1
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Persson LJ, Sahin C, Landreh M, Marklund EG. High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method. Anal Chem 2024; 96:15023-15030. [PMID: 39231152 PMCID: PMC11411496 DOI: 10.1021/acs.analchem.4c03272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. (J. Chem. Theory Comput., 2020, 16, 6938-6949), showing that it significantly enhances the performance of gas-phase simulations of large proteins. We assess how to achieve adequate accuracy and optimal performance with FMM, finding that it expands the accessible size range and time scales dramatically. Additionally, we simulate a 460 kDa ferritin complex over microsecond time scales, alongside complementary ion mobility (IM)-MS experiments, uncovering conformational changes that are not apparent from the IM-MS data alone.
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Affiliation(s)
- Louise J Persson
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165 Solna, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstro̷m-Lang Centre for Protein Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165 Solna, Sweden
- Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
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2
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Quiton SJ, Wu H, Xing X, Lin L, Head-Gordon M. The Staggered Mesh Method: Accurate Exact Exchange Toward the Thermodynamic Limit for Solids. J Chem Theory Comput 2024. [PMID: 39213528 DOI: 10.1021/acs.jctc.4c00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
In periodic systems, the Hartree-Fock (HF) exchange energy exhibits the slowest convergence of all HF energy components as the system size approaches the thermodynamic limit. We demonstrate that the recently proposed staggered mesh method for Fock exchange energy [Xing, Li, and Lin, Math. Comp., 2024], which is specifically designed to sidestep certain singularities in exchange energy evaluation, can expedite the finite-size convergence rate for the exact exchange energy across a range of insulators and semiconductors when compared to the regular and truncated Coulomb methods. This remains true even for two computationally cheaper versions of this new method, which we call non-SCF and split-SCF staggered mesh. Additionally, a sequence of numerical tests on simple solids showcases the staggered mesh method's ability to improve convergence toward the thermodynamic limit for band gaps, bulk moduli, equilibrium lattice dimensions, energies, and phonon force constants.
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Affiliation(s)
- Stephen Jon Quiton
- College of Chemistry, University of California, Berkeley, California 94720, United States
| | - Hamlin Wu
- College of Chemistry, University of California, Berkeley, California 94720, United States
| | - Xin Xing
- Department of Mathematics, University of California, Berkeley, California 94720, United States
| | - Lin Lin
- Department of Mathematics, University of California, Berkeley, California 94720, United States
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Martin Head-Gordon
- College of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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3
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Oliveira NFB, Ladokhin AS, Machuqueiro M. Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain. Biophys J 2024:S0006-3495(24)00589-7. [PMID: 39215463 DOI: 10.1016/j.bpj.2024.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/16/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
Protonation of key residues in the diphtheria toxin translocation (T)-domain triggered by endosomal acidification is critical for inducing a series of conformational transitions critical for the cellular entry of the toxin. Previous experiments revealed the importance of histidine residues in modulating pH-dependent transitions. They suggested the presence of a "safety latch" preventing premature refolding of the T-domain by a yet poorly understood mechanism. Here, we used constant-pH molecular dynamics simulations to systematically investigate the protonation sequence in the wild-type T-domain and the following mutants: H223Q, H257Q, E259Q, and H223Q/H257Q. Comparison of these computational results with previous experimental data on T-domain stability and activity with the H-to-Q replacements confirms the role of H223 (pKa = 6.5) in delaying the protonation of the main trigger, H257 (pKa = 2.2 in the WT and pKa = 4.9 in H223Q). Our calculations also reveal a very low pKa for a neighboring acidic residue E259, which does not get protonated even during simulations at pH 3. This residue also contributes to the formation of the safety latch, with the pKa of H257 increasing from 2.2 to 5.1 upon E259Q replacement. In contrast, the latter replacement has virtually no effect on the protonation of the H223. Thus, we conclude that the interplay of the protonation in the H223/H257/E259 triad has evolved to prevent triggering the accidental refolding of the T-domain by a fluctuation in the protonation of the main trigger at neutral pH, before the incorporation of the toxin inside the endosome. Subsequent acidification of the endosome overcomes the safety latch and triggers conformational switching via repulsion of H223+ and H257+. This protonation/conformation relationship corroborates experimental findings and offers a detailed stepwise molecular description of the transition mechanism, which can be instrumental in optimizing the potential applications of the T-domain for targeted delivery of therapies to tumors and other diseased acidic tissues.
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Affiliation(s)
- Nuno F B Oliveira
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, Kansas, USA.
| | - Miguel Machuqueiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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4
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Kim M, Biswas S, Barraza Alvarez I, Christopher P, Wong BM, Mangolini L. Nonthermal Plasma Activation of Adsorbates: The Case of CO on Pt. JACS AU 2024; 4:2979-2988. [PMID: 39211584 PMCID: PMC11350585 DOI: 10.1021/jacsau.4c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Nonthermal plasmas provide a unique approach to electrically driven heterogeneous catalytic processes. Despite much interest from the community, fundamental activation pathways in these processes remain poorly understood. Here, we investigate how exposure to a nonthermal plasma sustained in an argon nonreactive atmosphere affects the desorption of carbon monoxide (CO) from platinum nanoparticles. Temperature-programmed desorption measurements indicate that the plasma reduces the effective binding energy (BE) of CO to Pt surfaces by as much as ∼0.3 eV, with the reduction in the BE scaling linearly with the plasma density. We find that the effective CO BE is most strongly reduced for under-coordinated sites (steps and edges) compared to well-coordinated sites (terraces). Density functional theory calculations suggest that this is due to plasma-induced charging and electric fields at the catalyst surface, which preferentially affect under-coordinated sites. This study provides direct experimental evidence of plasma-induced nonthermal activation of the adsorbate-catalyst couple.
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Affiliation(s)
- Minseok Kim
- Department
of Mechanical Engineering, University of
California, Riverside, Riverside, California 92521, United States
| | - Sohag Biswas
- Materials
Science & Engineering Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Isabel Barraza Alvarez
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93117, United States
| | - Phillip Christopher
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93117, United States
| | - Bryan M. Wong
- Materials
Science & Engineering Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Lorenzo Mangolini
- Department
of Mechanical Engineering, University of
California, Riverside, Riverside, California 92521, United States
- Materials
Science & Engineering Program, University
of California, Riverside, Riverside, California 92521, United States
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5
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Verma S, Nair NN. A Comprehensive Study of Factors Affecting the Prediction of the p Ka Shift of Asp 26 in Thioredoxin Protein. J Phys Chem B 2024; 128:7304-7312. [PMID: 39023356 DOI: 10.1021/acs.jpcb.4c01516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The stable protonation state of ionizable amino acids in a protein can be predicted by computing the pKa shift of that residue within the protein environment. Thermodynamic Integration (TI) is an ideal molecular dynamics-based approach for predicting the pKa shift of ionizable protein residues. Here, we probe TI-based simulation protocols for their ability to accurately predict the pKa shift of Asp26 in thioredoxin. While implicit solvent models can predict the pKa shift accurately, explicit solvent models result in substantial errors. To understand the underlying reason for this surprising discrepancy, we investigate the role of various factors such as solvent models, conformational sampling, background charges, and polarization.
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Affiliation(s)
- Shivani Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India
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6
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Sun Z, Procacci P. Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems. Phys Chem Chem Phys 2024; 26:19887-19899. [PMID: 38990073 DOI: 10.1039/d4cp01804d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
As a contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest SAMPL challenges, using an alchemical molecular dynamics technique we have examined the impact of force field parameterization and ionic strength in connection with guest charge neutralization on computed dissociation free energies in two typical SAMPL heavily charged macrocyclic hosts encapsulating small protonated amines with disparate binding affinities. We have shown that the methodological treatment for host neutralization, with explicit ions or with the background neutralizing plasma in the context of alchemical calculations under periodic boundary conditions, has a moderate effect on the calculated affinities. On the other hand, we have shown that seemingly small differences in the force field parameterization in highly symmetric hosts can produce systematic effects on the structural features that can have a significant impact on the predicted binding affinities.
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Affiliation(s)
- Zhaoxi Sun
- Changping Laboratory, Beijing 102206, China
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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7
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Malani M, Hiremath MS, Sharma S, Jhunjhunwala M, Gayen S, Hota C, Nirmal J. Interaction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction. J Biomol Struct Dyn 2024; 42:5207-5218. [PMID: 37340665 DOI: 10.1080/07391102.2023.2226717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
Chronic disease patients (cancer, arthritis, cardiovascular diseases) undergo long-term systemic drug treatment. Membrane transporters in ocular barriers could falsely recognize these drugs and allow their trafficking into the eye from systemic circulation. Hence, despite their pharmacological activity, these drugs accumulate and cause toxicity at the non-target site, such as the eye. Since around 40% of clinically used drugs are organic cation in nature, it is essential to understand the role of organic cation transporter (OCT1) in ocular barriers to facilitate the entry of systemic drugs into the eye. We applied machine learning techniques and computer simulation models (molecular dynamics and metadynamics) in the current study to predict the potential OCT1 substrates. Artificial intelligence models were developed using a training dataset of a known substrates and non-substrates of OCT1 and predicted the potential OCT1 substrates from various systemic drugs causing ocular toxicity. Computer simulation studies was performed by developing the OCT1 homology model. Molecular dynamic simulations equilibrated the docked protein-ligand complex. And metadynamics revealed the movement of substrates across the transporter with minimum free energy near the binding pocket. The machine learning model showed an accuracy of about 80% and predicted the potential substrates for OCT1 among systemic drugs causing ocular toxicity - not known earlier, such as cyclophosphamide, bupivacaine, bortezomib, sulphanilamide, tosufloxacin, topiramate, and many more. However, further invitro and invivo studies are required to confirm these predictions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Malani
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Manthan S Hiremath
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Surbhi Sharma
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Manisha Jhunjhunwala
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Chittaranjan Hota
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Jayabalan Nirmal
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
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8
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Rodriguez Rodriguez ER, Nordvang RT, Petersson M, Rendsvig JKH, Arendrup EW, Fernández Quintero ML, Jenkins TP, Laustsen AH, Thrane SW. Fit-for-purpose heterodivalent single-domain antibody for gastrointestinal targeting of toxin B from Clostridium difficile. Protein Sci 2024; 33:e5035. [PMID: 38923049 PMCID: PMC11201815 DOI: 10.1002/pro.5035] [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: 12/11/2023] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024]
Abstract
Single-domain antibodies (sdAbs), such as VHHs, are increasingly being developed for gastrointestinal (GI) applications against pathogens to strengthen gut health. However, what constitutes a suitable developability profile for applying these proteins in a gastrointestinal setting remains poorly explored. Here, we describe an in vitro methodology for the identification of sdAb derivatives, more specifically divalent VHH constructs, that display extraordinary developability properties for oral delivery and functionality in the GI environment. We showcase this by developing a heterodivalent VHH construct that cross-inhibits the toxic activity of the glycosyltransferase domains (GTDs) from three different toxinotypes of cytotoxin B (TcdB) from lineages of Clostridium difficile. We show that the VHH construct possesses high stability and binding activity under gastric conditions, in the presence of bile salts, and at high temperatures. We suggest that the incorporation of early developability assessment could significantly aid in the efficient discovery of VHHs and related constructs fit for oral delivery and GI applications.
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Affiliation(s)
| | | | - Marcus Petersson
- Bactolife A/SCopenhagen EastDenmark
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | | | | | - Timothy P. Jenkins
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Andreas H. Laustsen
- Bactolife A/SCopenhagen EastDenmark
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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9
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Hanifi K, Scrosati PM, Konermann L. MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation. J Phys Chem B 2024; 128:5973-5986. [PMID: 38864851 DOI: 10.1021/acs.jpcb.4c01241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Electrospray ionization (ESI) mass spectrometry is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation mechanism (IEM)]. Here, we tackle this problem by examining the effects of various MD settings on the ESI behavior of the 9-residue peptide bradykinin in acidic aqueous droplets. Several parameters were found to significantly affect the kinetic competition between peptide IEM and CRM. By systematically probing the droplet behavior, we uncovered problems associated with certain settings, including peptide/solvent temperature imbalances, unexpected peptide deceleration during IEM, and a dependence of the ESI mechanism on the water model. We also noted different simulation outcomes for different force fields. On the basis of comprehensive tests, we propose a set of "best practice" parameter settings for MD simulations of ESI droplets. The strategies used here should be transferable to other types of droplet simulations, paving the way toward a more solid understanding of ESI mechanisms.
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Affiliation(s)
- Kasra Hanifi
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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10
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Wang M, Fan B, Lu W, Ryde U, Chang Y, Han D, Lu J, Liu T, Gao Q, Chen C, Xu Y. Unraveling the Binding Mode of Cyclic Adenosine-Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations. Molecules 2024; 29:2650. [PMID: 38893524 PMCID: PMC11173896 DOI: 10.3390/molecules29112650] [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: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The stimulator of interferon genes (STING) plays a significant role in immune defense and protection against tumor proliferation. Many cyclic dinucleotide (CDN) analogues have been reported to regulate its activity, but the dynamic process involved when the ligands activate STING remains unclear. In this work, all-atom molecular dynamics simulations were performed to explore the binding mode between human STING (hSTING) and four cyclic adenosine-inosine monophosphate analogs (cAIMPs), as well as 2',3'-cGMP-AMP (2',3'-cGAMP). The results indicate that these cAIMPs adopt a U-shaped configuration within the binding pocket, forming extensive non-covalent interaction networks with hSTING. These interactions play a significant role in augmenting the binding, particularly in interactions with Tyr167, Arg238, Thr263, and Thr267. Additionally, the presence of hydrophobic interactions between the ligand and the receptor further contributes to the overall stability of the binding. In this work, the conformational changes in hSTING upon binding these cAIMPs were also studied and a significant tendency for hSTING to shift from open to closed state was observed after binding some of the cAIMP ligands.
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Affiliation(s)
- Meiting Wang
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
- Department of Computational Chemistry, Chemical Centre, Lund University, SE-221 00 Lund, Sweden;
| | - Baoyi Fan
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Wenfeng Lu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Ulf Ryde
- Department of Computational Chemistry, Chemical Centre, Lund University, SE-221 00 Lund, Sweden;
| | - Yuxiao Chang
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Di Han
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Jiarui Lu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Taigang Liu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China;
| | - Changpo Chen
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions of Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Yongtao Xu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China; (M.W.); (D.H.); (J.L.); (T.L.)
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11
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Champion C, Hünenberger PH, Riniker S. Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations. J Chem Theory Comput 2024; 20:4350-4362. [PMID: 38742760 PMCID: PMC11137823 DOI: 10.1021/acs.jctc.4c00370] [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: 03/22/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a mixture of protonation and/or tautomeric states at physiological pH. Intrinsically, standard classical molecular dynamics (MD) simulations cannot describe such equilibria between states, which negatively impacts the prediction of key molecular properties in silico. Following the formalism described by de Oliveira and co-workers (J. Chem. Theory Comput. 2019, 15, 424-435) to consider the influence of all states on the binding process based on alchemical free-energy calculations, we demonstrate in this work that the multistate method replica-exchange enveloping distribution sampling (RE-EDS) is well suited to describe molecules with multiple protonation and/or tautomeric states in a single simulation. We apply our methodology to a series of eight inhibitors of factor Xa with two protonation states and a series of eight inhibitors of glycogen synthase kinase 3β (GSK3β) with two tautomeric states. In particular, we show that given a sufficient phase-space overlap between the states, RE-EDS is computationally more efficient than standard pairwise free-energy methods.
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Affiliation(s)
- Candide Champion
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H. Hünenberger
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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12
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Ray R, Nait Mohamed FA, Maurer DP, Huang J, Alpay BA, Ronsard L, Xie Z, Han J, Fernandez-Quintero M, Phan QA, Ursin RL, Vu M, Kirsch KH, Prum T, Rosado VC, Bracamonte-Moreno T, Okonkwo V, Bals J, McCarthy C, Nair U, Kanekiyo M, Ward AB, Schmidt AG, Batista FD, Lingwood D. Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity 2024; 57:1141-1159.e11. [PMID: 38670113 PMCID: PMC11096021 DOI: 10.1016/j.immuni.2024.03.022] [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: 12/12/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
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Affiliation(s)
- Rashmi Ray
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
| | - Daniel P Maurer
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Jiachen Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Berk A Alpay
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Monica Fernandez-Quintero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020 Innsbruck, Austria
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Rebecca L Ursin
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mya Vu
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Victoria C Rosado
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte-Moreno
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julia Bals
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron G Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Biology, The Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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13
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Kılıç M, Ensing B. Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation. J Phys Chem B 2024; 128:3069-3080. [PMID: 38518376 DOI: 10.1021/acs.jpcb.3c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Flavins play an important role in many oxidation and reduction processes in biological systems. For example, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment; however, the underlying molecular interactions of this effect are still unknown. Using hybrid quantum mechanics/molecular mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution, and two different protein environments, in particular, a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight into how specific polarization of the flavin by its environment tunes the reduction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counterion configurations and by artifacts at the QM/MM boundary. We make suggestions for how these issues can be overcome.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
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14
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Marini-Rapoport O, Fernández-Quintero ML, Keswani T, Zong G, Shim J, Pedersen LC, Mueller GA, Patil SU. Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies. Clin Exp Immunol 2024; 216:25-35. [PMID: 38346116 PMCID: PMC10929694 DOI: 10.1093/cei/uxae005] [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: 10/13/2023] [Revised: 12/08/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In peanut allergy, Arachis hypogaea 2 (Ara h 2) and Arachis hypogaea 6 (Ara h 6) are two clinically relevant peanut allergens with known structural and sequence homology and demonstrated cross-reactivity. We have previously utilized X-ray crystallography and epitope binning to define the epitopes on Ara h 2. We aimed to quantitatively characterize the cross-reactivity between Ara h 2 and Ara h 6 on a molecular level using human monoclonal antibodies (mAbs) and structural characterization of allergenic epitopes. We utilized mAbs cloned from Ara h 2 positive single B cells isolated from peanut-allergic, oral immunotherapy-treated patients to quantitatively analyze cross-reactivity between recombinant Ara h 2 (rAra h 2) and Ara h 6 (rAra h 6) proteins using biolayer interferometry and indirect inhibitory ELISA. Molecular dynamics simulations assessed time-dependent motions and interactions in the antibody-antigen complexes. Three epitopes-conformational epitopes 1.1 and 3, and the sequential epitope KRELRNL/KRELMNL-are conserved between Ara h 2 and Ara h 6, while two more conformational and three sequential epitopes are not. Overall, mAb affinity was significantly lower to rAra h 6 than it was to rAra h 2. This difference in affinity was primarily due to increased dissociation of the antibodies from rAra h 6, a phenomenon explained by the higher conformational flexibility of the Ara h 6-antibody complexes in comparison to Ara h 2-antibody complexes. Our results further elucidate the cross-reactivity of peanut 2S albumins on a molecular level and support the clinical immunodominance of Ara h 2.
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Affiliation(s)
- Orlee Marini-Rapoport
- Harvard University, Cambridge, MA, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tarun Keswani
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Guangning Zong
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jane Shim
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Sarita U Patil
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
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15
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Fischer AL, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibl F, Quoika PK, Gschwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics. J Chem Theory Comput 2024; 20:2321-2333. [PMID: 38373307 PMCID: PMC10938642 DOI: 10.1021/acs.jctc.3c01106] [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: 10/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
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Affiliation(s)
- Anna-Lena
M. Fischer
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Anna Tichy
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Robert F. Wild
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Patrick K. Quoika
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | | | - Stefano Forli
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Andrew B. Ward
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Klaus R. Liedl
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Martin Zacharias
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | - Monica L. Fernández-Quintero
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
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16
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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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17
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Blow KE, Whale TF, Quigley D, Sosso GC. Understanding the impact of ammonium ion substitutions on heterogeneous ice nucleation. Faraday Discuss 2024; 249:114-132. [PMID: 37782066 DOI: 10.1039/d3fd00097d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Understanding the mechanisms underpinning heterogeneous ice nucleation in the presence of ionic inclusions is important for fields such as cryopreservation and for improved models of climate and weather prediction. Feldspar and ammonium are both present in significant quantities in the atmosphere, and experimental evidence has shown that feldspar can nucleate ice from ammonium-containing solutions at temperatures warmer than water alone. In recent work, Whale hypothesised that this increase in nucleation temperature is due to an increase in configurational entropy when an ammonium ion is included in the ice hydrogen bond network (T. F. Whale, J. Chem. Phys., 2022, 156, 144503). In this work, we investigate the impact of the inclusion of an ammonium ion on the hydrogen bond network by direct enumeration of the number of structures found using Rick's algorithm. We also determine the energy of these systems and thus compare the effects of enthalpy and entropy to test Whale's hypothesis. We find that the inclusion of an ammonium ion increases the total number of configurations under conditions consistent with a realistic surface charge. We also find that the enthalpic contribution is dominant in determining the location of the ammonium ion within the structure, although we note that this neglects other practicalities of ice nucleation.
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Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Thomas F Whale
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David Quigley
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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18
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Petrov D, Perthold JW, Oostenbrink C, de Groot BL, Gapsys V. Guidelines for Free-Energy Calculations Involving Charge Changes. J Chem Theory Comput 2024; 20:914-925. [PMID: 38164763 PMCID: PMC10809403 DOI: 10.1021/acs.jctc.3c00757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes are considered, in the context of both free-energy calculations and sampling. We find that ensuring that no net-charge changes take place, while maintaining a neutral simulation box, may be sufficient provided that the simulation boxes are large enough. Addition of salt to the solution (when appropriate) can further alleviate the remaining artifacts in the sampling or the calculated free-energy differences. We provide practical guidelines to avoid finite-size artifacts.
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Affiliation(s)
- Drazen Petrov
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Jan Walther Perthold
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Chris Oostenbrink
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg
30, Beerse B-2340, Belgium
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19
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Doyle M, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME. Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography. J Am Chem Soc 2023; 145:14621-14635. [PMID: 37369071 PMCID: PMC10347547 DOI: 10.1021/jacs.3c01412] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 06/29/2023]
Abstract
Structural dynamics of water and its hydrogen-bonding networks play an important role in enzyme function via the transport of protons, ions, and substrates. To gain insights into these mechanisms in the water oxidation reaction in Photosystem II (PS II), we have performed crystalline molecular dynamics (MD) simulations of the dark-stable S1 state. Our MD model consists of a full unit cell with 8 PS II monomers in explicit solvent (861 894 atoms), enabling us to compute the simulated crystalline electron density and to compare it directly with the experimental density from serial femtosecond X-ray crystallography under physiological temperature collected at X-ray free electron lasers (XFELs). The MD density reproduced the experimental density and water positions with high fidelity. The detailed dynamics in the simulations provided insights into the mobility of water molecules in the channels beyond what can be interpreted from experimental B-factors and electron densities alone. In particular, the simulations revealed fast, coordinated exchange of waters at sites where the density is strong, and water transport across the bottleneck region of the channels where the density is weak. By computing MD hydrogen and oxygen maps separately, we developed a novel Map-based Acceptor-Donor Identification (MADI) technique that yields information which helps to infer hydrogen-bond directionality and strength. The MADI analysis revealed a series of hydrogen-bond wires emanating from the Mn cluster through the Cl1 and O4 channels; such wires might provide pathways for proton transfer during the reaction cycle of PS II. Our simulations provide an atomistic picture of the dynamics of water and hydrogen-bonding networks in PS II, with implications for the specific role of each channel in the water oxidation reaction.
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Affiliation(s)
- Margaret
D. Doyle
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Asmit Bhowmick
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David C. Wych
- Computer,
Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center
for Non-linear Studies, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United States
| | - Louise Lassalle
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Philipp S. Simon
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - James Holton
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Biochemistry and Biophysics, University
of California, San Francisco, San
Francisco, California 94158, United States
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nicholas K. Sauter
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Vittal K. Yachandra
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan F. Kern
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Michael E. Wall
- Computer,
Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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20
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Goncalves BG, Banerjee IA. A computational and laboratory approach for the investigation of interactions of peptide conjugated natural terpenes with EpHA2 receptor. J Mol Model 2023; 29:204. [PMID: 37291458 DOI: 10.1007/s00894-023-05596-3] [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: 07/06/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
CONTEXT Ephrin type A receptor 2 (EphA2) is a well-known drug target for cancer treatment due to its overexpression in numerous types of cancers. Thus, it is crucial to determine the binding interactions of this receptor with both the ligand-binding domain (LBD) and the kinase-binding domain (KBD) through a targeted approach in order to modulate its activity. In this work, natural terpenes with inherent anticancer properties were conjugated with short peptides YSAYP and SWLAY that are known to bind to the LBD of EphA2 receptor. We examined the binding interactions of six terpenes (maslinic acid, levopimaric acid, quinopimaric acid, oleanolic, polyalthic, and hydroxybetulinic acid) conjugated to the above peptides with the ligand-binding domain (LBD) of EphA2 receptor computationally. Additionally, following the "target-hopping approach," we also examined the interactions of the conjugates with the KBD. Our results indicated that most of the conjugates showed higher binding interactions with the EphA2 kinase domain compared to LBD. Furthermore, the binding affinities of the terpenes increased upon conjugating the peptides with the terpenes. In order to further investigate the specificity toward EphA2 kinase domain, we also examined the binding interactions of the terpenes conjugated to VPWXE (x = norleucine), as VPWXE has been shown to bind to other RTKs. Our results indicated that the terpenes conjugated to SWLAY in particular showed high efficacy toward binding to the KBD. We also designed conjugates where in the peptide portion and the terpenes were separated by a butyl (C4) group linker to examine if the binding interactions could be enhanced. Docking studies showed that the conjugates with linkers had enhanced binding with the LBD compared to those without linkers, though binding remained slightly higher without linkers toward the KBD. As a proof of concept, maslinate and oleanolate conjugates of each of the peptides were then tested with F98 tumor cells which are known to overexpress EphA2 receptor. Results indicated that the oleanolate-amido-SWLAY conjugates were efficacious in reducing the cell proliferation of the tumor cells and may be potentially developed and further studied for targeting tumor cells overexpressing the EphA2 receptor. To test if these conjugates could bind to the receptor and potentially function as kinase inhibitors, we conducted SPR analysis and ADP-Glo assay. Our results indicated that OA conjugate with SWLAY showed the highest inhibition. METHODS Docking studies were carried out using AutoDock Vina, v.1.2.0; Molecular Dynamics and MMGBSA calculations were carried out through Schrodinger Software DESMOND.
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Affiliation(s)
- Beatriz G Goncalves
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA.
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21
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Martin GM, Fernández-Quintero ML, Lee WH, Pholcharee T, Eshun-Wilson L, Liedl KR, Pancera M, Seder RA, Wilson IA, Ward AB. Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9. Nat Commun 2023; 14:2815. [PMID: 37198165 PMCID: PMC10192352 DOI: 10.1038/s41467-023-38509-2] [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: 12/12/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
A primary objective in malaria vaccine design is the generation of high-quality antibody responses against the circumsporozoite protein of the malaria parasite, Plasmodium falciparum (PfCSP). To enable rational antigen design, we solved a cryo-EM structure of the highly potent anti-PfCSP antibody L9 in complex with recombinant PfCSP. We found that L9 Fab binds multivalently to the minor (NPNV) repeat domain, which is stabilized by a unique set of affinity-matured homotypic, antibody-antibody contacts. Molecular dynamics simulations revealed a critical role of the L9 light chain in integrity of the homotypic interface, which likely impacts PfCSP affinity and protective efficacy. These findings reveal the molecular mechanism of the unique NPNV selectivity of L9 and emphasize the importance of anti-homotypic affinity maturation in protective immunity against P. falciparum.
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Affiliation(s)
- Gregory M Martin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Monica L Fernández-Quintero
- Department of General, Inorganic, and Theoretical Chemistry, Center for Chemistry and Biomedicine, The University of Innsbruck; Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tossapol Pholcharee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Biochemistry, University of Oxford, Oxford, OX1 3DR, UK
| | - Lisa Eshun-Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Klaus R Liedl
- Department of General, Inorganic, and Theoretical Chemistry, Center for Chemistry and Biomedicine, The University of Innsbruck; Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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22
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Zhang Z, Šponer J, Bussi G, Mlýnský V, Šulc P, Simmons CR, Stephanopoulos N, Krepl M. Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. J Chem Inf Model 2023; 63:2794-2809. [PMID: 37126365 PMCID: PMC10170514 DOI: 10.1021/acs.jcim.3c00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered "half-closed" intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials.
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Affiliation(s)
- Zhengyue Zhang
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Petr Šulc
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 241/27, 783 71 Olomouc, Czech Republic
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23
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Kasparyan G, Hub JS. Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation. J Chem Theory Comput 2023; 19:2676-2683. [PMID: 37052575 DOI: 10.1021/acs.jctc.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Electric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of mean force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes, and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charge imbalance as the membrane capacitance changes.
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Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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24
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Seidler CA, Kokot J, Fernández-Quintero ML, Liedl KR. Structural Characterization of Nanobodies during Germline Maturation. Biomolecules 2023; 13:380. [PMID: 36830754 PMCID: PMC9953242 DOI: 10.3390/biom13020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in combination with molecular dynamics simulations to capture a broad conformational space and to reconstruct the thermodynamics and kinetics of conformational transitions in the antigen-binding site, the paratope. By kinetically characterizing the loop movements of the paratope, we found that, with an increase in affinity, the state populations shift towards the binding competent conformation. The contacts contributing to antigen binding, and those who contribute to the overall stability, show a clear trend towards less variable but more intense contacts. Additionally, these investigated nanobodies clearly follow the conformational selection paradigm, as the binding competent conformation pre-exists within the structural ensembles without the presence of the antigen.
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Affiliation(s)
| | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
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25
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Wells NGM, Smith CA. Predicting binding affinity changes from long-distance mutations using molecular dynamics simulations and Rosetta. Proteins 2023. [PMID: 36757060 DOI: 10.1002/prot.26477] [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: 10/13/2022] [Revised: 01/20/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023]
Abstract
Computationally modeling how mutations affect protein-protein binding not only helps uncover the biophysics of protein interfaces, but also enables the redesign and optimization of protein interactions. Traditional high-throughput methods for estimating binding free energy changes are currently limited to mutations directly at the interface due to difficulties in accurately modeling how long-distance mutations propagate their effects through the protein structure. However, the modeling and design of such mutations is of substantial interest as it allows for greater control and flexibility in protein design applications. We have developed a method that combines high-throughput Rosetta-based side-chain optimization with conformational sampling using classical molecular dynamics simulations, finding significant improvements in our ability to accurately predict long-distance mutational perturbations to protein binding. Our approach uses an analytical framework grounded in alchemical free energy calculations while enabling exploration of a vastly larger sequence space. When comparing to experimental data, we find that our method can predict internal long-distance mutational perturbations with a level of accuracy similar to that of traditional methods in predicting the effects of mutations at the protein-protein interface. This work represents a new and generalizable approach to optimize protein free energy landscapes for desired biological functions.
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Affiliation(s)
- Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
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26
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Henrique Santana Silveira P, Pita SSDR. Druggable sites identification in Streptococcus mutans VicRK system evaluated by catechols. J Biomol Struct Dyn 2023; 41:12000-12015. [PMID: 36703608 DOI: 10.1080/07391102.2023.2166118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/26/2022] [Indexed: 01/28/2023]
Abstract
Dental caries is a global public health problem, being the most common non-communicable disease. Streptococcus mutans, the causative agent of human cariogenic dental biofilms, produce glycosyltransferases (Gtfs) whose gene expression is modulated by the VicRK system, which makes them a promising target for dental biofilm inhibitor developments. Bioinformatics have playing a significant role in drug discovery programs mainly in novel hit identification. In this study, potential inhibitors against the S. mutans VicK system have been identified through Structure-based Virtual Screening performed between the VicK druggable sites followed byMolecular Dynamic simulations (MD) with binding affinity analysis by MM-PBSA approach. First, VicK protein was downloaded from PDB, and druggability analyses were performed by PockDrug and FTMap servers describing three interaction sites (S1, S2, and S3) that covered the most important domains for stability and activity. Next, a catechol virtual screening (n = 383) was performed on AutoDock4.2, and better-docked catechols showed strong binding affinity interaction through hydrogen bonding, hydrophobic interactions, and π-stacking with VicK auto kinase and phosphatase activity sites. Ligand efficiency indexes were also calculated (LE, LELP, LLE, and BEI) and showed optimal values. Furthermore, a 200 ns MD simulation run showed stability (RMSD and RMSF) and a high number of hydrogen bonds into peltatoside and maritimein, the two best VicK complexes. These results supported that catechols could potentially inhibit exopolysaccharides synthesis and be used in the biofilm management of new anti-cariogenic and antimicrobial agents.
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Affiliation(s)
- Paulo Henrique Santana Silveira
- Multidisciplinary Institute in Health, Campus Anísio Teixeira, Federal University of Bahia (UFBA - IMS/CAT), Vitória da Conquista, Bahia, Brasil
| | - Samuel Silva da Rocha Pita
- Laboratory of Bioinformatic and Molecular Modelling (LaBiMM), Pharmacy College, Ondina Campus, Federal University of Bahia (UFBA), Salvador, Bahia, Brasil
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27
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Zlobin A, Belyaeva J, Golovin A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. J Chem Inf Model 2023; 63:546-560. [PMID: 36633836 DOI: 10.1021/acs.jcim.2c01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes' mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.
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Affiliation(s)
- Alexander Zlobin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Julia Belyaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrey Golovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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28
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Lazaridis T. Molecular origins of asymmetric proton conduction in the influenza M2 channel. Biophys J 2023; 122:90-98. [PMID: 36403086 PMCID: PMC9822799 DOI: 10.1016/j.bpj.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
The M2 proton channel of influenza A is embedded into the viral envelope and allows acidification of the virion when the external pH is lowered. In contrast, no outward proton conductance is observed when the internal pH is lowered, although outward current is observed at positive voltage. Residues Trp41 and Asp44 are known to play a role in preventing pH-driven outward conductance, but the mechanism for this is unclear. We investigate this issue using classical molecular dynamics simulations with periodic proton hops. When all key His37 residues are neutral, inward proton movement is much more facile than outward movement if the His are allowed to shuttle the proton. The preference for inward movement increases further as the charge on the His37 increases. Analysis of the trajectories reveals three factors accounting for this asymmetry. First, in the outward direction, Asp44 traps the hydronium by strong electrostatic interactions. Secondly, Asp44 and Trp41 orient the hydronium with the protons pointing inward, hampering outward Grotthus hopping. As a result, the effective barrier is lower in the inward direction. Trp41 adds to the barrier by weakly H-bonding to potential H+ acceptors. Finally, for charged His, the H3O+ in the inner vestibule tends to get trapped at lipid-lined fenestrations of the cone-shaped channel. Simulations qualitatively reproduce the experimentally observed higher outward conductance of mutants. The ability of positive voltage, unlike proton gradient, to induce an outward current appears to arise from its ability to bias H3O+ and the waters around it toward more H-outward orientations.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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29
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Xu Y, Fan B, Gao Y, Chen Y, Han D, Lu J, Liu T, Gao Q, Zhang JZ, Wang M. Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation. Molecules 2022; 27:molecules27238358. [PMID: 36500451 PMCID: PMC9739212 DOI: 10.3390/molecules27238358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is a histone-modifying enzyme, which is a significant target for anticancer drug research. In this work, 40 reported tetrahydroquinoline-derivative inhibitors targeting LSD1 were studied to establish the three-dimensional quantitative structure-activity relationship (3D-QSAR). The established models CoMFA (Comparative Molecular Field Analysis (q2 = 0.778, Rpred2 = 0.709)) and CoMSIA (Comparative Molecular Similarity Index Analysis (q2 = 0.764, Rpred2 = 0.713)) yielded good statistical and predictive properties. Based on the corresponding contour maps, seven novel tetrahydroquinoline derivatives were designed. For more information, three of the compounds (D1, D4, and Z17) and the template molecule 18x were explored with molecular dynamics simulations, binding free energy calculations by MM/PBSA method as well as the ADME (absorption, distribution, metabolism, and excretion) prediction. The results suggested that D1, D4, and Z17 performed better than template molecule 18x due to the introduction of the amino and hydrophobic groups, especially for the D1 and D4, which will provide guidance for the design of LSD1 inhibitors.
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Affiliation(s)
- Yongtao Xu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Baoyi Fan
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Yunlong Gao
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Yifan Chen
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Di Han
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - John Zenghui Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Meiting Wang
- School of Medical Engineering & Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang Medical University, Xinxiang 453003, China
- Department of Theoretical Chemistry, Chemical Centre, Lund University, SE-221 00 Lund, Sweden
- Correspondence:
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30
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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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31
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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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32
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George A, Mondal S, Purnaprajna M, Athri P. Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors. ACS OMEGA 2022; 7:32877-32896. [PMID: 36157750 PMCID: PMC9494432 DOI: 10.1021/acsomega.2c03189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucidate spatial and temporal properties of the building blocks of life, such as deoxyribonucleic acid (DNA) and protein, across microsecond (μs) time scales using femtosecond (fs) time steps. A principal bottleneck toward extending MD calculations to larger time scales is the long-range electrostatic force measuring component of the naive nonbonded force computation algorithm, which scales with a complexity of (N, number of atoms). In this review, we present various methods to determine electrostatic interactions in often-used open-source MD packages as well as the implementation details that facilitate acceleration of the electrostatic interaction calculation.
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Affiliation(s)
- Anu George
- Department
of Computer Science and Engineering, Amrita
School of Engineering, Bengaluru 560035, Amrita Vishwa Vidyapeetham, India
| | | | - Madhura Purnaprajna
- Department
of Computer Science and Engineering, PES
University, Bengaluru 560085, India
| | - Prashanth Athri
- Department
of Computer Science and Engineering, Amrita
School of Engineering, Bengaluru 560035, Amrita Vishwa Vidyapeetham, India
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33
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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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34
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Silvestri A, Raiteri P, Gale JD. Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability. J Chem Theory Comput 2022; 18:5901-5919. [PMID: 36073829 DOI: 10.1021/acs.jctc.2c00787] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative example. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for individual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na+ and Cl- are found to be surprisingly different and of opposite sign, despite the ions having very similar hydration free energies.
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Affiliation(s)
- Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
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35
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Fernández-Quintero ML, Fischer ALM, Kokot J, Waibl F, Seidler CA, Liedl KR. The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles. Front Immunol 2022; 13:953917. [PMID: 36177031 PMCID: PMC9514858 DOI: 10.3389/fimmu.2022.953917] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
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36
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Loche P, Scalfi L, Ali Amu M, Schullian O, Bonthuis D, Rotenberg B, Netz RR. Effects of surface rigidity and metallicity on dielectric properties and ion interactions at aqueous hydrophobic interfaces. J Chem Phys 2022; 157:094707. [DOI: 10.1063/5.0101509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using classical molecular dynamics simulations we investigate the dielectric properties at interfaces of water with graphene, graphite, hexane and water vapor. For graphite we compare metallic and non-metallic versions. At the vapor-liquid water and hexane-water interfaces the laterally averaged dielectric profiles are significantly broadened due to interfacial roughness and only slightly anisotropic. In contrast, at the rigid graphene surface the dielectric profiles are strongly anisotropic and the perpendicular dielectric profile exhibits pronounced oscillations and sign changes. The interfacial dielectric excess, characterized by the shift of the dielectric-dividing-surface with respect to the Gibbs-dividing-surface, is positive for all surfaces, showing that water has an enhanced dielectric response at hydrophobic surfaces. The dielectric-dividing-surface positions vary significantly among the different surfaces, which points to pronounced surface-specific dielectric behavior. The interfacial repulsion of a chloride ion is shown to be dominated by electrostatic interactions for the soft fluid-fluid interfaces and by non-electrostatic Lennard-Jones interactions for the rigid graphene-water interface. A linear tensorial dielectric model for the ion-interface interaction with sharp dielectric interfaces located on the dielectric-dividing-surface positions works well for graphene but fails for vapor and hexane, because these interfaces are smeared out. The repulsion of chloride from the metallic and non-metallic graphite versions differs very little, which reflects the almost identical interfacial water structure and can be understood based on linear continuum dielectric theory. Interface flexibility shows up mostly in the non-linear Coulomb part of the ion-interface interaction, which changes significantly close to the interfaces and signals the breakdown of linear dielectric continuum theory.
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Affiliation(s)
| | - Laura Scalfi
- Freie Universitat Berlin Fachbereich Physik, Germany
| | | | - Otto Schullian
- Max Planck Institute of Colloids and Interfaces, Germany
| | - Douwe Bonthuis
- Institute of Theoretical and Computational Physics, Graz University of Technology Institute of Theoretical and Computational Physics, Austria
| | | | - Roland R. Netz
- Physics, Freie Universitat Berlin Fachbereich Physik, Germany
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37
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Thakur A, Bansode D, Ghare P, Sakpal S. Molecular docking and dynamic simulation of approved drugs targeting against spike protein (6VXX) of 2019-nCoV (novel coronavirus). J INDIAN CHEM SOC 2022. [PMCID: PMC9197568 DOI: 10.1016/j.jics.2022.100571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Shi W, He B, Pu B, Ren Y, Avdeev M, Shi S. Software for Evaluating Long-Range Electrostatic Interactions Based on the Ewald Summation and Its Application to Electrochemical Energy Storage Materials. J Phys Chem A 2022; 126:5222-5230. [PMID: 35900935 DOI: 10.1021/acs.jpca.2c02591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrochemical characteristics such as open-circuit voltage and ionic conductivity of electrochemical energy storage materials are easily affected, typically negatively, by mobile ion/vacancy ordering. Ordered phases can be identified based on the lattice gas model and electrostatic energy screening. However, the evaluation of long-range electrostatic energy is not straightforward because of the conditional convergence. The Ewald method decomposes the electrostatic energy into a real space part and a reciprocal space part, achieving a fast convergence in each. Due to its high computational efficiency, Ewald-based techniques are widely used in analyzing characteristics of electrochemical energy storage materials. In this work, we present software not only integrating Ewald techniques for two-dimensional and three-dimensional periodic systems but also combining the Ewald method with the lattice matching algorithm and bond valence. It is aimed to become a useful tool for screening stable structures and interfaces and identifying the ionic transport channels of cation conductors.
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Affiliation(s)
- Wei Shi
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China.,Zhejiang Laboratory, Hangzhou 311100, China
| | - Bing He
- School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China
| | - Bowei Pu
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China
| | - Yuan Ren
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China
| | - Maxim Avdeev
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, NSW 2234, Australia.,School of Chemistry, The University of Sydney, Sydney 2006, Australia
| | - Siqi Shi
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China.,Zhejiang Laboratory, Hangzhou 311100, China.,Materials Genome Institute, Shanghai University, Shanghai 200444, China
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39
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Sun Z, Wang M, He Q, Liu Z. Molecular Modeling of Ionic Liquids: Force‐Field Validation and Thermodynamic Perspective from Large‐Scale Fast‐Growth Solvation Free Energy Calculations. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Mao Wang
- NCS Testing Technology Co., Ltd. No. 13, Gaoliangqiao Xiejie Beijing 100081 China
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio‐Engineering Co., Ltd. North Century Avenue 333 Ningbo 315100 China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
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40
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Procacci P. Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach. J Chem Theory Comput 2022; 18:4014-4026. [PMID: 35642423 PMCID: PMC9202353 DOI: 10.1021/acs.jctc.2c00295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 12/02/2022]
Abstract
In the context of advanced hit-to-lead drug design based on atomistic molecular dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between two chemically distant compounds. The method (termed NE-RBFE) relies on the enhanced sampling of the end-states in bulk and in the bound state via Hamiltonian Replica Exchange, alchemically connected by a series of independent and fast nonequilibrium (NE) simulations. The technique has been implemented in a bidirectional fashion, applying the Crooks theorem to the NE work distributions for RBFE predictions. The dissipation of the NE process, negatively affecting accuracy, has been minimized by introducing a smooth regularization based on shifted electrostatic and Lennard-Jones non bonded potentials. As a challenging testbed, we have applied our method to the calculation of the RBFEs in the recent host-guest SAMPL international contest, featuring a macrocyclic host with guests varying in the net charge, volume, and chemical fingerprints. Closure validation has been successfully verified in cycles involving compounds with disparate Tanimoto coefficients, volume, and net charge. NE-RBFE is specifically tailored for massively parallel facilities and can be used with little or no code modification on most of the popular software packages supporting nonequilibrium alchemical simulations, such as Gromacs, Amber, NAMD, or OpenMM. The proposed methodology bypasses most of the entanglements and limitations of the standard single topology RBFE approach for strictly congeneric series based on free-energy perturbation, such as slowly relaxing cavity water, sampling issues along the alchemical stratification, and the need for highly overlapping molecular fingerprints.
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Affiliation(s)
- Piero Procacci
- Dipartimento di Chimica “Ugo
Schiff”, Università degli
Studi di Firenze, Via
della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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41
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Oliveira NF, Machuqueiro M. Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. J Chem Inf Model 2022; 62:2550-2560. [PMID: 35442654 PMCID: PMC9775199 DOI: 10.1021/acs.jcim.2c00233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have designed a protocol combining constant-pH molecular dynamics (CpHMD) simulations with an umbrella sampling (US) scheme (US-CpHMD) to study the mechanism of ADP/ATP transport (import and export) by their inner mitochondrial membrane carrier protein [ADP/ATP carrier (AAC)]. The US scheme helped overcome the limitations of sampling the slow kinetics involved in these substrates' transport, while CpHMD simulations provided an unprecedented realism by correctly capturing the associated protonation changes. The import of anionic substrates along the mitochondrial membrane has a strong energetic disadvantage due to a smaller substrate concentration and an unfavorable membrane potential. These limitations may have created an evolutionary pressure on AAC to develop specific features benefiting the import of ADP. In our work, the potential of mean force profiles showed a clear selectivity in the import of ADP compared to ATP, while in the export, no selectivity was observed. We also observed that AAC sequestered both substrates at longer distances in the import compared to the export process. Furthermore, only in the import process do we observe transient protonation of both substrates when going through the AAC cavity, which is an important advantage to counteract the unfavorable mitochondrial membrane potential. Finally, we observed a substrate-induced disruption of the matrix salt-bridge network, which can promote the conformational transition (from the C- to M-state) required to complete the import process. This work unraveled several important structural features where the complex electrostatic interactions were pivotal to interpreting the protein function and illustrated the potential of applying the US-CpHMD protocol to other transport processes involving membrane proteins.
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42
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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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43
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van Teijlingen A, Swanson HWA, Lau KHA, Tuttle T. Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization. J Phys Chem Lett 2022; 13:4046-4051. [PMID: 35486900 PMCID: PMC9109222 DOI: 10.1021/acs.jpclett.2c00544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.
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44
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Procacci P, Guarnieri G. SAMPL9 blind predictions using nonequilibrium alchemical approaches. J Chem Phys 2022; 156:164104. [PMID: 35490003 DOI: 10.1063/5.0086640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present our blind predictions for the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL), ninth challenge, focusing on the binding of WP6 (carboxy-pillar[6]arene) with ammonium/diammonium cationic guests. Host-guest binding free energies have been calculated using the recently developed virtual double system single box approach, based on the enhanced sampling of the bound and unbound end-states followed by fast switching nonequilibrium alchemical simulations [M. Macchiagodena et al., J. Chem. Theory Comput. 16, 7160 (2020)]. As far as Pearson and Kendall coefficients are concerned, performances were acceptable and, in general, better than those we submitted for calixarenes, cucurbituril-like open cavitand, and beta-cyclodextrines in previous SAMPL host-guest challenges, confirming the reliability of nonequilibrium approaches for absolute binding free energy calculations. In comparison with previous submissions, we found a rather large mean signed error that we attribute to the way the finite charge correction was addressed through the assumption of a neutralizing background plasma.
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Affiliation(s)
- Piero Procacci
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Guido Guarnieri
- ENEA, Portici Research Centre, DTE-ICT-HPC, P.le E. Fermi, 1, I-80055 Portici, NA, Italy
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45
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Loche P, Bonthuis DJ, Netz RR. Molecular dynamics simulations of the evaporation of hydrated ions from aqueous solution. Commun Chem 2022; 5:55. [PMID: 36698011 PMCID: PMC9814746 DOI: 10.1038/s42004-022-00669-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/22/2022] [Indexed: 01/28/2023] Open
Abstract
Although important for atmospheric processes and gas-phase catalysis, very little is known about the hydration state of ions in the vapor phase. Here we study the evaporation energetics and kinetics of a chloride ion from liquid water by molecular dynamics simulations. As chloride permeates the interface, a water finger forms and breaks at a chloride separation of ≈ 2.8 nm from the Gibbs dividing surface. For larger separations from the interface, about 7 water molecules are estimated to stay bound to chloride in saturated water vapor, as corroborated by continuum dielectrics and statistical mechanics models. This ion hydration significantly reduces the free-energy barrier for evaporation. The effective chloride diffusivity in the transition state is found to be about 6 times higher than in bulk, which reflects the highly mobile hydration dynamics as the water finger breaks. Both effects significantly increase the chloride evaporation flux from the quiescent interface of an electrolyte solution, which is predicted from reaction kinetic theory.
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Affiliation(s)
- Philip Loche
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
- Fachbereich Physik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Douwe J Bonthuis
- Institute of Theoretical and Computational Physics, Graz University of Technology, 8010, Graz, Austria
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, 14195, Berlin, Germany.
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46
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Wu Z, Biggin PC. Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers. J Chem Theory Comput 2022; 18:2657-2672. [PMID: 35315270 PMCID: PMC9082507 DOI: 10.1021/acs.jctc.1c01251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Absolute
binding free-energy (ABFE) calculations are playing an
increasing role in drug design, especially as they can be performed
on a range of disparate compounds and direct comparisons between them
can be made. It is, however, especially important to ensure that they
are as accurate as possible, as unlike relative binding free-energy
(RBFE) calculations, one does not benefit as much from a cancellation
of errors during the calculations. In most modern implementations
of ABFE calculations, a particle mesh Ewald scheme is typically used
to treat the electrostatic contribution to the free energy. A central
requirement of such schemes is that the box preserves neutrality throughout
the calculation. There are many ways to deal with this problem that
have been discussed over the years ranging from a neutralizing plasma
with a post hoc correction term through to a simple co-alchemical
ion within the same box. The post hoc correction approach is the most
widespread. However, the vast majority of these studies have been
applied to a soluble protein in a homogeneous solvent (water or salt
solution). In this work, we explore which of the more common approaches
would be the most suitable for a simulation box with a lipid bilayer
within it. We further develop the idea of the so-called Rocklin correction
for lipid-bilayer systems and show how such a correction could work.
However, we also show that it will be difficult to make this generalizable
in a practical way and thus we conclude that the use of a “co-alchemical
ion” is the most useful approach for simulations involving
lipid membrane systems.
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Affiliation(s)
- Zhiyi Wu
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, U.K
| | - Philip C Biggin
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, U.K
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47
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Zofchak ES, Zhang Z, Marioni N, Duncan TJ, Sachar HS, Chamseddine A, Freeman BD, Ganesan V. Cation–Ligand Interactions Dictate Salt Partitioning and Diffusivity in Ligand-Functionalized Polymer Membranes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Everett S. Zofchak
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Zidan Zhang
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Nico Marioni
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Tyler J. Duncan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Harnoor S. Sachar
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alyssa Chamseddine
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benny D. Freeman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Venkat Ganesan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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48
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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49
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Guthmiller JJ, Han J, Utset HA, Li L, Lan LYL, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, de la Peña AT, Rosado V, Dugan HL, Zheng NY, Tepora ME, Bitar DJ, Changrob S, Strohmeier S, Huang M, García-Sastre A, Liedl KR, Bloom JD, Nachbagauer R, Palese P, Krammer F, Coughlan L, Ward AB, Wilson PC. Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Nature 2022; 602:314-320. [PMID: 34942633 PMCID: PMC8828479 DOI: 10.1038/s41586-021-04356-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection1. However, viral mutants that escape broadly neutralizing antibodies have been reported2,3. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine4,5, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | | | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Moderna Inc., Cambridge, MA, USA
| | | | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George O'Dell
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alec W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lauren Gentles
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Victoria Rosado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Micah E Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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Fernández-Quintero ML, Kroell KB, Grunewald LJ, Fischer ALM, Riccabona JR, Liedl KR. CDR loop interactions can determine heavy and light chain pairing preferences in bispecific antibodies. MAbs 2022; 14:2024118. [PMID: 35090383 PMCID: PMC8803122 DOI: 10.1080/19420862.2021.2024118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
As the current biotherapeutic market is dominated by antibodies, the design of different antibody formats, like bispecific antibodies, is critical to the advancement of the field. In contrast to monovalent antibodies, which consist of two identical antigen-binding sites, bispecific antibodies can target two different epitopes by containing two different antigen-binding sites. Thus, the rise of new formats as successful therapeutics has reignited the interest in advancing and facilitating the efficient production of bispecific antibodies. Here, we investigate the influence of point mutations in the antigen-binding site, the paratope, on heavy and light chain pairing preferences by using molecular dynamics simulations. In agreement with experiments, we find that specific residues in the antibody variable domain (Fv), i.e., the complementarity-determining region (CDR) L3 and H3 loops, determine heavy and light chain pairing preferences. Excitingly, we observe substantial population shifts in CDR-H3 and CDR-L3 loop conformations in solution accompanied by a decrease in bispecific IgG yield. These conformational changes in the CDR3 loops induced by point mutations also influence all other CDR loop conformations and consequentially result in different CDR loop states in solution. However, besides their effect on the obtained CDR loop ensembles, point mutations also lead to distinct interaction patterns in the VH-VL interface. By comparing the interaction patterns among all investigated variants, we observe specific contacts in the interface that drive heavy and light chain pairing. Thus, these findings have broad implications in the field of antibody engineering and design because they provide a mechanistic understanding of antibody interfaces, by identifying critical factors driving the pairing preferences, and thus can help to advance the design of bispecific antibodies.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lukas J Grunewald
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena M Fischer
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Jakob R Riccabona
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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