1
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Péczka N, Ranđelović I, Orgován Z, Csorba N, Egyed A, Petri L, Ábrányi-Balogh P, Gadanecz M, Perczel A, Tóvári J, Schlosser G, Takács T, Mihalovits LM, Ferenczy GG, Buday L, Keserű GM. Contribution of Noncovalent Recognition and Reactivity to the Optimization of Covalent Inhibitors: A Case Study on KRas G12C. ACS Chem Biol 2024. [PMID: 38991015 DOI: 10.1021/acschembio.4c00217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Covalent drugs might bear electrophiles to chemically modify their targets and have the potential to target previously undruggable proteins with high potency. Covalent binding of drug-size molecules includes a noncovalent recognition provided by secondary interactions and a chemical reaction leading to covalent complex formation. Optimization of their covalent mechanism of action should involve both types of interactions. Noncovalent and covalent binding steps can be characterized by an equilibrium dissociation constant (KI) and a reaction rate constant (kinact), respectively, and they are affected by both the warhead and the scaffold of the ligand. The relative contribution of these two steps was investigated on a prototypic drug target KRASG12C, an oncogenic mutant of KRAS. We used a synthetically more accessible nonchiral core derived from ARS-1620 that was equipped with four different warheads and a previously described KRAS-specific basic side chain. Combining these structural changes, we have synthesized novel covalent KRASG12C inhibitors and tested their binding and biological effect on KRASG12C by various biophysical and biochemical assays. These data allowed us to dissect the effect of scaffold and warhead on the noncovalent and covalent binding event. Our results revealed that the atropisomeric core of ARS-1620 is not indispensable for KRASG12C inhibition, the basic side chain has little effect on either binding step, and warheads affect the covalent reactivity but not the noncovalent binding. This type of analysis helps identify structural determinants of efficient covalent inhibition and may find use in the design of covalent agents.
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Affiliation(s)
- Nikolett Péczka
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Ivan Ranđelović
- Department of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Noémi Csorba
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Attila Egyed
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - László Petri
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Márton Gadanecz
- Protein Modeling Research Group, Laboratory of Structural Chemistry and Biology, ELTE Institute of Chemistry, Budapest 1117, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány. 1/A, Budapest 1117, Hungary
| | - András Perczel
- Protein Modeling Research Group, Laboratory of Structural Chemistry and Biology, ELTE Institute of Chemistry, Budapest 1117, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - Gitta Schlosser
- MTA-ELTE "Lendület", Ion Mobility Mass Spectrometry Research Group, Budapest 1117, Hungary
| | - Tamás Takács
- HUN-REN Research Centre for Natural Sciences, Signal Transduction and Functional Genomics Research Group, Budapest 1117, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest 1117, Hungary
| | - Levente M Mihalovits
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - László Buday
- HUN-REN Research Centre for Natural Sciences, Signal Transduction and Functional Genomics Research Group, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest 1111, Hungary
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2
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2024; 42:5912-5930. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [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: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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3
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Herman CE, Valiya Parambathu A, Asthagiri DN, Lenhoff AM. Polarizability Plays a Decisive Role in Modulating Association between Molecular Cations and Anions. J Phys Chem Lett 2023; 14:7020-7026. [PMID: 37523856 DOI: 10.1021/acs.jpclett.3c01566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Electrostatic interactions involving proteins depend on not only the ionic charges involved but also their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of different pairs of monovalent molecular ions that are relevant to protein-protein and protein-ligand interactions. Cationic analogues of the basic amino acid side chains are simulated, along with oxyanionic analogues of cation-exchange ligands and acidic amino acids. Experimentally observed association trends with respect to the cations, but not anions, are captured by a nonpolarizable model. An effective continuum correction to account for electronic polarizability can capture both trends better but at the expense of fidelity to the underlying free energy landscape for ion-pair association. A polarizable model proves decisive in capturing experimentally suggested trends with respect to both cations and anions; critically, the free energy landscape for ion-pair association is itself altered, thus altering configurational sampling.
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Affiliation(s)
- Chase E Herman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Arjun Valiya Parambathu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Dilipkumar N Asthagiri
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
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4
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Villot C, Lao KU. Electronic structure theory on modeling short-range noncovalent interactions between amino acids. J Chem Phys 2023; 158:094301. [PMID: 36889981 DOI: 10.1063/5.0138032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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5
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Shin S, Willard AP. Quantifying the Molecular Polarization Response of Liquid Water Interfaces at Heterogeneously Charged Surfaces. J Chem Theory Comput 2023; 19:1843-1852. [PMID: 36866865 DOI: 10.1021/acs.jctc.2c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water's hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water's collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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6
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Liu H, Fu H, Chipot C, Shao X, Cai W. Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. J Chem Inf Model 2022; 62:3863-3873. [PMID: 35920605 DOI: 10.1021/acs.jcim.2c00678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The strength of salt bridges resulting from the interaction of cations and anions is modulated by their environment. However, polarization of the solvent molecules by the charged moieties makes the accurate description of cation-anion interactions in an aqueous solution by means of a pairwise additive potential energy function and classical combination rules particularly challenging. In this contribution, aiming at improving the representation of solvent-exposed salt-bridge interactions with an all-atom non-polarizable force field, we put forth here a parametrization strategy. First, the interaction of a cation and an anion is characterized by hybrid quantum mechanical/molecular mechanics (QM/MM) potential of mean force (PMF) calculations, whereby constantly exchanging solvent molecules around the ions are treated at the quantum mechanical level. The Lennard-Jones (LJ) parameters describing the salt-bridge ion pairs are then optimized to match the reference QM/MM PMFs through the so-called nonbonded FIX, or NBFIX, feature of the CHARMM force field. We apply the new set of parameters, coined CHARMM36m-SBFIX, to the calculation of association constants for the ammonium-acetate and guanidinium-acetate complexes, the osmotic pressures for glycine zwitterions, guanidinium, and acetate ions, and to the simulation of both folded and intrinsically disordered proteins. Our findings indicate that CHARMM36m-SBFIX improves the description of solvent-exposed salt-bridge interactions, both structurally and thermodynamically. However, application of this force field to the standard binding free-energy calculation of a protein-ligand complex featuring solvent-excluded salt-bridge interactions leads to a poor reproduction of the experimental value, suggesting that the parameters optimized in an aqueous solution cannot be readily transferred to describe solvent-excluded salt-bridge interactions. Put together, owing to their sensitivity to the environment, modeling salt-bridge interactions by means of a single, universal set of LJ parameters remains a daunting theoretical challenge.
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Affiliation(s)
- Han Liu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, F-54506 Vandœuvre-lès-Nancy, France.,Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana 61801, Illinois, United States.,Department of Biochemistry and Molecular Biology and Gordon Center for Integrative Science, The University of Chicago, Chicago 60637, Illinois, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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7
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Biriukov D, Wang HW, Rampal N, Tempra C, Kula P, Neuefeind JC, Stack AG, Předota M. The "good," the "bad," and the "hidden" in neutron scattering and molecular dynamics of ionic aqueous solutions. J Chem Phys 2022; 156:194505. [PMID: 35597655 DOI: 10.1063/5.0093643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We characterize a concentrated 7.3 m CaCl2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca2+-Cl- interactions were primarily "hidden" in the Ca-NDIS signal due to overlapping with Ca2+-Ow and Ca2+-Hw contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models "on average," the question "which model is the best" has not been answered but replaced by the question "which model is better for a given research." An overall "good" model can still be inappropriate or, in some instances, "bad" and, unfortunately, produce erroneous results. The accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.
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Affiliation(s)
- Denys Biriukov
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Hsiu-Wen Wang
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Nikhil Rampal
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Patrik Kula
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Joerg C Neuefeind
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Andrew G Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Milan Předota
- Department of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
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8
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Feng JJ, Chen JN, Kang W, Wu YD. Accurate Structure Prediction for Protein Loops Based on Molecular Dynamics Simulations with RSFF2C. J Chem Theory Comput 2021; 17:4614-4628. [PMID: 34170125 DOI: 10.1021/acs.jctc.1c00341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein loops, connecting the α-helices and β-strands, are involved in many important biological processes. However, due to their conformational flexibility, it is still challenging to accurately determine three-dimensional (3D) structures of long loops experimentally and computationally. Herein, we present a systematic study of the protein loop structure prediction via a total of ∼850 μs molecular dynamics (MD) simulations. For a set of 15 long (10-16 residues) and solvent-exposed loops, we first evaluated the performance of four state-of-the-art loop modeling algorithms, DaReUS-Loop, Sphinx, Rosetta-NGK, and MODELLER, on each loop, and none of them could accurately predict the structures for most loops. Then, temperature replica exchange molecular dynamics (REMD) simulations were conducted with three recent force fields, RSFF2C with TIP3P water model, CHARMM36m with CHARMM-modified TIP3P, and AMBER ff19SB with OPC. We found that our recently developed residue-specific force field RSFF2C performed the best and successfully predicted 12 out of 15 loops with a root-mean-square deviation (RMSD) < 1.5 Å. As an alternative with lower computational cost, normal MD simulations at high temperatures (380, 500, and 620 K) were investigated. Temperature-dependent performance was observed for each force field, and, for RSFF2C+TIP3P, we found that three independent 100-ns MD simulations at 500 K gave comparable results with REMD simulations. These results suggest that MD simulations, especially with enhanced sampling techniques such as replica exchange, with the RSFF2C force field could be useful for accurate loop structure prediction.
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Affiliation(s)
- Jia-Jie Feng
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jia-Nan Chen
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Kang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Shenzhen Bay Laboratory, Shenzhen 518132, China
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9
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Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
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Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
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10
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Okajima R, Hiraoka S, Yamashita T. Environmental Effects on Salt Bridge Stability in the Protein-Protein Interface: The Case of Hen Egg-White Lysozyme and Its Antibody, HyHEL-10. J Phys Chem B 2021; 125:1542-1549. [PMID: 33544613 DOI: 10.1021/acs.jpcb.0c09248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We studied the stability of two salt bridges between hen egg-white lysozyme (HEL) and its antibody, HyHEL-10, by using molecular dynamics simulations. It was observed that one salt bridge, D32H-K97Y, was stable, whereas the other, D99H-K97Y, was not. To understand this difference, we compared several reduced salt bridge models that incorporated the salt bridges and nearby residues. The results showed the importance of nearby residues, especially Y33H and W98H. Furthermore, to understand the effects of nearby salt bridges, we investigated two mutants, D32HA and D99HA. We found that the D32HA mutation considerably stabilized the D99H-K97Y salt bridge. The reduced model analysis indicated that this can be largely attributed to a conformational change of the main chain.
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Affiliation(s)
- Ryo Okajima
- Department of Basic Science, Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.,Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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11
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Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021; 153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
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Affiliation(s)
- E Duboué-Dijon
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - M Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Delcroix
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - H Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
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12
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Bergues-Pupo AE, Lipowsky R, Vila Verde A. Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. SOFT MATTER 2020; 16:9917-9928. [PMID: 33030193 DOI: 10.1039/d0sm01166e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single alpha helices (SAHs) stable in isolated form are often found in motor proteins where they bridge functional domains. Understanding the mechanical response of SAHs is thus critical to understand their function. The quasi-static force-extension relation of a small number of SAHs is known from single-molecule experiments. Unknown, or still controversial, are the molecular scale details behind those observations. We show that the deformation mechanism of SAHs pulled from the termini at pull speeds approaching the quasi-static limit differs from that of typical helices found in proteins, which are stable only when interacting with other protein domains. Using molecular dynamics simulations with atomistic resolution at low pull speeds previously inaccessible to simulation, we show that SAHs start unfolding from the termini at all pull speeds we investigated. Unfolding proceeds residue-by-residue and hydrogen bond breaking is not the main event determining the barrier to unfolding. We use the molecular simulation data to test the cooperative sticky chain model. This model yields excellent fits of the force-extension curves and quantifies the distance, xE = 0.13 nm, to the transition state, the natural frequency of bond vibration, ν0 = 0.82 ns-1, and the height, V0 = 2.9 kcal mol-1, of the free energy barrier associated with the deformation of single residues. Our results demonstrate that the sticky chain model could advantageously be used to analyze experimental force-extension curves of SAHs and other biopolymers.
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Affiliation(s)
- Ana Elisa Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Paren BA, Thurston BA, Neary WJ, Kendrick A, Kennemur JG, Stevens MJ, Frischknecht AL, Winey KI. Percolated Ionic Aggregate Morphologies and Decoupled Ion Transport in Precise Sulfonated Polymers Synthesized by Ring-Opening Metathesis Polymerization. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Benjamin A. Paren
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
| | - Bryce A. Thurston
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - William J. Neary
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Aaron Kendrick
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Justin G. Kennemur
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Karen I. Winey
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
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14
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Mendes de Oliveira D, Zukowski SR, Palivec V, Hénin J, Martinez-Seara H, Ben-Amotz D, Jungwirth P, Duboué-Dijon E. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys Chem Chem Phys 2020; 22:24014-24027. [DOI: 10.1039/d0cp02987d] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We combine Raman-MCR vibrational spectroscopy experiments with ab initio and classical MD simulations to gain molecular insights into carboxylate–cation binding.
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Affiliation(s)
| | | | - Vladimir Palivec
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Jérôme Hénin
- CNRS, Université de Paris
- UPR 9080
- Laboratoire de Biochimie Théorique
- 13 Rue Pierre et Marie Curie
- Paris
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Dor Ben-Amotz
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
| | - Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- 16610 Prague 6
- Czech Republic
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15
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Melcr J, Piquemal JP. Accurate Biomolecular Simulations Account for Electronic Polarization. Front Mol Biosci 2019; 6:143. [PMID: 31867342 PMCID: PMC6904368 DOI: 10.3389/fmolb.2019.00143] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022] Open
Abstract
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.
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Affiliation(s)
- Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR7616 CNRS, Paris, France
- Institut Universitaire de France, Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
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