1
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Kolocouris A, Arkin I, Glykos NM. A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent. Phys Chem Chem Phys 2022; 24:25391-25402. [PMID: 36239696 DOI: 10.1039/d2cp02881f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here, we have carried out a proof-of-concept molecular dynamics (MD) simulation with adaptive tempering in a membrane mimetic environment to study the folding of single-pass membrane peptides. We tested the influenza A M2 viroporin, influenza B M2 viroporin, and protein E from coronaviruses MERS-Cov-2 and SARS-CoV-2 peptides with known experimental secondary structures in membrane bilayers. The two influenza-derived peptides are significantly different in the peptide sequence and secondary structure and more polar than the two coronavirus-derived peptides. Through a total of more than 50 μs of simulation time that could be accomplished in trifluoroethanol (TFE), as a membrane model, we characterized comparatively the folding behavior, helical stability, and helical propensity of these transmembrane peptides that match perfectly their experimental secondary structures, and we identified common motifs that reflect their quaternary organization and known (or not) biochemical function. We showed that BM2 is organized into two structurally distinct parts: a significantly more stable N-terminal half, and a fast-converting C-terminal half that continuously folds and unfolds between α-helical structures and non-canonical structures, which are mostly turns. In AM2, both the N-terminal half and C-terminal half are very flexible. In contrast, the two coronavirus-derived transmembrane peptides are much more stable and fast helix-formers when compared with the influenza ones. In particular, the SARS-derived peptide E appears to be the fastest and most stable helix-former of all the four viral peptides studied, with a helical structure that persists almost without disruption for the whole of its 10 μs simulation. By comparing the results with experimental observations, we benchmarked TFE in studying the conformation of membrane and hydrophobic peptides. This work provided accurate results suggesting a methodology to run long MD simulations and predict structural properties of biologically important membrane peptides.
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Affiliation(s)
- Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Greece.
| | - Isaiah Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, 91904, Israel
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
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2
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Moharana TR, Nagaraj R. In silico folding of hydrophobic peptides that form β-hairpin structures in solution. J Pept Sci 2022; 28:e3427. [PMID: 35595709 DOI: 10.1002/psc.3427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Peptides designed with residues that have a high propensity to occur in β-turns form β-hairpin structures in apolar as well as in polar organic solvents such as dimethyl sulfoxide (DMSO). Due to limited solubility, their conformations have not been investigated experimentally in water. We have examined the conformations of four of such designed peptides that fold into well-defined β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by molecular dynamics simulations (MDS). The peptides folded into β-hairpin structures in water, starting from the fully extended conformation. However, in DMSO, neither folding nor unfolding was observed during MDS, when the starting structures were unfolded and folded, respectively. The lack of folding in DMSO was investigated by constructing folding free energy landscapes by umbrella sampling. The folding free energy landscape is smooth in water while in DMSO folded and unfolded structures are separated by high-energy barriers. The folding free energy is less in DMSO compared to water due to a more stable unfolded structure in DMSO compared to water, which in turn is due to stabilization of the unfolded state by hydrophobic interactions in DMSO. This finding will be helpful to researchers to accurately model and/or design small peptide structures in water and organic solvents.
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3
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Cui H, Vedder M, Schwaneberg U, Davari MD. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents. Methods Mol Biol 2022; 2397:179-202. [PMID: 34813065 DOI: 10.1007/978-1-0716-1826-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.
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Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Markus Vedder
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
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4
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Sadhukhan D, Hsu PJ, Kuo JL, Patwari GN. Is Dissociation of HCl in DMSO Clusters Bistable? J Phys Chem A 2021; 125:10351-10358. [PMID: 34821498 DOI: 10.1021/acs.jpca.1c08627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dissociation of HCl embedded in dimethyl sulfoxide (DMSO) clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. A large number of distinct structures (about 1500) consisting of up to five DMSO molecules were considered in the present work for statistical reliability. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm-1 along the H-Cl bond. However, a large number of exceptions wherein the electric field values much higher than the critical electric field of 138 MV cm-1 did not result in dissociation of HCl were observed, in addition to several cases wherein the HCl dissociates with an electric field less than the critical electric field. On the other hand, the MP2 level calculations reveal that the critical electric field for HCl dissociation is about 181 MV cm-1 with almost no exceptions. A comparison of calculations carried out using the MP2 and the B3LYP-D3 levels suggests that the dissociation of HCl embedded in DMSO clusters is bistable at the B3LYP-D3 level, which is an artifact, suggesting that care must be exercised in interpreting the processes of proton transfer. The answer to the question raised as the title of this paper is NO.
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Affiliation(s)
- Debopriya Sadhukhan
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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5
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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6
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Tsoras AN, Wong KM, Paravastu AK, Champion JA. Rational Design of Antigen Incorporation Into Subunit Vaccine Biomaterials Can Enhance Antigen-Specific Immune Responses. Front Immunol 2020; 11:1547. [PMID: 32849524 PMCID: PMC7396695 DOI: 10.3389/fimmu.2020.01547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/11/2020] [Indexed: 12/29/2022] Open
Abstract
Peptide subunit vaccines increase safety by reducing the risk of off-target responses and improving the specificity of the induced adaptive immune response. The immunogenicity of most soluble peptides, however, is often insufficient to produce robust and lasting immunity. Many biomaterials and delivery vehicles have been developed for peptide antigens to improve immune response while maintaining specificity. Peptide nanoclusters (PNC) are a subunit peptide vaccine material that has shown potential to increase immunogenicity of peptide antigens. PNC are comprised only of crosslinked peptide antigen and have been synthesized from several peptide antigens as small as 8 amino acids in length. However, as with many peptide vaccine biomaterials, synthesis requires adding residues to the peptide and/or engaging amino acids within the antigen epitope covalently to form a stable material. The impact of antigen modifications made to enable biomaterial incorporation or formation is rarely investigated, since the goal of most studies is to compare the soluble antigen with biomaterial form of antigen. This study investigates PNC as a platform vaccine biomaterial to evaluate how peptide modification and biomaterial formation with different crosslinking chemistries affect epitope-specific immune cell presentation and activation. Several types of PNC were synthesized by desolvation from the model peptide epitope SIINFEKL, which is derived from the immunogenic protein ovalbumin. SIINFEKL was altered to include extra residues on each end, strategically chosen to enable multiple conjugation chemistry options for incorporation into PNC. Several crosslinking methods were used to control which functional groups were used to stabilize the PNC, as well as the reducibility of the crosslinking. These variations were evaluated for immune responses and biodistribution following in vivo immunization. All modified antigen formulations still induced comparable immune responses when incorporated into PNC compared to unmodified soluble antigen alone. However, some crosslinking methods led to a significant increase in desirable immune responses while others did not, suggesting that not all PNC were processed the same. These results help guide future peptide vaccine biomaterial design, including PNC and a wide variety of conjugated and self-assembled peptide antigen materials, to maximize and tune the desired immune response.
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Affiliation(s)
| | | | | | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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7
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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8
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Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W. β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 2018; 122:11895-11905. [DOI: 10.1021/acs.jpcb.8b08308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sylwia Berbeć
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | | | - Agnieszka Hernik-Magoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | - Grzegorz Ścibisz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
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9
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Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. Cell Surf 2018; 2:54-66. [PMID: 30046666 PMCID: PMC6053601 DOI: 10.1016/j.tcsw.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.
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Affiliation(s)
- Avinash S. Punekar
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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10
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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11
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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12
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Takis PG, Papavasileiou KD, Peristeras LD, Boulougouris GC, Melissas VS, Troganis AN. Unscrambling micro-solvation of –COOH and –NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies. Phys Chem Chem Phys 2017; 19:13710-13722. [DOI: 10.1039/c7cp01592e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigates the interactions of –COOH and –NH groups in neat DMSO solutions, with special focus on their thermodynamics and kinetics.
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Affiliation(s)
- Panteleimon G. Takis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
| | - Konstantinos D. Papavasileiou
- National Center for Scientific Research “Demokritos”
- Institute of Nanoscience and Nanotechnology
- Molecular Thermodynamics and Modelling of Materials Laboratory (MTMML)
- GR-153 10 Aghia Paraskevi Attikis
- Greece
| | - Loukas D. Peristeras
- National Center for Scientific Research “Demokritos”
- Institute of Nanoscience and Nanotechnology
- Molecular Thermodynamics and Modelling of Materials Laboratory (MTMML)
- GR-153 10 Aghia Paraskevi Attikis
- Greece
| | - Georgios C. Boulougouris
- Department of Molecular Biology and Genetics
- Democritus University of Thrace
- GR-681 00 Alexandroupolis
- Greece
| | | | - Anastassios N. Troganis
- Department of Biological Applications and Technology
- University of Ioannina
- GR-451 10 Ioannina
- Greece
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13
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Salvi AM, Moscarelli P, Bochicchio B, Lanza G, Castle JE. Combined effects of solvation and aggregation propensity on the final supramolecular structures adopted by hydrophobic, glycine-rich, elastin-like polypeptides. Biopolymers 2016; 99:292-313. [PMID: 23426573 DOI: 10.1002/bip.22160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 08/11/2012] [Accepted: 09/14/2012] [Indexed: 01/25/2023]
Abstract
Previous work on elastin-like polypeptides (ELPs) made of hydrophobic amino acids of the type XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) has consistently shown that differing dominant supramolecular structures were formed when the suspending media were varied: helical, amyloid-like fibers when suspended in water and globules evolving into "string of bead" structures, poly(ValGlyGlyValGly), or cigar-like bundles, poly(ValGlyGlyLeuGly), when suspended in methyl alcohol. Comparative experiments with poly(LeuGlyGlyValGly) have further indicated that the interface energy plays a significant role and that solvation effects act in concomitance with the intrinsic aggregation propensity of the repeat sequence. Continuing our investigation on ELPs using surface (X-ray photoelectron spectroscopy, atomic force microscopy) and bulk (circular dichroism, Fourier transform infrared spectroscopy) techniques for their characterization, here we have compared the effect of suspending solvents (H(2)O, dimethylsulfoxide, ethylene glycol, and MeOH) on poly(ValGlyGlyValGly), the polypeptide most inclined to form long and well-refined helical fibers in water, searching for the signature of intermolecular interactions occurring between the polypeptide chains in the given suspension. The influence of sequence specificities has been studied by comparing poly(ValGlyGlyValGly) and poly(LeuGlyGlyValGly) with a similar degree of polymerization. Deposits on substrates of the polypeptides were characterized taking into account the differing evaporation rate of solvents, and tests on their stability in ultra high vacuum were performed. Finally, combining experimental and computational studies, we have revaluated the three-dimensional modeling previously proposed for the supramolecular assembly in water of poly(ValGlyGlyValGly). The results were discussed and rationalized also in the light of published data.
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Affiliation(s)
- Anna M Salvi
- Dipartimento di Chimica 'Antonio Mario Tamburro,' Università della Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy.
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14
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Richard T, Papastamoulis Y, Waffo-Teguo P, Monti JP. 3D NMR structure of a complex between the amyloid beta peptide (1–40) and the polyphenol ε-viniferin glucoside: Implications in Alzheimer's disease. Biochim Biophys Acta Gen Subj 2013; 1830:5068-74. [DOI: 10.1016/j.bbagen.2013.06.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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15
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Mirtič A, Grdadolnik J. The structure of poly-l-lysine in different solvents. Biophys Chem 2013; 175-176:47-53. [DOI: 10.1016/j.bpc.2013.02.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
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16
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Kamerzell TJ, Pace AL, Li M, Danilenko DM, Mcdowell M, Gokarn YR, John Wang Y. Polar Solvents Decrease the Viscosity of High Concentration IgG1 Solutions Through Hydrophobic Solvation and Interaction: Formulation and Biocompatibility Considerations. J Pharm Sci 2013; 102:1182-93. [DOI: 10.1002/jps.23453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/23/2012] [Accepted: 01/03/2013] [Indexed: 02/06/2023]
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17
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Shukla RT, Sasidhar YU. Energetics of β-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: an MD simulation study. Phys Chem Chem Phys 2013; 15:18571-83. [DOI: 10.1039/c3cp52166d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dzwolak W, Kalinowski J, Johannessen C, Babenko V, Zhang G, Keiderling TA. On the DMSO-Dissolved State of Insulin: A Vibrational Spectroscopic Study of Structural Disorder. J Phys Chem B 2012; 116:11863-71. [DOI: 10.1021/jp3062674] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wojciech Dzwolak
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093
Warsaw, Poland
| | - Jarosław Kalinowski
- Institute of High
Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw, Poland
| | - Christian Johannessen
- Manchester Interdisciplinary
Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Viktoria Babenko
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093
Warsaw, Poland
| | - Ge Zhang
- Department of Chemistry, University of Illinois at Chicago, 845
West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, United
States
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845
West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, United
States
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Kaur H, Sasidhar YU. For the Sequence YKGQ, the Turn and Extended Conformational Forms Are Separated by Small Barriers and the Turn Propensity Persists Even at High Temperatures: Implications for Protein Folding. J Phys Chem B 2012; 116:3850-60. [DOI: 10.1021/jp210227s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Yellamraju U. Sasidhar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Srivastava KR, Kumar A, Goyal B, Durani S. Stereochemistry and Solvent Role in Protein Folding: Nuclear Magnetic Resonance and Molecular Dynamics Studies of Poly-l and Alternating-l,d Homopolypeptides in Dimethyl Sulfoxide. J Phys Chem B 2011; 115:6700-8. [DOI: 10.1021/jp200743w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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Zhang R, Wu WJ. Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/05/504-508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Bordag N, Keller S. α-Helical transmembrane peptides: A “Divide and Conquer” approach to membrane proteins. Chem Phys Lipids 2010; 163:1-26. [PMID: 19682979 DOI: 10.1016/j.chemphyslip.2009.07.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022]
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Duarte AMS, de Jong ER, Koehorst RBM, Hemminga MA. Conformational studies of peptides representing a segment of TM7 from H+-VO-ATPase in SDS micelles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:639-46. [PMID: 19669749 PMCID: PMC2841257 DOI: 10.1007/s00249-009-0522-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/09/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, positively charged arginine residue located in the center of both peptides has a destabilizing effect on the helical conformation of the SDS-solubilized peptides, leading to beta-sheet formation and subsequent aggregation.
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Affiliation(s)
- Afonso M. S. Duarte
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
- Present Address: Cellular Protein Chemistry Laboratory, Utrecht University, Utrecht, The Netherlands
| | - Edwin R. de Jong
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Rob B. M. Koehorst
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Marcus A. Hemminga
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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Teixeira PCN, de Souza CAM, de Freitas MS, Foguel D, Caffarena ER, Alves LA. Predictions suggesting a participation of beta-sheet configuration in the M2 domain of the P2X(7) receptor: a novel conformation? Biophys J 2009; 96:951-63. [PMID: 19186133 DOI: 10.1016/j.bpj.2008.10.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 10/15/2008] [Indexed: 11/18/2022] Open
Abstract
Scanning experiments have shown that the putative TM2 domain of the P2X(7) receptor (P2X(7)R) lines the ionic pore. However, none has identified an alpha-helix structure, the paradigmatic secondary structure of ion channels in mammalian cells. In addition, some researchers have suggested a beta-sheet conformation in the TM2 domain of P2X(2). These data led us to investigate a new architecture within the P2X receptor family. P2X(7)R is considered an intriguing receptor because its activation induces nonselective large pore formation, in contrast to the majority of other ionic channel proteins in mammals. This receptor has two states: a low-conductance channel (approximately 10 pS) and a large pore (> 400 pS). To our knowledge, one fundamental question remains unanswered: Are the P2X(7)R channel and the pore itself the same entity or are they different structures? There are no structural data to help solve this question. Thus, we investigated the hydrophobic M2 domain with the aim of predicting the fitted position and the secondary structure of the TM2 segment from human P2X(7)R (hP2X(7)R). We provide evidence for a beta-sheet conformation, using bioinformatics algorithms and molecular-dynamics simulation in conjunction with circular dichroism in different environments and Fourier transform infrared spectroscopy. In summary, our study suggests the possibility that a segment composed of residues from part of the M2 domain and part of the putative TM2 segment of P2X(7)R is partially folded in a beta-sheet conformation, and may play an important role in channel/pore formation associated with P2X(7)R activation. It is important to note that most nonselective large pores have a transmembrane beta-sheet conformation. Thus, this study may lead to a paradigmatic change in the P2X(7)R field and/or raise new questions about this issue.
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