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Kumar A, Kumar A, Kumar P, Garg N, Giri R. SARS-CoV-2 NSP1 C-terminal (residues 131-180) is an intrinsically disordered region in isolation. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2021; 2:100007. [PMID: 34189489 PMCID: PMC8020630 DOI: 10.1016/j.crviro.2021.100007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023]
Abstract
The NSP1- C terminal structure in complex with ribosome using cryo-EM is available now, and the N-terminal region structure in isolation is also deciphered in literature. However, as a reductionist approach, the conformation of NSP1- C terminal region (NSP1-CTR; amino acids 131-180) has not been studied in isolation. We found that NSP1-CTR conformation is disordered in an aqueous solution. Further, we examined the conformational propensity towards alpha-helical structure using trifluoroethanol, we observed induction of helical structure conformation using CD spectroscopy. Additionally, in SDS, NSP1-CTR shows a conformational change from disordered to ordered, possibly gaining alpha-helix in part. But in the presence of neutral lipid DOPC, a slight change in conformation is observed, which implies the possible role of hydrophobic interaction and electrostatic interaction on the conformational changes of NSP1. Fluorescence-based studies have shown a blue shift and fluorescence quenching in the presence of SDS, TFE, and lipid vesicles. In agreement with these results, fluorescence lifetime and fluorescence anisotropy decay suggest a change in conformational dynamics. The zeta potential studies further validated that the conformational dynamics are primarily because of hydrophobic interaction. These experimental studies were complemented through Molecular Dynamics (MD) simulations, which have shown a good correlation and testifies our experiments. We believe that the intrinsically disordered nature of the NSP1-CTR will have implications for enhanced molecular recognition feature properties of this IDR, which may add disorder to order transition and disorder-based binding promiscuity with its interacting proteins.
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Affiliation(s)
- Amit Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Ankur Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
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2
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Mandal T, Larson RG. Prediction of striped cylindrical micelles (SCMs) formed by dodecyl-β-d-maltoside (DDM) surfactants. SOFT MATTER 2018; 14:2694-2700. [PMID: 29565444 DOI: 10.1039/c8sm00274f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using fully atomistic and coarse-grained (CG) molecular dynamics (MD) simulations, we report, for the first time, the self-assembly of initially randomly dispersed dodecyl-β-d-maltoside (DDM) surfactants into a striped cylindrical micelle (SCM) with lamellae of surfactant heads and tails alternating along the cylindrical axis, with both heads and tails in contact with the water. By changing the interaction strength of the head group with water relative to itself, we find that such micelles are most likely for head groups with marginal solubility in the water solvent. Unlike the surfactants in a regular cylindrical micelle, whose tails are in the fluid micelle interior, the diffusion of DDM surfactants along the micelle body is blocked by the lamellar patterning. As a consequence, branches cannot slide along the micelle body and surfactant molecules cannot exchange between the micelle body and the branch, which should have a significant impact on the rheological properties of these micelles.
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Affiliation(s)
- Taraknath Mandal
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI-48109, USA.
| | - Ronald G Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI-48109, USA.
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Allen DT, Lorenz CD. A novel method for constructing continuous intrinsic surfaces of nanoparticles. J Mol Model 2017; 23:219. [PMID: 28674837 PMCID: PMC5495850 DOI: 10.1007/s00894-017-3378-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/22/2017] [Indexed: 12/28/2022]
Abstract
In recent years, the field of nanotechnology has become increasingly prevalent in the disciplines of science and engineering due to it’s abundance of application areas. Therefore, the ability to study and characterize these materials is more relevant than ever. Despite the wealth of simulation and modeling studies of nanoparticles reported in the literature, a rigorous description of the interface of such materials is rarely included in analyses which are pivotal to understanding interfacial behavior. We propose a novel method for constructing the continuous intrinsic surface of nanoparticles, which has been applied to a model system consisting of a sodium dodecyl sulfate micelle in the presence of testosterone propionate. We demonstrate the advantages of using our continuous intrinsic surface definition as a means to elucidate the true interfacial structure of the micelle, the interfacial properties of the hydrating water molecules, and the position of the drug (testosterone propionate) within the micelle. Additionally, we discuss the implications of this algorithm for future work in the simulation of nanoparticles.
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Affiliation(s)
- Daniel T Allen
- Theory & Simulation of Condensed Matter Group, Department of Physics, Strand Campus, King's College London, Strand, London, WC2R 2LS, UK
| | - Christian D Lorenz
- Theory & Simulation of Condensed Matter Group, Department of Physics, Strand Campus, King's College London, Strand, London, WC2R 2LS, UK.
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4
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Baldissera G, dos Santos Cabrera MP, Chahine J, Ruggiero JR. Role of Peptide–Peptide Interactions in Aggregation: Protonectins Observed in Equilibrium and Replica Exchange Molecular Dynamics Simulations. Biochemistry 2015; 54:2262-9. [DOI: 10.1021/bi501210e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gisele Baldissera
- Faculdade de Tecnologia de Catanduva, 15800-020 Catanduva, SP, Brazil
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5
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Interaction of cyclic and linear Labaditin peptides with anionic and zwitterionic micelles. J Colloid Interface Sci 2015; 438:39-46. [PMID: 25454423 DOI: 10.1016/j.jcis.2014.09.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 01/31/2023]
Abstract
Conformational changes of the cyclic (Lo) peptide Labaditin (VWTVWGTIAG) and its linear analogue (L1) promoted by presence of anionic sodium dodecyl sulfate (SDS) and zwitterionic L-α-Lysophosphatidylcholine (LPC) micelles were investigated. Results from λ(max) blue-shift of tryptophan fluorescence emission combined with Stern-Volmer constants values and molecular dynamics (MD) simulations indicated that L1 interacts with SDS micelles to a higher extent than does Lo. Further, the MD simulation demonstrated that both Lo and L1 interact similarly with LPC micelles, being preferentially located at the micelle/water interface. The peptide-micelle interaction elicits conformational changes in the peptides. Lo undergoes limited modifications and presents unordered structure in both LPC and SDS micelles. On the other hand, L1 displays a random-coil structure in aqueous medium, pH 7.0, and it acquires a β-structure upon interaction with SDS and LPC, albeit with structural differences in each medium.
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6
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Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution. J Mol Model 2014; 20:2469. [DOI: 10.1007/s00894-014-2469-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
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Hong Z, Damodaran K, Asher SA. Sodium dodecyl sulfate monomers induce XAO peptide polyproline II to α-helix transition. J Phys Chem B 2014; 118:10565-75. [PMID: 25121643 PMCID: PMC4161145 DOI: 10.1021/jp504133m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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XAO peptide (Ac–X2A7O2–NH2; X: diaminobutyric
acid side chain, −CH2CH2NH3+; O: ornithine side chain,
−CH2CH2CH2NH3+) in aqueous solution shows a predominantly polyproline II
(PPII) conformation without any detectable α-helix-like conformations.
Here we demonstrate by using circular dichroism (CD), ultraviolet
resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy
that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce
formation of α-helix-like conformations. The stoichiometry and
the association constants of SDS and XAO were determined from the
XAO–SDS diffusion coefficients measured by pulsed field gradient
NMR. We developed a model for the formation of XAO–SDS aggregate
α-helix-like conformations. Using UVRR spectroscopy, we calculated
the Ramachandran ψ angle distributions of aggregated XAO peptides.
We resolved α-, π- and 310- helical conformations
and a turn conformation. XAO nucleates SDS aggregation at SDS concentrations
below the SDS critical micelle concentration. The XAO4–SDS16 aggregates have four SDS molecules bound to each XAO to
neutralize the four side chain cationic charges. We propose that the
SDS alkyl chains partition into a hydrophobic core to minimize the
hydrophobic area exposed to water. Neutralization of the flanking
XAO charges enables α-helix formation. Four XAO–SDS4 aggregates form a complex with an SDS alkyl chain-dominated
hydrophobic core and a more hydrophilic shell where one face of the
α-helix peptide contacts the water environment.
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Affiliation(s)
- Zhenmin Hong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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Kong X, Li Z, Lu D, Liu Z, Wu J. Multiscale simulation of surfactant–aquaporin complex formation and water permeability. RSC Adv 2014. [DOI: 10.1039/c4ra03759f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Molecular dynamics simulation reveals distinctive roles of electrostatic and hydrophobic interactions in surfactant (SDS)–protein (AqpZ) complex formation and functionality.
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Affiliation(s)
- Xian Kong
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
- Department of Chemical & Environmental Engineering
- University of California
| | - Zhixian Li
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Diannan Lu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Zheng Liu
- Department of Chemical Engineering
- Tsinghua University
- Beijing, China
| | - Jianzhong Wu
- Department of Chemical & Environmental Engineering
- University of California
- Riverside, USA
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Neale C, Ghanei H, Holyoake J, Bishop RE, Privé GG, Pomès R. Detergent-mediated protein aggregation. Chem Phys Lipids 2013; 169:72-84. [PMID: 23466535 PMCID: PMC5007131 DOI: 10.1016/j.chemphyslip.2013.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.
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Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Hamed Ghanei
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - John Holyoake
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Gilbert G. Privé
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Campbell Family Cancer Research Institute, UHN, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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