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Dabhade A, Chaudhury S. Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions. Chem Asian J 2021; 16:3354-3362. [PMID: 34410041 DOI: 10.1002/asia.202100905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 11/06/2022]
Abstract
Coarse-grained molecular dynamics simulations are performed to understand the behavior of diblock polyelectrolytes in solutions of divalent salt by studying the conformations of chains over a wide range of salt concentrations. The polymer molecules are modeled as bead spring chains with different charged fractions and the counterions and salt ions are incorporated explicitly. Upon addition of a divalent salt, the salt cations replace the monovalent counterions, and the condensation of divalent salt cations onto the polyelectrolyte increases, and the chains favor to collapse. The condensation of ions changes with the salt concentration and depends on the charged fraction. Also, the degree of collapse at a given salt concentration changes with the increasing valency of the counterion due to the bridging effect. As a quantitative measure of the distribution of counterions around the polyelectrolyte chain, we study the radial distribution function between monomers on different polyelectrolytes and the counterions inside the counterion worm surrounding a polymer chain at different concentrations of the divalent salt. Our simulation results show a strong dependence of salt concentration on the conformational properties of diblock copolymers and indicate that it can tune the self-assembly behaviors of such charged polyelectrolyte block copolymers.
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Affiliation(s)
- Akash Dabhade
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
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Samanta M, Chaudhury S. Coarse-grained molecular dynamics simulations study of the conformational properties of single polyelectrolyte diblock copolymers. Biophys Chem 2020; 266:106437. [PMID: 32771806 DOI: 10.1016/j.bpc.2020.106437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
We use coarse-grained molecular dynamics simulations to study a single di block polyelectrolyte chain in solution. We analyze the conformational properties of the chain and localization of counterions as a function of the charge fraction, backbone stiffness, Bjerrum length, and counterion valence. The interplay between the excluded-volume effects and the electrostatic interactions among charged residues leads to variation in block-polyelectrolyte architecture. Our computational findings indicate that varying such system properties lead to nontrivial effects and can be a powerful mechanism to tune the conformational properties of block polyelectrolytes.
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Affiliation(s)
- Mrityunjay Samanta
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India.
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Campeggio J, Bortoli M, Orian L, Zerbetto M, Polimeno A. Multiscale modeling of reaction rates: application to archetypal S N2 nucleophilic substitutions. Phys Chem Chem Phys 2020; 22:3455-3465. [PMID: 31984980 DOI: 10.1039/c9cp03841h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers' theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al., J. Comput. Chem. 2019, 40, 679-705]. This, in turn, allows to keep into account barrier recrossing, i.e. the transmission coefficient that is employed in correcting transition state theory evaluations. To test the capabilities and the flaws of the approach we use as case studies two archetypal SN2 reactions. First, we consider to the standard substitution of chloride ion to bromomethane. The rate constant at 295.15 K is evaluated to k/c⊖ = 2.7 × 10-6 s-1 (with c⊖ = 1 M), which compares well to the experimental value of 3.3 × 10-6 s-1 [R. H. Bathgate and E. A. Melwyn-Hughes, J. Chem. Soc 1959, 2642-2648]. Then, the method is applied to the SN2 reaction of methylthiolate to dimethyl disulfide in water. In biology, such an interconversion of thiols and disulfides is an important metabolic topic still not entirely rationalized. The predicted rate constant is k/c⊖ = 7.7 × 103 s-1. No experimental data is available for such a reaction, but it is in accord with the fact that the alkyl thiolates to dialkyl disulfides substitutions in water have been found to be fast reactions [S. M. Bachrach, J. M. Hayes, T. Dao and J. L. Mynar, Theor. Chem. Acc. 2002, 107, 266-271].
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Affiliation(s)
- Jonathan Campeggio
- Dipartimento di Sicenze Chimiche, Universià degli Studi di Padova, Via Marzolo 1, Padova, Italy.
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Wang F, Orioli S, Ianeselli A, Spagnolli G, A Beccara S, Gershenson A, Faccioli P, Wintrode PL. All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding. Biophys J 2019; 114:2083-2094. [PMID: 29742402 DOI: 10.1016/j.bpj.2018.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022] Open
Abstract
Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α1-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α1-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.
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Affiliation(s)
- Fang Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Simone Orioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Alan Ianeselli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Giovanni Spagnolli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Silvio A Beccara
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts.
| | - Pietro Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland.
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Röder K, Wales DJ. Predicting Pathways between Distant Configurations for Biomolecules. J Chem Theory Comput 2018; 14:4271-4278. [DOI: 10.1021/acs.jctc.8b00370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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Ianeselli A, Orioli S, Spagnolli G, Faccioli P, Cupellini L, Jurinovich S, Mennucci B. Atomic Detail of Protein Folding Revealed by an Ab Initio Reappraisal of Circular Dichroism. J Am Chem Soc 2018; 140:3674-3682. [DOI: 10.1021/jacs.7b12399] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alan Ianeselli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Simone Orioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Giovanni Spagnolli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Pietro Faccioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University, Fatehgarh; Sahib-140406, Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Life Sciences Institute; University of Michigan; Ann Arbor, MI USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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