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Nanavare P, Choudhury AR, Sarkar S, Maity A, Chakrabarti R. Structure and Orientation of Water and Choline Chloride Molecules Around a Methane Hydrophobe: A Computer Simulation Study. Chemphyschem 2022; 23:e202200446. [DOI: 10.1002/cphc.202200446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/18/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Pooja Nanavare
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Asha Rani Choudhury
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Soham Sarkar
- TU Darmstadt: Technische Universitat Darmstadt Eduard-Zintl-Institute für Anorganische und Physikalische Chemie INDIA
| | - Atanu Maity
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Rajarshi Chakrabarti
- Indian Institute of Technology Bombay Chemistry Indian Institute of Technology BombayPowaiIndia 400076 Mumbai INDIA
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Paul S, Paul S. Molecular insights into the urea-choline- O-sulfate interactions in aqueous solution. Phys Chem Chem Phys 2021; 23:25317-25334. [PMID: 34747954 DOI: 10.1039/d1cp02821a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Urea and choline-O-sulfate (COS) are both osmolytes, but have opposite effects on protein structure. Urea has been well-known for years to destabilize protein structure. Though COS has been revealed as an osmoprotective molecule against urea induced denaturation of proteins, the mechanism of this compensation is still unexplored. This study focuses on a theoretical investigation of the interdependent behavior of urea and COS in a mixture, to explore how urea becomes a weaker denaturing agent in the presence of COS. In this study, we have considered every possible interaction among the solute (urea and COS) and solvent (water) both at room temperature and high temperature, employing two different force field parameters i.e., CHARMM General Force Field parameters (CGenFF) and General AMBER Force Field (GAFF) parameters through classical molecular dynamics simulation studies. Different techniques have been used to analyze the average interactions between COS and urea as well as their solvation properties, which show that in the presence of COS, urea becomes a less effective denaturant than when alone. The water-water interaction shows that the mixed osmolyte solution of urea and COS strengthens the water hydrogen bonding network. The enhanced solvation of urea and COS in the urea-COS mixture and their mutual interactions, results in the exclusion of free urea as well as COS from the solution. This synergistic behavior of urea and COS could be the major reason behind COS counteracting urea's denaturation of proteins.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Paul S, Paul S. Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:14496-14510. [PMID: 34184696 DOI: 10.1039/d1cp00825k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human calcitonin (hCT) is a 32-residue amino acid poly-peptide hormone which is secreted by the C-cells (also known as parafollicular cells) of thyroid glands. It acts to inhibit osteoclast cell hormones by reducing the cell function and regulating calcium and phosphate in blood. hCT has a high tendency to assemble into protofilaments with β-sheet conformations. Amyloid fibril formation of hCT reduces its bio-activity and limits its application as a therapeutic drug. Salmon calcitonin (sCT), which also carries the same disulfide bridge at the N and C-terminus, but differs at the 16 residue position from hCT, has less propensity to aggregate than hCT. Human calcitonin has much higher bio-activity than sCT if its aggregation propensity is reduced. Substituting the key residues which are responsible for the aggregation of hCT, is one of the ways to reduce its aggregation and fibril formation. hCT analogues with less aggregation tendency can be exploited as therapeutic drugs. In this work, we study the amyloidogenic behavior of hCT and its peptide based derivatives i.e., sCT, phCT, N17H hCT, Y12L hCT and DM hCT, through classical molecular dynamics (MD) simulations. Our study reveals that sCT is the least aggregation prone derivative, and the double mutation at position 12 and 17 can reduce the aggregation propensity of this peptide. Also, we have applied these mutant variants of hCT as peptide inhibitors in the self-aggregation of hCT. This study could help in understanding and preparing peptide-based inhibitors for hCT fibrillation and their applications as therapeutic drugs.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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Paul S, Kumari K, Paul S. Molecular Insight into the Effects of Enhanced Hydrophobicity on Amyloid-like Aggregation. J Phys Chem B 2020; 124:10048-10061. [PMID: 33115237 DOI: 10.1021/acs.jpcb.0c06000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Generally, hydrophobic amino acids provide hydrophobic interactions during peptide aggregation. However, besides the hydrophobic amino acids, some hydrophilic amino acids, such as glutamine, are also considered to be essential elements in many self-aggregating peptides. For example, huntingtin contains polyglutamine at its N-terminus and the yeast prion Sup35 protein has the GNNQQNY sequence, a peptide well-known for its ability for amyloid fibril formation. However, despite the frequent emergence of glutamine in self-assembling systems, the molecular mechanism of amyloid formation involving this unique amino acid has not been well documented. It is still not clear how this hydrophilic amino acid is responsible for the hydrophobic interaction in the self-association process. Therefore, in this study, we have carried out classical molecular dynamics simulations of the GNNQQNY peptide and its derivatives in pure water. We quantify the propensity for the formation of β-sheet conformation with an increasing glutamine number in the peptide sequence. In addition, we assess the importance of the hydrophobicity of the dimethanediyl group present in glutamine (as well as in glutamic acid) for the self-association of the peptides through nonpolar solvent medium simulations.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Komal Kumari
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Paul S, Paul S. In silico study of osmolytic effects of choline-O-sulfate on urea induced unfolding of Trp-cage mini-protein: An atomistic view from replica exchange molecular dynamics simulation. Arch Biochem Biophys 2020; 695:108484. [DOI: 10.1016/j.abb.2020.108484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022]
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The conformational stability of terminal helices of λ-repressor protein in aqueous dodine and choline-O-sulfate solutions. Int J Biol Macromol 2020; 154:1332-1346. [DOI: 10.1016/j.ijbiomac.2019.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022]
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Maity A, Sarkar S, Theeyancheri L, Chakrabarti R. Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions. Chemphyschem 2020; 21:552-567. [DOI: 10.1002/cphc.201901078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/22/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Atanu Maity
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Soham Sarkar
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Ligesh Theeyancheri
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Rajarshi Chakrabarti
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
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Paul S, Paul S. Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation. J Comput Chem 2019; 40:1957-1968. [PMID: 31062393 DOI: 10.1002/jcc.25851] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 11/06/2022]
Abstract
Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11-20 and 23-36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide-peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
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Masutani K, Yamamori Y, Kim K, Matubayasi N. Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. J Chem Phys 2019; 150:145101. [DOI: 10.1063/1.5088395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Keiichi Masutani
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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Paul S, Paul S. Inhibitory Effect of Choline-O-sulfate on Aβ16–22 Peptide Aggregation: A Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:3475-3489. [DOI: 10.1021/acs.jpcb.9b02727] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
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