochemical properties, physiological outcomes, and tastes of foods. This review highlights several examples of advanced computer simulations at molecular, mesoscale, and multiscale levels that shed light on the mechanisms at play in foods, thereby facilitating their control. It includes a practical simulation toolbox for those new to in silico modeling.
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Affiliation(s)
- Fernando Luís Barroso da Silva
- School of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, BR-14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paolo Carloni
- Institute for Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - David Cheung
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Grazia Cottone
- Department of Physics and Chemistry, University of Palermo, 90128 Palermo, Italy
| | - Serena Donnini
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - E Allen Foegeding
- Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Muhammad Gulzar
- UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | | | | | - Donal MacKernan
- UCD School of Physics, University College Dublin, Dublin 4, Ireland
| | | | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Erik E Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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21
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Youssefian S. Conformational Transformation of pH-Responsive Hairy Cellulose NanoCrystalloids in Salt-Free Dilute Solutions. Biomacromolecules 2019; 20:2839-2851. [PMID: 31241307 DOI: 10.1021/acs.biomac.9b00592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among biomaterials, pH-responsive nanoparticles have promising potential for overcoming nonspecific therapeutic delivery by taking advantage of the pH gradient between physiological and pathological states. This article discusses pH-dependent conformations of an organic nanoparticle that has a needle-shaped body from crystalline cellulose, sandwiched between two amorphous regions from chemically nanoengineered dicarboxylated cellulose (DCC). Computational study on a single free DCC chain elucidated that in a salt-free dilute solution, the chain undergoes a major transformation between pH ∼ 3 and ∼6.3. Through this transformation, the DCC chain nature varies from globular neutral polymer to coiled quasi-neutral polymer and finally to rodlike polyelectrolyte. Study on the particle nanostructure indicated that, at pH ∼ 3, the conformation of the amorphous regions is analogous to that of polymer brushes in poor solvents, whereas at pH ∼ 5, the conformation changes to that of quasi-neutral polymer brushes in good solvents. For pH > 6.3, the conformation transforms into that of star-like polyelectrolytes. The height of the amorphous region exhibits a regressive trend up to pH ∼ 6.3, followed by a progressive trend up to pH ∼ 10. Study on the hydrodynamic properties revealed a sharp decline in the diffusion rate as the pH varies from ∼3 to ∼5, followed by a plateau for higher pH. It was demonstrated that, at pH ∼ 3, the nanoparticle may form a coherent nanophase with a rodlike structure. These results may provide insight into designing pH-responsive nanocelluloses with a controlled expansion and diffusion coefficient.
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Affiliation(s)
- Sina Youssefian
- Department of Civil Engineering , Johns Hopkins University , Baltimore , Maryland , United States.,Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Cambridge , Massachusetts , United States.,Department of Mechanical Engineering , Worcester Polytechnic Institute , Worcester , Massachusetts , United States
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22
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Barroso da Silva FL, Sterpone F, Derreumaux P. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. J Chem Theory Comput 2019; 15:3875-3888. [DOI: 10.1021/acs.jctc.9b00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/no, Ribeirão Preto, São Paulo BR-14040-903, Brazil
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Fabio Sterpone
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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23
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Abstract
An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry & Physics, Graduate Center, City University of New York , 365 Fifth Ave, New York, New York 10016, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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24
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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25
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Barroso da Silva FL, Derreumaux P, Pasquali S. Fast coarse-grained model for RNA titration. J Chem Phys 2017; 146:035101. [PMID: 28109220 DOI: 10.1063/1.4972986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.
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Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ave. do café, s/no, BR-14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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26
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Barroso da Silva FL, MacKernan D. Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations. J Chem Theory Comput 2017; 13:2915-2929. [DOI: 10.1021/acs.jctc.6b01114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento
de Fı́sica e Quı́mica, Faculdade
de Ciências Farmacêuticas de Ribeirão Preto,
Av. do café, s/no. − Universidade de São Paulo, BR-14040-903 Ribeirão Preto, São Paulo, Brazil
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27
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Sharma A, Smith JD, Walters KB, Rick SW. Constant pH simulations of pH responsive polymers. J Chem Phys 2016; 145:234906. [DOI: 10.1063/1.4972062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Arjun Sharma
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - J. D. Smith
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Keisha B. Walters
- School of Chemical Engineering, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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28
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Dobrev P, Donnini S, Groenhof G, Grubmüller H. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pK(a) Calculations. J Chem Theory Comput 2016; 13:147-160. [PMID: 27966355 DOI: 10.1021/acs.jctc.6b00807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.
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Affiliation(s)
- Plamen Dobrev
- Theoretical & Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Helmut Grubmüller
- Theoretical & Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 2016; 12:5411-5421. [PMID: 27709966 DOI: 10.1021/acs.jctc.6b00552] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.
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Affiliation(s)
- Yandong Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Wei Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Jason A Wallace
- University of Oklahoma College of Dentistry , Oklahoma City, Oklahoma 73117, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
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Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
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