1
|
Asakereh I, Rutbeek NR, Singh M, Davidson D, Prehna G, Khajehpour M. The Streptococcus phage protein paratox is an intrinsically disordered protein. Protein Sci 2024; 33:e5037. [PMID: 38801244 PMCID: PMC11129628 DOI: 10.1002/pro.5037] [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: 01/18/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
The bacteriophage protein paratox (Prx) blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces the ability of Streptococcus to uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the Prx:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that Prx may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of Prx in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions Prx is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces Prx folding. However, the solute stabilized fold is different from the conformation Prx adopts when it is bound to ComR. Furthermore, we have characterized Prx folding thermodynamics and folding kinetics through steady-state fluorescence and stopped flow kinetic measurements. Our results show that Prx is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein Prx is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized fold is likely the predominant form of Prx in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing in Streptococcus, by a combination of conformational selection and induced-fit binding mechanisms.
Collapse
Affiliation(s)
- Iman Asakereh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Nicole R. Rutbeek
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Manvir Singh
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - David Davidson
- Department of ChemistryUniversity of ManitobaWinnipegManitobaCanada
| | - Gerd Prehna
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
| | | |
Collapse
|
2
|
Vijayanathan M, Vadakkepat AK, Mahendran KR, Sharaf A, Frandsen KEH, Bandyopadhyay D, Pillai MR, Soniya EV. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity. Commun Biol 2024; 7:566. [PMID: 38745065 PMCID: PMC11093982 DOI: 10.1038/s42003-024-06152-2] [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: 12/29/2021] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS's steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
Collapse
Affiliation(s)
- Mallika Vijayanathan
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Abhinav Koyamangalath Vadakkepat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE17HB, UK
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
| | - Kristian E H Frandsen
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Eppurath Vasudevan Soniya
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
He W, Huang X, Kelimu A, Li W, Cui C. Streamlined Efficient Synthesis and Antioxidant Activity of γ-[Glutamyl] (n≥1)-tryptophan Peptides by Glutaminase from Bacillus amyloliquefaciens. Molecules 2023; 28:4944. [PMID: 37446606 DOI: 10.3390/molecules28134944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
As a group of naturally occurring peptides in various foods, γ-glutamyl peptides possess a unique Kokumi taste and health benefits. However, few studies have focused on the functionality of γ-glutamyl peptides. In this study, the γ-[glutamyl] (n=1, 2, 3)-tryptophan peptides were synthesized from a solution of glutamine (Gln) and tryptophan (Trp) employing L-glutaminase from Bacillus amyloliquefaciens. Four different γ-glutamyl peptides were identified from the reaction mixture by UPLC-Q-TOF-MS/MS. Under optimal conditions of pH 10, 37 °C, 3 h, 0.1 mol/L Gln: 0.1 mol/L Trp = 1:3, and glutaminase at 0.1% (m/v), the yields of γ-l-glutamyl-l-tryptophan (γ-EW), γ-l-glutamyl-γ-l-glutamyl-l-tryptophan (γ-EEW) and γ-l-glutamyl-γ-l-glutamyl-γ-l-glutamyl-l-tryptophan (γ-EEEW) were 51.02%, 26.12% and 1.91% respectively. The antioxidant properties of the reaction mixture and the two peptides (γ-EW, γ-EEW) identified from the reaction media were further compared. Results showed that γ-EW exhibited the highest DPPH•, ABTS•+ and O2•--scavenging activity (EC50 = 0.2999 mg/mL, 67.6597 μg/mL and 5.99 mg/mL, respectively) and reducing power (EC50 = 4.61 mg/mL), while γ-EEW demonstrated the highest iron-chelating activity (76.22%). Thus, the synthesized mixture may be used as a potential source of antioxidant peptides for food and nutraceutical applications.
Collapse
Affiliation(s)
- Wenjiang He
- Infinitus (China) Co., Ltd., Guangzhou 510640, China
| | - Xiaoling Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Abulimiti Kelimu
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Nongda East Road 311, Urumqi 830052, China
| | - Wenzhi Li
- Infinitus (China) Co., Ltd., Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| |
Collapse
|
5
|
Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Interactions between Rigid Polyelectrolytes Mediated by Ordering and Orientation of Multivalent Nonspherical Ions in Salt Solutions. PHYSICAL REVIEW LETTERS 2023; 130:158202. [PMID: 37115871 DOI: 10.1103/physrevlett.130.158202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/23/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Multivalent ions in solutions with polyelectrolytes (PEs) induce electrostatic correlations that can drastically change ion distributions around the PEs and their mutual interactions. Using coarse-grained molecular dynamics simulations, we show how in addition to valency, ion shape and concentration can be harnessed as tools to control rigid like-charged PE-PE interactions. We demonstrate a correlation between the orientational ordering of aspherical ions and how they mediate the effective PE-PE attraction induced by multivalency. The interaction type, strength, and range can thus be externally controlled in ionic solutions. Our results can be used as generic guidelines to tune the self-assembly of like-charged polyelectrolytes by variation of the characteristics of the ions.
Collapse
Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| |
Collapse
|
6
|
Kunche L, Natarajan U. Conformations and Solvation of Synthetic Polymers in Water by Generalized Born Implicit-Solvent Molecular Dynamics Simulations: Stereoisomers of Poly(acrylic acid) and Poly(methacrylic acid). J Phys Chem B 2023; 127:1244-1253. [PMID: 36705523 DOI: 10.1021/acs.jpcb.2c06658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present the GB-OBC model as an approach for implicit-solvent MD simulations of a synthetic macromolecule in water. The model is tested and found to be successful in reproducing the chain dimensions and predicting the free energy of solvation of carboxylic acid vinyl polymers. The influence of stereochemistry and the hydrophobic nature of the polymer was investigated as a function of chain length (20 < N < 600) for poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMA). The dimensionless parameters of the GB-OBC model were parameterized to be applicable to PAA and PMA. Scaling relations for chain dimensions obtained using implicit-solvent MD simulations in this study are in good agreement with those from experiments, theory of solvated chains in good solvents, and all-atom MD simulations in explicit water. Results show that ⟨Rg2⟩/NL2 is greater for the atactic chain as compared to the isotactic chain, for PAA as well as PMA. ⟨Rg2⟩/NL2 values of chains attain constancy in water for N = 200, with the values being greater for PMA. The PMA chain is conformationally more perturbed than the PAA chain, for both isotactic and atactic stereochemistry. The solvation free energy ΔGhyd of PAA and PMA in water is negative for all chain lengths (N = 20-600) and becomes more favorable with an increase in molecular weight. The ΔGhyd values for isotactic and atactic chains are identical at lower values of N but differ slightly for N > 300. Irrespective of the hydrophobic nature of the polymer, the atactic chain is thermodynamically more soluble in water as compared to the isotactic chain. The isotactic chain is less hydrophilic as compared to the atactic chain due to the closer proximity of the COOH groups along the backbone. This implicit solvent method is an effective way to accurately simulate the configurational properties and solvation of synthetic polymers in water.
Collapse
Affiliation(s)
- Lakshmikumar Kunche
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai600036, India
| | - Upendra Natarajan
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai600036, India
| |
Collapse
|
7
|
Zhu Q, Ge Y, Li W, Ma J. Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters. J Chem Theory Comput 2023; 19:396-411. [PMID: 36592097 DOI: 10.1021/acs.jctc.2c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Polarization plays important roles in charged and hydrogen bonding containing systems. Much effort ranging from the construction of physics-based models to quantum mechanism (QM)-based and machine learning (ML)-assisted models have been devoted to incorporating the polarization effect into the conventional force fields at different levels, such as atomic and coarse grained (CG). The application of polarizable force fields or polarization models was limited by two aspects, namely, computational cost and transferability. Different from physics-based models, no predetermining parameters were required in the QM-based approaches. Taking advantage of both the accuracy of QM calculations and efficiency of molecular mechanism (MM) and ML, polarization effects could be treated more efficiently while maintaining the QM accuracy. The computational cost could be reduced with variable electrostatic parameters, such as the charge, dipole, and electronic dielectric constant with the help of linear scaling fragmentation-based QM calculations and ML models. Polarization and entropy effects on the prediction of partition coefficient of druglike molecules are demonstrated by using both explicit or implicit all-atom molecular dynamics simulations and machine learning-assisted models. Directions and challenges for future development are also envisioned.
Collapse
Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Yang Ge
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| |
Collapse
|
8
|
Fukuda I, Nakamura H. Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference. Biophys Rev 2022; 14:1315-1340. [PMID: 36659982 PMCID: PMC9842848 DOI: 10.1007/s12551-022-01029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.
Collapse
Affiliation(s)
- Ikuo Fukuda
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima, Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| |
Collapse
|
9
|
Ruiz-Rodríguez MA, Cooper CD, Rocchia W, Casalegno M, López de los Santos Y, Raos G. Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode. J Phys Chem B 2022; 126:8777-8790. [PMID: 36269122 PMCID: PMC9639099 DOI: 10.1021/acs.jpcb.2c05371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.
Collapse
Affiliation(s)
| | - Christopher D. Cooper
- Department
of Mechanical Engineering and Centro Científico Tecnológico
de Valparaíso, Universidad Técnica
Federico Santa María, Valparaíso, 2340000, Chile
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, 16163Genova, Italy
| | - Mosè Casalegno
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy
| | - Yossef López de los Santos
- Centre
Armand-Frappier Santé, Biotechnologie, Institut national de
la recherche scientifique (INRS), Université
du Québec, Laval, QuébecHV7 1B7, Canada
| | - Guido Raos
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy,
| |
Collapse
|
10
|
Lee AJ, Rackers JA, Bricker WP. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Biophys J 2022; 121:3883-3895. [PMID: 36057785 PMCID: PMC9674991 DOI: 10.1016/j.bpj.2022.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
One of the fundamental limitations of accurately modeling biomolecules like DNA is the inability to perform quantum chemistry calculations on large molecular structures. We present a machine learning model based on an equivariant Euclidean neural network framework to obtain accurate ab initio electron densities for arbitrary DNA structures that are much too large for conventional quantum methods. The model is trained on representative B-DNA basepair steps that capture both base pairing and base stacking interactions. The model produces accurate electron densities for arbitrary B-DNA structures with typical errors of less than 1%. Crucially, the error does not increase with system size, which suggests that the model can extrapolate to large DNA structures with negligible loss of accuracy. The model also generalizes reasonably to other DNA structural motifs such as the A- and Z-DNA forms, despite being trained on only B-DNA configurations. The model is used to calculate electron densities of several large-scale DNA structures, and we show that the computational scaling for this model is essentially linear. We also show that this machine learning electron density model can be used to calculate accurate electrostatic potentials for DNA. These electrostatic potentials produce more accurate results compared with classical force fields and do not show the usual deficiencies at short range.
Collapse
Affiliation(s)
- Alex J Lee
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico
| | - Joshua A Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico.
| | - William P Bricker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
| |
Collapse
|
11
|
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
Collapse
Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
12
|
Rahnamoun A, O'Hearn KA, Kaymak MC, Li Z, Merz KM, Aktulga HM. A Polarizable Cationic Dummy Metal Ion Model. J Phys Chem Lett 2022; 13:5334-5340. [PMID: 35675715 DOI: 10.1021/acs.jpclett.2c01279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can fluctuate to respond to the environment. This model includes explicit polarization and ion-induced interactions and can be coupled with nonpolarizable or polarizable water models, making it more transferable to simpler force fields. This approach allows us to enhance the original fixed charge CDA model where the charge distribution cannot adapt to the local solvent structure. To illustrate the new CDApol model, we examined properties of the Zn2+, Al3+, and Zr4+ ions in aqueous solution. The polarizable model and Lennard-Jones parameters were refined for octahedrally coordinated Zn2+, Al3+, and Zr4+ CDAs to reproduce thermodynamic and geometrical properties. Using this locally polarizable model, we were able to obtain the experimental hydration free energy, ion-oxygen distance, and coordination number coupled with the standard 12-6 Lennard-Jones model. This model can be used in myriad additional applications where local polarization and charge transfer is important.
Collapse
Affiliation(s)
- Ali Rahnamoun
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Kurt A O'Hearn
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Mehmet Cagri Kaymak
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Zhen Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| |
Collapse
|
13
|
Vahid H, Scacchi A, Yang X, Ala-Nissila T, Sammalkorpi M. Modified Poisson–Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions. J Chem Phys 2022; 156:214906. [DOI: 10.1063/5.0092273] [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
We present a soft-potential-enhanced Poisson–Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based model for polyelectrolytes (PEs) in monovalent salt solutions as well as compared to a full atomistic molecular dynamics simulation with the explicit solvent. We demonstrate that our modification enables the SPB theory to accurately predict monovalent ion distributions around a rodlike PE in a wide range of ion and charge distribution conditions in the weak-coupling regime. These include excess salt concentrations up to 1M and ion sizes ranging from small ions, such as Na+ or Cl−, to softer and larger ions with a size comparable to the PE diameter. The work provides a simple way to implement an enhancement that effectively captures the influence of ion size and species into the PB theory in the context of PEs in aqueous salt solutions.
Collapse
Affiliation(s)
- Hossein Vahid
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
| | - Xiang Yang
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| |
Collapse
|
14
|
Hunley C, Mohsin M, Marucho M. Electrical impulse characterization along actin filaments in pathological conditions. COMPUTER PHYSICS COMMUNICATIONS 2022; 275:108317. [PMID: 35369107 PMCID: PMC8967275 DOI: 10.1016/j.cpc.2022.108317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The simplicity of the theoretical formulation, and high performance of the Mathematica software, enable the analysis of multiple conditions without computational restrictions. The program is based on a multi-scale (atomic → monomer → filament) approach capable of accounting for the atomistic details of a protein molecular structure, its biological environment, and their impact on the travel distance, velocity, and attenuation of monovalent ionic wave packets propagating along microfilaments. The interactive component allows investigators to choose the experimental conditions (intracellular Vs in vitro), nucleotide state (ATP Vs ADP), actin isoform (alpha, gamma, beta, and muscle or non-muscle cell), as well as a conformation model that covers a variety of mutants and wild-type (the control) actin filament. We used the computational tool to analyze environmental changes such as temperature effects and pH changes of the surrounding solutions, as well as structural changes to an actin monomer due to radius changes. Additionally, we investigated for the first time the electrostatic consequences of actin mutations from different disease conditions. These studies may provide an unprecedented molecular understanding of why and how age, inheritance, and disease conditions induce dysfunctions in the biophysical mechanisms underlying the propagation of electrical signals along actin filaments.
Collapse
Affiliation(s)
- Christian Hunley
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA
| | - Md Mohsin
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA
| |
Collapse
|
15
|
Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
Collapse
Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| |
Collapse
|
16
|
Jon JS, Ri WK, Sin KR, Son YC, Jo KW, Pak JS, Kim SJ, Ri YJ, An YC. Derivation of the solvation effect-incorporated Poisson-Boltzmann equation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
17
|
Gabas F, Conte R, Ceotto M. Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation. J Phys Chem Lett 2022; 13:1350-1355. [PMID: 35109652 PMCID: PMC8842300 DOI: 10.1021/acs.jpclett.1c04087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.
Collapse
|
18
|
Electrical Propagation of Condensed and Diffuse Ions Along Actin Filaments. J Comput Neurosci 2022; 50:91-107. [PMID: 34392446 PMCID: PMC8818025 DOI: 10.1007/s10827-021-00795-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 02/03/2023]
Abstract
In this article, we elucidate the roles of divalent ion condensation and highly polarized immobile water molecules on the propagation of ionic calcium waves along actin filaments. We introduced a novel electrical triple layer model and used a non-linear Debye-Huckel theory with a non-linear, dissipative, electrical transmission line model to characterize the physicochemical properties of each monomer in the filament. This characterization is carried out in terms of an electric circuit model containing monomeric flow resistances and ionic capacitances in both the condensed and diffuse layers. We considered resting and excited states of a neuron using representative mono and divalent electrolyte mixtures. Additionally, we used 0.05V and 0.15V voltage inputs to study ionic waves along actin filaments in voltage clamp experiments. Our results reveal that the physicochemical properties characterizing the condensed and diffuse layers lead to different electrical conductive mediums depending on the ionic species and the neuron state. This region specific propagation mechanism provides a more realistic avenue of delivery by way of cytoskeleton filaments for larger charged cationic species. A new direct path for transporting divalent ions might be crucial for many electrical processes found in localized neuron elements such as at mitochondria and dendritic spines.
Collapse
|
19
|
Xu X, Jia X, Zhang Y. Dendritic polyelectrolytes with monovalent and divalent counterions: the charge regulation effect and counterion release. SOFT MATTER 2021; 17:10862-10872. [PMID: 34806740 DOI: 10.1039/d1sm01392k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The charge regulation and the release of counterions are extremely important and substantial in determining the charge state of polyelectrolytes and the interaction between polyelectrolytes and proteins. Going beyond monovalent to multivalent cations, it is well-known that the effects of ions are qualitatively different. Therefore, the well-accepted descriptions of the charge regulation and the counterion release based on monovalent ions do not immediately apply to systems with multivalent ions. Here, we study the key structural and electrostatic features of charged dendrimers at hand of the pharmaceutically important dendritic polyglycerol sulfate (dPGS) macromolecule equilibrated with monovalent and divalent salts by molecular dynamics (MD) simulations. Following a simple but accurate scheme to determine its effective radius, the counterion condensed layer of the dPGS is determined with high accuracy and we observe the sequential replacement of condensed monovalent cations (MCs) to divalent cations (DCs) rendering a smaller dPGS effective charge versus the DC concentration. We resolve and track the release of counterions on the dPGS along its binding pathway with the plasma protein Human Serum Albumin (HSA). We find that the release of MCs remains favorable for the complexation leading to a considerable amount of release entropy as the driving force for complexation. The release of DCs only occurs above a certain DC concentration with a comparably smaller number of released ions than MCs. Its contribution to the binding free energy is small indicating a subtle cancellation between the entropy gain in releasing DCs and the enthalpy penalty from dissociating DCs from the dendrimer.
Collapse
Affiliation(s)
- Xiao Xu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
| | - Xu Jia
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
| | - Yuejun Zhang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
| |
Collapse
|
20
|
Chen Y, Krämer A, Charron NE, Husic BE, Clementi C, Noé F. Machine learning implicit solvation for molecular dynamics. J Chem Phys 2021; 155:084101. [PMID: 34470360 DOI: 10.1063/5.0059915] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent in a mean-field fashion with implicit solvent models. However, a challenge with existing implicit solvent models is that they often lack accuracy or certain physical properties compared to explicit solvent models as the many-body effects of the neglected solvent molecules are difficult to model as a mean field. Here, we leverage machine learning (ML) and multi-scale coarse graining (CG) in order to learn implicit solvent models that can approximate the energetic and thermodynamic properties of a given explicit solvent model with arbitrary accuracy, given enough training data. Following the previous ML-CG models CGnet and CGSchnet, we introduce ISSNet, a graph neural network, to model the implicit solvent potential of mean force. ISSNet can learn from explicit solvent simulation data and be readily applied to molecular dynamics simulations. We compare the solute conformational distributions under different solvation treatments for two peptide systems. The results indicate that ISSNet models can outperform widely used generalized Born and surface area models in reproducing the thermodynamics of small protein systems with respect to explicit solvent. The success of this novel method demonstrates the potential benefit of applying machine learning methods in accurate modeling of solvent effects for in silico research and biomedical applications.
Collapse
Affiliation(s)
- Yaoyi Chen
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Andreas Krämer
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | | | - Brooke E Husic
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Cecilia Clementi
- Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| |
Collapse
|
21
|
Jiménez-Grávalos F, Suárez D. A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy. J Chem Theory Comput 2021; 17:4981-4995. [PMID: 34279923 PMCID: PMC8901103 DOI: 10.1021/acs.jctc.1c00263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.
Collapse
Affiliation(s)
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain
| |
Collapse
|
22
|
Eguchi H, Kobayashi T, Yamada T, Rocabado DSR, Ishimoto T, Yamauchi M. Inversely polarized thermo-electrochemical power generation via the reaction of an organic redox couple on a TiO 2/Ti mesh electrode. Sci Rep 2021; 11:13929. [PMID: 34230515 PMCID: PMC8260709 DOI: 10.1038/s41598-021-93269-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
We demonstrate thermo-electrochemical (TEC) conversion using a biocompatible redox couple of lactic acid and pyruvic acid on earth-abundant TiO2. The TEC cell exhibited a positive Seebeck coefficient of 1.40 mV K-1. DFT calculations figured out that the adsorption of intermediate species and protons on TiO2 controls both the redox reaction and current polarity.
Collapse
Affiliation(s)
- Hiroto Eguchi
- Department of Chemistry, Graduate School of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takashi Kobayashi
- Division of Applied Chemistry, Graduate School of Engineering, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Teppei Yamada
- Division of Applied Chemistry, Graduate School of Engineering, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan. .,Center for Molecular Systems, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - David S Rivera Rocabado
- Graduate School of Nanobioscience, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Takayoshi Ishimoto
- Graduate School of Nanobioscience, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama, 236-0027, Japan. .,Smart Innovation Program, Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, Hiroshima, 739-8527, Japan.
| | - Miho Yamauchi
- Department of Chemistry, Graduate School of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan. .,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan. .,Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
| |
Collapse
|
23
|
Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
Collapse
Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| |
Collapse
|
24
|
Kozuch J, Schneider SH, Zheng C, Ji Z, Bradshaw RT, Boxer SG. Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case. J Phys Chem B 2021; 125:4415-4427. [PMID: 33900769 PMCID: PMC8522303 DOI: 10.1021/acs.jpcb.1c00578] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions underlie nearly all molecular processes in the condensed phase from solvation to catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach toward more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electric fields are correlated to conformation-dependent effects of the flexible PenG side chain, including both the local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in three-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.
Collapse
Affiliation(s)
- Jacek Kozuch
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Samuel H Schneider
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Chu Zheng
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Zhe Ji
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Richard T Bradshaw
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| |
Collapse
|
25
|
Abstract
JACFC is a Java web application (http://neuronanobiophysics.utsa.edu/) that provides both experts and non-experts in the field suitable tools for elucidating the molecular mechanisms modulating the electrical signal propagation, stability, and bundle formation of microtubules and actin filaments under different molecular (wild type, isoforms, mutants) and environmental (physiological and pathological) conditions. This acknowledgment might reveal the potential role of cytoskeleton filaments in neuronal activities, including molecular-level processing of information and neural regeneration. Molecular understanding of the polyelectrolyte properties of bionanowires, is also crucial for development of reliability, highly functioning small devices with biotechnological applications such as bionanosensors and computing bionanoprocessors.
Collapse
Affiliation(s)
- Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| |
Collapse
|
26
|
Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021; 17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson-Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson-Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.
Collapse
Affiliation(s)
- Rae A Corrigan
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Andrew C Thiel
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jack R Lynn
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Brandon D Walker
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Thomas L Casavant
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Louis Lagardere
- Department of Chemistry, Sorbonne Université, F-75005 Paris, France
| | | | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Michael J Schnieders
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States.,Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| |
Collapse
|
27
|
Cerar J, Jamnik A, Szilágyi I, Tomšič M. Solvation of nonionic poly(ethylene oxide) surfactant Brij 35 in organic and aqueous-organic solvents. J Colloid Interface Sci 2021; 594:150-159. [PMID: 33761392 DOI: 10.1016/j.jcis.2021.02.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/17/2022]
Abstract
HYPOTHESIS By combining the experimental small- and wide-angle x-ray scattering (SWAXS) method with molecular dynamics simulations and the theoretical 'complemented-system approach' it is possible to obtain detailed information about the intra- and inter-molecular structure and dynamics of the solvation and hydration of the surfactant in organic and mixed solvents, e.g., of the nonionic surfactant Brij 35 (C12E23) in alcohols and aqueous alcohol-rich ternary systems. This first application of the complemented-system approach to the surfactant system will promote the use of this powerful methodology that is based on experimental and calculated SWAXS data in studies of colloidal systems. By applying high-performance computing systems, such an approach is readily available for studies in the colloidal domain. EXPERIMENTS SWAXS experiments and MD simulations were performed for binary Brij 35/alcohol and ternary Brij 35/water/alcohol systems with ethanol, n-butanol and n-hexanol as the organic solvent component at 25 °C. FINDINGS We confirmed the presence of solvated Brij 35 monomers in the studied organic media, revealed their preferential hydration and discussed their structural and dynamic features at the intra- and inter-molecular levels. Anisotropic effective surfactant molecular conformations were found. The influence of the hydrophobicity of the organic solvent on the hydration phenomena of surfactant molecules was explained.
Collapse
Affiliation(s)
- Jure Cerar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Andrej Jamnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - István Szilágyi
- MTA-SZTE Lendület Biocolloids Research Group, Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Matija Tomšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
28
|
Majodina S, Ndima L, Abosede OO, Hosten EC, Lorentino CMA, Frota HF, Sangenito LS, Branquinha MH, Santos ALS, Ogunlaja AS. Physical stability enhancement and antimicrobial properties of a sodium ionic cocrystal with theophylline. CrystEngComm 2021. [DOI: 10.1039/d0ce01387k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, we have described the synthesis and characterisation of the theophylline hydrate (Theo hydrate), cocrystal (Theo–Phen·2H2O) and hydrated sodium co-crystal of theophylline (Na–(Theo)2ClO·2H2O), where Theo = theophylline and Phen = 1,10-phenathroline.
Collapse
Affiliation(s)
| | - Lubabalo Ndima
- Department of Chemistry
- Nelson Mandela University
- Port Elizabeth 6031
- South Africa
| | - Olufunso O. Abosede
- Department of Chemistry
- Nelson Mandela University
- Port Elizabeth 6031
- South Africa
| | - Eric C. Hosten
- Department of Chemistry
- Nelson Mandela University
- Port Elizabeth 6031
- South Africa
| | - Carolline M. A. Lorentino
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes
- Departamento de Microbiologia Geral
- Instituto de Microbiologia Paulo de Góes
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
| | - Heloísa F. Frota
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes
- Departamento de Microbiologia Geral
- Instituto de Microbiologia Paulo de Góes
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
| | - Leandro S. Sangenito
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes
- Departamento de Microbiologia Geral
- Instituto de Microbiologia Paulo de Góes
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
| | - Marta H. Branquinha
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes
- Departamento de Microbiologia Geral
- Instituto de Microbiologia Paulo de Góes
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
| | - André L. S. Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes
- Departamento de Microbiologia Geral
- Instituto de Microbiologia Paulo de Góes
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
| | - Adeniyi S. Ogunlaja
- Department of Chemistry
- Nelson Mandela University
- Port Elizabeth 6031
- South Africa
| |
Collapse
|
29
|
Borleske G, Zhou Y. Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation. JOURNAL OF COMPUTATIONAL PHYSICS 2020; 421:109725. [PMID: 32884156 PMCID: PMC7461612 DOI: 10.1016/j.jcp.2020.109725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is proposed to calculate these quantities on the dielectric interface from the numerical solutions of the Poisson-Boltzmann equation. Our method reconstructs a potential field locally in the least square sense on the polynomial basis enriched with Green's functions, the latter characterize the Coulomb potential induced by charges near the position of reconstruction. This enrichment resembles the decomposition of electrostatic potential into singular Coulomb component and the regular reaction field in the Generalized Born methods. Numerical experiments demonstrate that the enrichment recovery produces drastically more accurate and stable potential gradients on molecular surfaces compared to classical recovery techniques.
Collapse
|
30
|
Cifani C, Micioni Di Bonaventura E, Botticelli L, Del Bello F, Giorgioni G, Pavletić P, Piergentili A, Quaglia W, Bonifazi A, Schepmann D, Wünsch B, Vistoli G, Micioni Di Bonaventura MV. Novel Highly Potent and Selective Sigma1 Receptor Antagonists Effectively Block the Binge Eating Episode in Female Rats. ACS Chem Neurosci 2020; 11:3107-3116. [PMID: 32886484 PMCID: PMC8011929 DOI: 10.1021/acschemneuro.0c00456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
![]()
In
this paper, the benzo-cracking approach was applied to the potent
sigma1 (σ1) receptor antagonist 1 to
afford the less conformationally constrained 1,3-dioxane derivatives 2 and 3. To evaluate the effect of the increase
in the distance between the two hydrophobic structural elements that
flank the basic function, the cis and trans diastereomers of 4 and 5 were also prepared
and studied. Compounds 2 and 3 showed affinity
values at the σ1 receptor significantly higher than
that of the lead compound 1. In particular, 3 displayed unprecedented selectivity over the σ2 receptor, the phencyclidine site of the NMDA receptor, and opioid
receptor subtypes, as well as over the dopamine transporter. Docking
results supported the structure–activity relationship studies.
Due to its interesting biological profile, derivative 3, selected for an in vivo study in a validated preclinical
model of binge eating, was able to counteract the overeating of palatable
food only in binging rats, without affecting palatable food intake
in the control group and anxiety-like and depression-related behaviors
in female rats. This result strengthened the involvement of the σ1 receptor in the compulsive-like eating behavior and supported
the σ1 receptor as a promising target for the management
of eating disorders.
Collapse
Affiliation(s)
- Carlo Cifani
- School of Pharmacy, Pharmacology Unit, University of Camerino, Via Madonna delle Carceri 9, 62032 Camerino, Italy
| | | | - Luca Botticelli
- School of Pharmacy, Pharmacology Unit, University of Camerino, Via Madonna delle Carceri 9, 62032 Camerino, Italy
| | - Fabio Del Bello
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Gianfabio Giorgioni
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Pegi Pavletić
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Alessandro Piergentili
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Wilma Quaglia
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Alessandro Bonifazi
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie, Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie, Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milano, Italy
| | | |
Collapse
|
31
|
Albuquerque JV, Shirsat RN. Prelude to Molecular Dynamics‐II: Investigation of Potential Energy Surfaces Using Gaussian Charge Models. ChemistrySelect 2020. [DOI: 10.1002/slct.202002418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Rajendra N. Shirsat
- School of Chemical Sciences Goa University, Taleigao Plateau Taleigao Goa. 403 206 India
| |
Collapse
|
32
|
Ali HS, Higham J, de Visser SP, Henchman RH. Comparison of Free-Energy Methods to Calculate the Barriers for the Nucleophilic Substitution of Alkyl Halides by Hydroxide. J Phys Chem B 2020; 124:6835-6842. [PMID: 32648760 DOI: 10.1021/acs.jpcb.0c02264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calculating the free-energy barriers of liquid-phase chemical reactions with explicit solvent is a considerable challenge. Most studies use the energy and entropy of minimized single-point geometries of the reactants and transition state in implicit solvent using normal mode analysis (NMA). Explicit-solvent methods instead make use of the potential of mean force (PMF). Here, we propose a new energy-entropy (EE) method to calculate the Gibbs free energy of reactants and transition states in explicit solvent by combining quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations with multiscale cell correlation (MCC). We apply it to six nucleophilic substitution reactions of the hydroxide transfer to methyl and ethyl halides in water, where the halides are F, Cl, and Br. We compare EE-MCC Gibbs free energy barriers using two Hamiltonians, self-consistent charge density functional based tight-binding (SCC-DFTB) and B3LYP/6-31+G* density functional theory (DFT) with respective PMF values, EE-NMA values using B3LYP/6-31+G* and M06/6-31+G* DFT in implicit solvent and experimental values derived via transition state theory. The barriers using SCC-DFTB are found to agree well with the PMF and experiment and previous computational studies, being slightly higher but improving on the lower values obtained for the implicit solvent. Achieving convergence over many degrees of freedom remains a challenge for EE-MCC in explicit-solvent QM/MM systems, particularly for the more expensive B3LYP/6-31+G* and M06/6-31+G* DFT methods, but the insightful decomposition of entropy over all degrees of freedom should make EE-MCC a valuable tool for deepening the understanding of chemical reactions.
Collapse
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Jonathan Higham
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.,Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| |
Collapse
|
33
|
Zhang B, Zhang J, Kang Z, Liang L, Liu Y, Wang Q. On interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations. J Biomol Struct Dyn 2020; 39:5335-5347. [PMID: 32608321 DOI: 10.1080/07391102.2020.1786456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
P-glycoprotein (P-gp, MDR1), one of ATP-binding cassette transporters, may confer tumor cells cross-resistance to chemotherapeutics. A large amount of P-gp inhibitors were designed to inhibit the multidrug resistance (MDR) feature of P-gp. However, no sufficient researches were reported to explore the correlation between binding capacity and drug property by experiment. Without particular drug property found to inhibit the MDR feature of P-gp, the orientation of drug design is indefinite. In this work, 10 representative cancer drugs with various properties are used to bind with P-gp by molecular dynamics simulation. Binding free energy between P-gp and 10 drugs ranges -139 to -253 kJ/mol. It reveals that the promiscuity nature of P-gp is in light of the similar binding free energy in separate P-gp-ligand binding systems. The binding effect of P-gp and drugs correlates well with the size of drugs and has no apparent correlation with the polarity of each drug. The key reason is that van der Waal's interaction occupies most of the total binding free energy, and it is led by the number of atoms in the drugs. Two transmembrane segments (TM6 and TM12) and three types of amino acids (PHE, MET, and GLN) are vital in binding drugs with van der Waal's energy, which evident the influence between binding stability and size of drugs. This work provides the cause and theoretical basis for the promiscuity nature of P-gp.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bo Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Junqiao Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Lijun Liang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Yingchun Liu
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| |
Collapse
|
34
|
Palomino‐Hernandez O, Margreiter MA, Rossetti G. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Isr J Chem 2020. [DOI: 10.1002/ijch.202000021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Oscar Palomino‐Hernandez
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
- Computation-based Science and Technology Research CenterThe Cyprus Institute Nicosia 2121 Cyprus
- Institute of Life ScienceThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Michael A. Margreiter
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Jülich Supercomputing Centre (JSC)Forschungszentrum Jülich 52425 Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital AachenRWTH Aachen University Pauwelsstraße 30 52074 Aachen Germany
| |
Collapse
|
35
|
Meng W, Timsina R, Bull A, Andresen K, Qiu X. Additive Modulation of DNA-DNA Interactions by Interstitial Ions. Biophys J 2020; 118:3019-3025. [PMID: 32470322 DOI: 10.1016/j.bpj.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/04/2020] [Accepted: 04/28/2020] [Indexed: 11/26/2022] Open
Abstract
Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that DNA-DNA forces are observed to linearly depend on the partition of interstitial ions, suggesting the dominant role of ion-DNA coupling. Further implications are discussed in light of physical theories of electrostatic interactions and like-charge attraction.
Collapse
Affiliation(s)
- Wei Meng
- Key Lab of Biofabrication of Anhui Higher Education Institution Centre for Advanced Biofabrication, Hefei University, Hefei, Anhui, China; Department of Physics, George Washington University, Washington, District of Columbia
| | - Raju Timsina
- Department of Physics, George Washington University, Washington, District of Columbia
| | - Abby Bull
- Department of Physics, Gettysburg College, Gettysburg, Pennsylvania
| | - Kurt Andresen
- Department of Physics, Gettysburg College, Gettysburg, Pennsylvania.
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, District of Columbia.
| |
Collapse
|
36
|
Joy S, Periyasamy G. Influence of explicit water molecules on the charge migration dynamics of peptidomimetics: a DFT study. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02609-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
Duan G, Ji C, Zhang JZH. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv 2020; 10:15530-15540. [PMID: 35495446 PMCID: PMC9052371 DOI: 10.1039/d0ra01483d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).
Collapse
Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of Chemistry, New York University NY NY 10003 USA
- Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
| |
Collapse
|
38
|
Taylor Z, Marucho M. The Self-Adaptation Ability of Zinc Oxide Nanoparticles Enables Reliable Cancer Treatments. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E269. [PMID: 32033506 PMCID: PMC7075113 DOI: 10.3390/nano10020269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 11/26/2022]
Abstract
Optimal procedures for reliable anti-cancer treatments involve the systematic delivery of zinc oxide nanoparticles, which spread through the circulatory system. The success of these procedures may largely depend on the NPs' ability of self-adapting their physicochemical properties to overcome the different challenges facing at each stage on its way to the interior of a cancerous cell. In this article, we combine a multiscale approach, a unique nanoparticle model, and available experimental data to characterize the behavior of zinc oxide nanoparticles under different vessels rheology, pH levels, and biological environments. We investigate their ability to prevent aggregation, allow prolonged circulation time in the bloodstream, avoid clearance, conduct themselves through the capillarity system to reach damaged tissues, and selectively approach to target cancerous cells. Our results show that non-functionalized spherical zinc oxide nanoparticles with surface density N = 5.89 × 10-6 mol/m2, protonation and deprotonation rates pKa = 10.9 and pKb = -5.5, and NP size in the range of 20-50 nm are the most effective, smart anti-cancer agents for biomedical treatments.
Collapse
Affiliation(s)
- Zane Taylor
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA;
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| |
Collapse
|
39
|
Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. J Chem Theory Comput 2019; 15:6422-6432. [PMID: 31553600 PMCID: PMC6889957 DOI: 10.1021/acs.jctc.9b00519] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.
Collapse
Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
40
|
Jain V, Wilson WN, Rai N. Solvation effect on binding modes of model lignin dimer compounds on MWW 2D-zeolite. J Chem Phys 2019; 151:114708. [DOI: 10.1063/1.5112101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Varsha Jain
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Woodrow N. Wilson
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Neeraj Rai
- Dave C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| |
Collapse
|
41
|
Duan G, Ji C, Zhang JZH. A force consistent method for electrostatic energy calculation in fluctuating charge model. J Chem Phys 2019; 151:094105. [PMID: 31492061 DOI: 10.1063/1.5118224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A practical approach to include the polarization effect in a molecular force field is the fluctuating charge method in which atomic charges vary as the configuration of the molecular system changes. However, the use of the Coulomb formula to evaluate energy in a fluctuating charge method is theoretically inconsistent with the forces given by the fluctuating method. In this work, we propose a force-consistent method to correctly calculate electrostatic energies of molecular systems using a fluctuating charge model (Effective Polarizable Bond or EPB). In this protocol, the electrostatic energy is obtained by numerical interaction of the atomic forces along the MD trajectory, rather than using the default Coulomb formula in the EPB model. Test study on the benchmark Barnase-Barstar protein-protein interaction system demonstrates that although the total electrostatic energy of the system shows little deviation due to the averaging effect, specific residue-residue electrostatic interaction energy is affected and the level of the effect depends on the charges of the interacting residues with charged residues showing pronounced differences in calculated energies between using the current protocol and the standard Coulomb formula. It is recommended that the proposed numerical interaction method should be preferred in the calculation of electrostatic energy in fluctuating charge models used in molecular dynamics simulations.
Collapse
Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| |
Collapse
|
42
|
Pandey P, Aytenfisu AH, MacKerell AD, Mallajosyula SS. Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives. J Chem Theory Comput 2019; 15:4982-5000. [PMID: 31411469 PMCID: PMC6852669 DOI: 10.1021/acs.jctc.9b00327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.
Collapse
Affiliation(s)
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | | |
Collapse
|
43
|
Marucho M. A Java Application to Characterize Biomolecules and Nanomaterials in Electrolyte Aqueous Solutions. COMPUTER PHYSICS COMMUNICATIONS 2019; 242:104-119. [PMID: 31827306 PMCID: PMC6905646 DOI: 10.1016/j.cpc.2019.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The electrostatic, entropic and surface interactions between a macroion (nanoparticle or biomolecule), surrounding ions and water molecules play a fundamental role in the behavior and function of colloidal systems. However, the molecular mechanisms governing these phenomena are still poorly understood. One of the major limitations in procuring this understanding is the lack of appropriate computational tools. Additionally, only experts in the field with an extensive background in programming, who are trained in statistical mechanics, and have access to supercomputers are able to study these systems. To overcome these limitations, in this article, we present a free, multiplatform, portable Java software, which provides experts and non-experts in the field an easy and efficient way to obtain an accurate molecular characterization of electrical and structural properties of aqueous electrolyte mixture solutions around both cylindrical- and spherical-like rigid macroions under multiple conditions. These properties include the normalized ions and water density profile distributions, the mean electrostatic potential, the integrated charge, the zeta potential, the electrostatic potential energy, the particle crowding entropy energy, the ion-ion electrostatic direct correlation energy, and the ionic potential of mean force. The Java software does not require outstanding skills and comes with detailed user-guide documentation. The application is based on the so-called Classical Density Functional Theory Solver (CSDFTS), which was successfully applied to a variety of rod-like biopolymers, rigid-like globular proteins, nanoparticles, and nano-rods. CSDFTS implements several electrolyte and macroion models, uses different levels of approximation and takes advantage of high performance Fortran90 routines and optimized libraries. These features enable the software to run on single processor computers at low-to-moderate computational cost depending on the computer performance, the grid resolution, and the characterization of the macroion and the electrolyte solution, among other factors. As a unique feature, the software comes with a graphical user interface (GUI) that allows users to take advantage of the visually guided setup of the required input data to properly characterize the system and configure the solver. Several examples on nanomaterials and biomolecules are provided to illustrate the use of the GUI and the solver performance.
Collapse
Affiliation(s)
- Marcelo Marucho
- , website: https://www.utsa.edu/physics/faculty/MarceloMarucho.html
| |
Collapse
|
44
|
Tollefson MR, Litman JM, Qi G, O'Connell CE, Wipfler MJ, Marini RJ, Bernabe HV, Tollefson WTA, Braun TA, Casavant TL, Smith RJH, Schnieders MJ. Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophys J 2019; 117:602-612. [PMID: 31327459 DOI: 10.1016/j.bpj.2019.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Hearing loss is associated with ∼8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants. The majority of these variants are classified as "variants of uncertain significance" to reflect our inability to ascribe a phenotypic effect to the observed amino acid change. A promising source of pathogenicity information is biophysical simulation, although input protein structures often contain defects because of limitations in experimental data and/or only distant homology to a template. Here, we combine the polarizable atomic multipole optimized energetics for biomolecular applications force field, many-body optimization theory, and graphical processing unit acceleration to repack all deafness-associated proteins and thereby improve average structure MolProbity score from 2.2 to 1.0. We then used these optimized wild-type models to create over 60,000 structures for missense variants in the Deafness Variation Database, which are being incorporated into the Deafness Variation Database to inform deafness pathogenicity prediction. Finally, this work demonstrates that advanced polarizable atomic multipole force fields are efficient enough to repack the entire human proteome.
Collapse
Affiliation(s)
- Mallory R Tollefson
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Jacob M Litman
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Claire E O'Connell
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Matthew J Wipfler
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J Marini
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Hernan V Bernabe
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | | | - Terry A Braun
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Thomas L Casavant
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Richard J H Smith
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa.
| | - Michael J Schnieders
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Department of Biochemistry, University of Iowa, Iowa City, Iowa.
| |
Collapse
|
45
|
Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. Sci Rep 2019; 9:10477. [PMID: 31324834 PMCID: PMC6642143 DOI: 10.1038/s41598-019-46636-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.
Collapse
|
46
|
Lei H, Li J, Gao P, Stinis P, Baker NA. A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING 2019; 350:199-227. [PMID: 32038051 PMCID: PMC7007047 DOI: 10.1016/j.cma.2019.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The challenge of quantifying uncertainty propagation in real-world systems is rooted in the high-dimensionality of the stochastic input and the frequent lack of explicit knowledge of its probability distribution. Traditional approaches show limitations for such problems, especially when the size of the training data is limited. To address these difficulties, we have developed a general framework of constructing surrogate models on spaces of stochastic input with arbitrary probability measure irrespective of the mutual dependencies between individual components of the random inputs and the analytical form. The present Data-driven Sparsity-enhancing Rotation for Arbitrary Randomness (DSRAR) framework includes a data-driven construction of multivariate polynomial basis for arbitrary mutually dependent probability measures and a sparsity enhancement rotation procedure. This sparsity-enhancing rotation method was initially proposed in our previous work [1] for Gaussian density distributions, which may not be feasible for non-Gaussian distributions due to the loss of orthogonality after the rotation. To remedy such difficulties, we developed a new data-driven approach to construct orthonormal polynomials for arbitrary mutually dependent randomness, ensuring the constructed basis maintains the orthogonality/near-orthogonality with respect to the density of the rotated random vector, where directly applying the regular polynomial chaos including arbitrary polynomial chaos (aPC) [2] shows limitations due to the assumption of the mutual independence between the components of the random inputs. The developed DSRAR framework leads to accurate recovery, with only limited training data, of a sparse representation of the target functions. The effectiveness of our method is demonstrated in challenging problems such as partial differential equations and realistic molecular systems within high-dimensional (O(10)) conformational spaces where the underlying density is implicitly represented by a large collection of sample data, as well as systems with explicitly given non-Gaussian probabilistic measures.
Collapse
Affiliation(s)
- Huan Lei
- Pacific Northwest National Laboratory, Richland, WA
99352
| | - Jing Li
- Pacific Northwest National Laboratory, Richland, WA
99352
| | - Peiyuan Gao
- Pacific Northwest National Laboratory, Richland, WA
99352
| | - Panagiotis Stinis
- Pacific Northwest National Laboratory, Richland, WA
99352
- Department of Applied Mathematics, University of
Washington, Seattle, WA 98195
| | - Nathan A. Baker
- Pacific Northwest National Laboratory, Richland, WA
99352
- Division of Applied Mathematics, Brown University,
Providence, RI 02912
| |
Collapse
|
47
|
Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
Collapse
Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Sara Y Cheng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| |
Collapse
|
48
|
Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
49
|
Choi JM, Pappu RV. Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics. J Chem Theory Comput 2019; 15:1367-1382. [PMID: 30633502 PMCID: PMC10749164 DOI: 10.1021/acs.jctc.8b00573] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of examples to highlight the preservation of accuracies as well as examples that demonstrate the improvements. Our efforts show how the recent experimentally derived and computationally optimized coil-library landscapes can be used as a touchstone for quantifying errors and making improvements to molecular mechanics force fields.
Collapse
Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
| |
Collapse
|
50
|
Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| |
Collapse
|