1
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Hurwitz N, Zaidman D, Wolfson HJ. Pep–Whisperer: Inhibitory peptide design. Proteins 2022; 90:1886-1895. [DOI: 10.1002/prot.26384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Naama Hurwitz
- Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel
| | - Daniel Zaidman
- Department of Organic Chemistry Weizmann Institute of Science Rehovot Israel
| | - Haim J. Wolfson
- Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel
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2
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Sekar PC, Paul DM, Srinivasan E, Rajasekaran R. Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics-quantum and molecular mechanical approaches. J Mol Model 2021; 27:10. [PMID: 33392722 DOI: 10.1007/s00894-020-04652-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/16/2020] [Indexed: 01/09/2023]
Abstract
Ocellatin AMPs (antimicrobial peptides) are considered to be promising alternative therapeutics to conventional antibiotics. Three-dimensional (3D) structures of ocellatin-F1 with 25 residues have been reported to be potent in terms of bacterial membrane permeability. To investigate the influence of similar ocellatin peptides with 25 residues pertaining to antimicrobial effect, ocellatin-1, K1 and S1 peptides were modelled with ocellatin-F1 as template. Comparative analyses between these peptides were carried out, using computational approaches. From the results of in silico toxicity profile, all peptides were found to be non-toxic with no haemolytic activity. Further sequence analysis, net charge, hydrophobicity and hydrophobic moment revealed the membrane permeable efficacy of ocellatin-1 peptide. Besides, the investigation of peptide electronic structures through density functional theory and quantum chemical (HOMO and LUMO) calculations predicted ocellatin-1 to be a suitable peptide, which can be used as a scaffold for therapeutics. Furthermore, the determination of structural contours such as RMSD, RMSF and Rg through trajectory analysis revealed that ocellatin-1 exhibited strong structural stability. In addition, the trajectory analysis of elements of secondary structure illustrated the alpha helical conformations to be retained in all peptides, except ocellatin-1. On the aforementioned grounds, ocellatin-1 was found to possess the important role of peptide penetration of the bacterial membrane. This study becomes significant, since it is the first time where the structural importance of ocellatin peptides were explored in detail and the therapeutic potential of ocellatin-1 as a peptide-based antimicrobial drug have been theoretically revealed.
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Affiliation(s)
- P Chandra Sekar
- Bioinformatics Lab, Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - D Meshach Paul
- Bioinformatics Lab, Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India.
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3
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Breibeck J, Skerra A. The polypeptide biophysics of proline/alanine-rich sequences (PAS): Recombinant biopolymers with PEG-like properties. Biopolymers 2017; 109. [PMID: 29076532 PMCID: PMC5813227 DOI: 10.1002/bip.23069] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 12/14/2022]
Abstract
PAS polypeptides comprise long repetitive sequences of the small L‐amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half‐life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL‐1Ra. Data from size exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy and quantification of hydrodynamic and polar properties demonstrate that the biosynthetic PAS polypeptides exhibit random coil behavior in aqueous solution astonishingly similar to the chemical polymer poly‐ethylene glycol (PEG). The solvent‐exposed PAS peptide groups, in the absence of secondary structure, account for strong hydrophilicity, with negligible contribution by the Ser side chains. Notably, PAS polypeptides exceed PEG of comparable molecular mass in hydrophilicity and hydrodynamic volume while exhibiting lower viscosity. Their uniform monodisperse composition as genetically encoded polymers and their biological nature, offering biodegradability, render PAS polypeptides a promising PEG mimetic for biopharmaceutical applications.
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Affiliation(s)
- Joscha Breibeck
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany.,XL-protein GmbH, Lise-Meitner-Str. 30, 85354, Freising, Germany
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4
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du Preez LL, Patterton HG. The effect of epigenetic modifications on the secondary structures and possible binding positions of the N-terminal tail of histone H3 in the nucleosome: a computational study. J Mol Model 2017; 23:137. [PMID: 28353152 PMCID: PMC5391383 DOI: 10.1007/s00894-017-3308-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/06/2017] [Indexed: 11/05/2022]
Abstract
The roles of histone tails as substrates for reversible chemical modifications and dynamic cognate surfaces for the binding of regulatory proteins are well established. Despite these crucial roles, experimentally derived knowledge of the structure and possible binding sites of histone tails in chromatin is limited. In this study, we utilized molecular dynamics of isolated histone H3 N-terminal peptides to investigate its structure as a function of post-translational modifications that are known to be associated with defined chromatin states. We observed a structural preference for α-helices in isoforms associated with an inactive chromatin state, while isoforms associated with active chromatin states lacked α-helical content. The physicochemical effect of the post-translational modifications was highlighted by the interaction of arginine side-chains with the phosphorylated serine residues in the inactive isoform. We also showed that the isoforms exhibit different tail lengths, and, using molecular docking of the first 15 N-terminal residues of an H3 isoform, identified potential binding sites between the superhelical gyres on the octamer surface, close to the site of DNA entry/exit in the nucleosome. We discuss the possible functional role of the binding of the H3 tail within the nucleosome on both nucleosome and chromatin structure and stability.
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Affiliation(s)
- Louis L du Preez
- Department of Microbiological, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
| | - Hugh-G Patterton
- Division of Bioinformatics and Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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5
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Pushpanathan M, Pooja S, Gunasekaran P, Rajendhran J. Critical Evaluation and Compilation of Physicochemical Determinants and Membrane Interactions of MMGP1 Antifungal Peptide. Mol Pharm 2016; 13:1656-67. [PMID: 26987762 DOI: 10.1021/acs.molpharmaceut.6b00086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A growing issue of pathogen resistance to antibiotics has fostered the development of innovative approaches for novel drug development. Here, we report the physicochemical and biological properties of an antifungal peptide, MMGP1, based on computational analysis. Computation of physicochemical properties has revealed that the natural biological activities of MMGP1 are coordinated by its intrinsic properties such as net positive charge (+5.04), amphipathicity, high hydrophobicity, low hydrophobic moment, and higher isoelectric point (11.915). Prediction of aggregation hot spots in MMGP1 had revealed the presence of potentially aggregation-prone segments that can nucleate in vivo aggregation (on the membrane), whereas no aggregating regions were predicted for in vitro aggregation (in solutions) of MMGP1. This ability of MMGP1 to form oligomeric aggregates on membrane further substantiates its direct-cell penetrating potency. Monte Carlo simulation of the interactions of MMGP1 in the aqueous phase and different membrane environments revealed that increasing the proportion of acidic lipids on membrane had led to increase in the peptide helicity. Furthermore, the peptide adopts energetically favorable transmembrane configuration, by inserting peptide loop and helix termini into the membrane containing >60% of anionic lipids. The charged lipid-based insertion of MMGP1 into membrane might be responsible for the selectivity of peptide toward fungal cells. Additionally, MMGP1 possessed DNA-binding property. Computational docking has identified DNA-binding residues (TRP3, SER4, MET7, ARG8, PHE10, ALA11, GLY20, THR21, ARG22, MET23, TRP34, and LYS36) in MMGP1 crucial for its DNA-binding property. Furthermore, computational mutation analysis revealed that aromatic amino acids are crucial for in vivo aggregation, membrane insertion, and DNA-binding property of MMGP1. These data provide new insight into the molecular determinants of MMGP1 antifungal activity and also serves as the template for the design of novel peptide antibiotics.
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Affiliation(s)
- Muthuirulan Pushpanathan
- Laboratory of Gene Regulation and Development, National Institutes of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Sharma Pooja
- Department of Animal and Avian Sciences, University of Maryland , College Park, Maryland 20740, United States
| | - Paramasamy Gunasekaran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University , Madurai 625 021, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University , Madurai 625 021, India
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6
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Schlapschy M, Binder U, Börger C, Theobald I, Wachinger K, Kisling S, Haller D, Skerra A. PASylation: a biological alternative to PEGylation for extending the plasma half-life of pharmaceutically active proteins. Protein Eng Des Sel 2013; 26:489-501. [PMID: 23754528 PMCID: PMC3715784 DOI: 10.1093/protein/gzt023] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A major limitation of biopharmaceutical proteins is their fast clearance from
circulation via kidney filtration, which strongly hampers efficacy both in
animal studies and in human therapy. We have developed conformationally
disordered polypeptide chains with expanded hydrodynamic volume comprising the
small residues Pro, Ala and Ser (PAS). PAS sequences are hydrophilic, uncharged
biological polymers with biophysical properties very similar to poly-ethylene
glycol (PEG), whose chemical conjugation to drugs is an established method for
plasma half-life extension. In contrast, PAS polypeptides offer fusion to a
therapeutic protein on the genetic level, permitting Escherichia
coli production of fully active proteins and obviating in
vitro coupling or modification steps. Furthermore, they are
biodegradable, thus avoiding organ accumulation, while showing stability in
serum and lacking toxicity or immunogenicity in mice. We demonstrate that
PASylation bestows typical biologics, such as interferon, growth hormone or Fab
fragments, with considerably prolonged circulation and boosts bioactivity
in vivo.
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Affiliation(s)
- Martin Schlapschy
- Munich Center for Integrated Protein Science CIPS-M & Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
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7
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8
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Gofman Y, Haliloglu T, Ben-Tal N. Monte Carlo simulations of peptide-membrane interactions with the MCPep web server. Nucleic Acids Res 2012; 40:W358-63. [PMID: 22695797 PMCID: PMC3394254 DOI: 10.1093/nar/gks577] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The MCPep server (http://bental.tau.ac.il/MCPep/) is designed for non-experts wishing to perform Monte Carlo (MC) simulations of helical peptides in association with lipid membranes. MCPep is a web implementation of a previously developed MC simulation model. The model has been tested on a variety of peptides and protein fragments. The simulations successfully reproduced available empirical data and provided new molecular insights, such as the preferred locations of peptides in the membrane and the contribution of individual amino acids to membrane association. MCPep simulates the peptide in the aqueous phase and membrane environments, both described implicitly. In the former, the peptide is subjected solely to internal conformational changes, and in the latter, each MC cycle includes additional external rigid body rotational and translational motions to allow the peptide to change its location in the membrane. The server can explore the interaction of helical peptides of any amino-acid composition with membranes of various lipid compositions. Given the peptide’s sequence or structure and the natural width and surface charge of the membrane, MCPep reports the main determinants of peptide–membrane interactions, e.g. average location and orientation in the membrane, free energy of membrane association and the peptide’s helical content. Snapshots of example simulations are also provided.
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Affiliation(s)
- Yana Gofman
- Helmholtz-Zentrum, Department of Structure Research on Macromolecules, 21502 Geesthacht, Germany
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9
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Goh BC, Leong HW, Qu X, Chew LY. The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2012; 35:9704. [PMID: 22526978 DOI: 10.1140/epje/i2012-12027-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/10/2012] [Accepted: 03/28/2012] [Indexed: 05/31/2023]
Abstract
By introducing an additional hydrogen bond to hydrogen bond interaction in the force field of the CSAW (Conditioned Self-Avoiding Walk) model, we investigate into the mechanism of antiparallel β-sheet formation based on the folding of a short polyalanine in gas phase. Through our numerical simulation, we detect the possible presence of a transient helix during β-sheet formation, whose presence is shown to have slowed the formation of β-sheets by an order of magnitude. While we observe the mechanisms of nucleation, zipping and induction that drives the formation of a β-sheet, we uncover a new mechanism that involves transient β-turns and short β-sheets during the formation of long β-sheets. Our results have enabled us to provide an overview on the mechanisms of β-sheet formation via two main folding pathways: slow folding through the intermediate state of transient helix, and fast folding from the nucleation of β-turn.
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Affiliation(s)
- Boon Chong Goh
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
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10
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Linse P, Palenčár P, Bleha T. A New Two-State Polymer Folding Model and Its Application to α-Helical Polyalanine. J Phys Chem B 2011; 115:11448-54. [DOI: 10.1021/jp2019395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Per Linse
- Physical Chemistry, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Peter Palenčár
- Polymer Institute, Slovak Academy of Science, 845 41 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Science, 845 41 Bratislava, Slovakia
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11
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Janzsó G, Bogár F, Hudoba L, Penke B, Rákhely G, Leitgeb B. Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: A molecular dynamics study. Comput Biol Chem 2011; 35:240-50. [DOI: 10.1016/j.compbiolchem.2011.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 05/23/2011] [Accepted: 05/24/2011] [Indexed: 11/29/2022]
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12
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Leitgeb B, Janzsó G, Hudoba L, Penke B, Rákhely G, Bogár F. Helix and H-bond formations of alanine-based peptides containing basic amino acids. Struct Chem 2011. [DOI: 10.1007/s11224-011-9824-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Palenčár P, Bleha T. Molecular dynamics simulations of the folding of poly(alanine) peptides. J Mol Model 2011; 17:2367-74. [PMID: 21360173 DOI: 10.1007/s00894-011-0997-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/26/2011] [Indexed: 11/29/2022]
Abstract
The secondary structures and the shapes of long-chain polyalanine (PA) molecules were investigated by all-atom molecular dynamics simulations using a modified Amber force field. Homopolymers of polyaminoacids such as PA are convenient models to study the mechanism of protein folding. It was found that the conformational structures of PA peptides are highly sensitive to the chain length. In the absence of solvent, straight α-helices dominate in short (n ∼ 20) peptides at room temperature. A shape transition occurs at a chain length n of 40-45; the compact helix-turn-helix structure (the double-leg hairpin) becomes favored over a straight α-helix. For n=60, double-leg and the triple-leg hairpins are the only structures present in PA molecules. An exploration of a chain organization in a cubic cavity revealed a clear predisposition of PA molecules for additional breaks in α-helices and the formation of multifolded hairpins. Furthermore, under confinement the hairpin structure becomes much looser, the antiparallel positions of helical stems are disturbed, and a sizeable proportion of the helical stems are transformed from α-helices into 3(10)-helices.
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Affiliation(s)
- Peter Palenčár
- Polymer Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 41, Bratislava, Slovakia
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14
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Gordon-Grossman M, Kaminker I, Gofman Y, Shai Y, Goldfarb D. W-Band pulse EPR distance measurements in peptides using Gd3+–dipicolinic acid derivatives as spin labels. Phys Chem Chem Phys 2011; 13:10771-80. [DOI: 10.1039/c1cp00011j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Dorosz J, Gofman Y, Kolusheva S, Otzen D, Ben-Tal N, Nielsen NC, Jelinek R. Membrane interactions of novicidin, a novel antimicrobial peptide: phosphatidylglycerol promotes bilayer insertion. J Phys Chem B 2010; 114:11053-60. [PMID: 20690652 DOI: 10.1021/jp1052248] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novicidin is an antimicrobial peptide derived from ovispirin, a cationic peptide which originated from the ovine cathelicidin SMAP-29. Novicidin, however, has been designed to minimize the cytotoxic properties of SMAP-29 and ovisipirin toward achieving potential therapeutic applications. We present an analysis of membrane interactions and lipid bilayer penetration of novicidin, using an array of biophysical techniques and biomimetic membrane assemblies, complemented by Monte Carlo (MC) simulations. The data indicate that novicidin interacts minimally with zwitterionic bilayers, accounting for its low hemolytic activity. Negatively charged phosphatidylglycerol, on the other hand, plays a significant role in initiating membrane binding of novicidin, and promotes peptide insertion into the interface between the lipid headgroups and the acyl chains. The significant insertion into bilayers containing negative phospholipids might explain the enhanced antibacterial properties of novicidin. Overall, this study highlights two distinct outcomes for membrane interactions of novicidin, and points to a combination between electrostatic attraction to the lipid/water interface and penetration into the subsurface lipid headgroups region as important determinants for the biological activity of novicidin.
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Affiliation(s)
- Jerzy Dorosz
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva 84105, Israel
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16
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17
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Gofman Y, Linser S, Rzeszutek A, Shental-Bechor D, Funari SS, Ben-Tal N, Willumeit R. Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS. J Phys Chem B 2010; 114:4230-7. [PMID: 20201501 DOI: 10.1021/jp909154y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used Monte Carlo simulations and biophysical measurements to study the interaction of NKCS, a derivative of the antimicrobial peptide NK-2, with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) membrane. The simulations showed that NKCS adsorbed on the membrane surface and the dominant conformation featured two amphipathic helices connected by a hinge region. We designed two mutants in the hinge to investigate the interplay between helicity and membrane affinity. Simulations with a Leu-to-Pro substitution showed that the helicity and membrane affinity of the mutant (NKCS-[LP]) decreased. Two Ala residues were added to NKCS to produce a sequence that is compatible with a continuous amphipathic helix structure (NKCS-[AA]), and the simulations showed that the mutant adsorbed on the membrane surface with a particularly high affinity. The circular dichroism spectra of the three peptides also showed that NKCS-[LP] is the least helical and NKCS-[AA] is the most. However, the activity of the peptides, determined in terms of their antimicrobial potency and influence on the temperature of the transition of the lipid to hexagonal phase, displayed a complex behavior: NKCS-[LP] was the least potent and had the smallest influence on the transition temperature, and NKCS was the most potent and had the largest effect on the temperature.
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Affiliation(s)
- Yana Gofman
- GKSS Research Center, 21502 Geesthacht, Germany
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18
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Gordon-Grossman M, Gofman Y, Zimmermann H, Frydman V, Shai Y, Ben-Tal N, Goldfarb D. A Combined Pulse EPR and Monte Carlo Simulation Study Provides Molecular Insight on Peptide−Membrane Interactions. J Phys Chem B 2009; 113:12687-95. [DOI: 10.1021/jp905129b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michal Gordon-Grossman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yana Gofman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Herbert Zimmermann
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Veronica Frydman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yechiel Shai
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Nir Ben-Tal
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Daniella Goldfarb
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
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19
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Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J Phys Chem B 2009; 113:267-74. [PMID: 19067549 DOI: 10.1021/jp805309e] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.
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Affiliation(s)
- Yassmine Chebaro
- Institut de Biologie Physico-Chimique et Universite Paris 7 Denis Diderot, 75005 Paris, France
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20
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Vitalis A, Pappu RV. Methods for Monte Carlo simulations of biomacromolecules. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2009; 5:49-76. [PMID: 20428473 PMCID: PMC2860296 DOI: 10.1016/s1574-1400(09)00503-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.
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Affiliation(s)
- Andreas Vitalis
- Department of Biomedical Engineering, Molecular Biophysics Program, Center for Computational Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130-4899, USA
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Lei J, Huang K. Dynamics of alpha helix formation in the CSAW model. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2008; 27:197-204. [PMID: 18825424 DOI: 10.1140/epje/i2007-10371-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 09/03/2008] [Indexed: 05/26/2023]
Abstract
We study the folding dynamics of polyalanine (Ala20), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic force and internal hydrogen bonding. We find that large-scale structures form before small-scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain, one near each end. The evolution of small- and large-scale structures involves different mechanisms. While the former can be described by rate equations that govern the growth of helical content, the latter is akin to the relaxation of an elastic solid.
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Affiliation(s)
- J Lei
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, 100084 Beijing, China.
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Craig JA, Rexeisen EL, Mardilovich A, Shroff K, Kokkoli E. Effect of linker and spacer on the design of a fibronectin-mimetic peptide evaluated via cell studies and AFM adhesion forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:10282-10292. [PMID: 18693703 DOI: 10.1021/la702434p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The design of a fibronectin-mimetic peptide that specifically binds to the alpha 5beta 1 integrin has been widely studied because of this integrin's participation in many physiological and pathological processes. A promising design for such a peptide includes both the primary binding site RGD and the synergy site PHSRN connected by a linker and extended off of a surface by a spacer. Our original hypothesis was that the degree of hydrophobicity/hydrophilicity between the two sequences (RGD and PHSRN) in fibronectin is an important parameter in designing a fibronectin-mimetic peptide (Mardilovich, A.; Kokkoli, E. Biomacromolecules 2004, 5, 950-957). A peptide-amphiphile, PR_b, that was previously designed in our laboratory employed a hydrophobic tail connected to the N terminus of a peptide headgroup that was composed of a spacer, the synergy site sequence, a linker mimicking both the distance and hydrophobicity/hydrophilicity present in the native protein fibronectin (thus presenting an overall "neutral" linker), and finally the primary binding sequence. Even though our previous work (Mardilovich, A.; Craig, J. A.; McCammon, M. Q.; Garg, A.; Kokkoli, E. Langmuir 2006, 22, 3259-3264) demonstrated that PR_b is a promising sequence compared to fibronectin, this is the first study that tests our hypothesis by comparing PR_b to other peptides with hydrophobic or hydrophilic linkers. Furthermore, different peptide-amphiphiles were designed that could be used to study the effect of building blocks systematically, such as the peptide headgroup linker length and hydrophobicity/hydrophilicity as well as the headgroup spacer length on integrin adhesion. Circular dichroism spectroscopy was first employed, and the collected spectra demonstrated that only one peptide-amphiphile exhibited a secondary structure. Their surface topography was evaluated by taking atomic force microscopy (AFM) images of Langmuir-Blodgett peptide-amphiphile membranes supported on mica. Their adhesion was first evaluated with AFM force measurements between the different sequences and an AFM tip functionalized with purified integrins. The amphiphiles were further characterized via 1-12 h cell studies that examined human umbilical vein endothelial cell adhesion and extracellular matrix fibronectin production. The AFM studies were in good agreement with the cell studies. Overall, the adhesion studies validated our hypothesis and demonstrated for the first time that a "neutral" linker, which more closely mimics the cell adhesion domain of fibronectin, supports higher levels of adhesion compared to other peptide designs with a hydrophobic or hydrophilic linker or even fibronectin. Neutral linker lengths that were within the distance found between PHSRN and RGD in fibronectin performed equally well. However, the 10 amino acid neutral linker gave slightly better cell adhesion than did the control fibronectin at all times. Also, a short spacer was shown to give higher adhesion than other sequences with no spacer or a longer spacer, suggesting that a short spacer is necessary to extend the sequence further away from the interface. In conclusion, this work outlines a logical approach that can be applied for the rational design of any protein-mimetic peptide with two binding sites.
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Affiliation(s)
- Jennifer A Craig
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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Ulmschneider JP, Ulmschneider MB, Di Nola A. Monte carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins 2007; 69:297-308. [PMID: 17600830 DOI: 10.1002/prot.21519] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An efficient Monte Carlo (MC) algorithm using concerted backbone rotations is combined with a recently developed implicit membrane model to simulate the folding of the hydrophobic transmembrane domain M2TM of the M2 protein from influenza A virus and Sarcolipin at atomic resolution. The implicit membrane environment is based on generalized Born theory and has been calibrated against experimental data. The MC sampling has previously been used to fold several small polypeptides and been shown to be equivalent to molecular dynamics (MD). In combination with a replica exchange algorithm, M2TM is found to form continuous membrane spanning helical conformations for low temperature replicas. Sarcolipin is only partially helical, in agreement with the experimental NMR structures in lipid bilayers and detergent micelles. Higher temperature replicas exhibit a rapidly decreasing helicity, in agreement with expected thermodynamic behavior. To exclude the possibility of an erroneous helical bias in the simulations, the model is tested by sampling a synthetic Alanine-rich polypeptide of known helicity. The results demonstrate there is no overstabilization of helical conformations, indicating that the implicit model captures the essential components of the native membrane environment for M2TM and Sarcolipin.
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Abstract
In this article, we perform a dynamic Monte Carlo simulation study of the helix-coil transition by using a bond-fluctuation lattice model. The results of the simulations are compared with those predicted by the Zimm-Bragg statistical thermodynamic theory with propagation and nucleation parameters determined from simulation data. The Zimm-Bragg theory provides a satisfactory description of the helix-coil transition of a homopolypeptide chain of 32 residues (N = 32). For such a medium-length chain, however, the analytical equation based on a widely-used large-N approximation to the Zimm-Bragg theory is not suitable to predict the average length of helical blocks at low temperatures when helicity is high. We propose an analytical large-eigenvalue (lambda) approximation. The new equation yields a significantly improved agreement on the average helix-block length with the original Zimm-Bragg theory for both medium and long chain lengths in the entire temperature range. Nevertheless, even the original Zimm-Bragg theory does not provide an accurate description of helix-coil transition for longer chains. We assume that the single-residue nucleation of helix formation as suggested in the original Zimm-Bragg model might be responsible for this deviation. A mechanism of nucleation by a short helical block is proposed by us and provides a significantly improved agreement with our simulation data.
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Affiliation(s)
- Yantao Chen
- Department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China
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Couch VA, Cheng N, Nambiar K, Fink W. Structural characterization of alpha-helices of implicitly solvated poly-alanine. J Phys Chem B 2007; 110:3410-9. [PMID: 16494355 DOI: 10.1021/jp055209j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural characteristics of alpha-helices in poly-alanine-based peptides have been investigated via molecular dynamics simulation with the goal of understanding the basic features of peptide simulations within the context of a model system, classical molecular dynamics with generalized Born (GB) solvation, and to shed insight into the formation and stabilization of alpha-helices in short peptides. The effects of peptide length, terminal charges, proline substitution, and temperature on the alpha-helical secondary structure have been studied. The simulations have shown that distinct secondary structure begins to develop in peptides with lengths approaching 10 residues while ambiguous structures occur in shorter peptides. The helical content of peptides with lengths > or =10 amino acids is observed to be nearly constant up to (Ala)(40). Interestingly, terminal charges and proline in the second position from the N-terminus alter the secondary structure locally with little effect on the overall alpha-helical content of the peptide. The free energy profile of helix formation was also investigated. A large increase in free energy accompanying the formation of helices with more than two consecutive hydrogen bonds in the (i, i + 4) pattern was observed while the free energy increases linearly with additional hydrogen bonds. Values for the change in enthalpy and entropy of helix nucleation and propagation are reported. Additionally the results obtained from the GB model are compared to explicit solvent simulations of two synthetic alanine-based peptides.
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Affiliation(s)
- Vernon A Couch
- Department of Chemistry, University of California, Davis, California 95616, USA.
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Shental-Bechor D, Haliloglu T, Ben-Tal N. Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method. Biophys J 2007; 93:1858-71. [PMID: 17496025 PMCID: PMC1959530 DOI: 10.1529/biophysj.106.103812] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a computational model of the interaction between hydrophobic cations, such as the antimicrobial peptide, Magainin2, and membranes that include anionic lipids. The peptide's amino acids were represented as two interaction sites: one corresponds to the backbone alpha-carbon and the other to the side chain. The membrane was represented as a hydrophobic profile, and its anionic nature was represented by a surface of smeared charges. Thus, the Coulombic interactions between the peptide and the membrane were calculated using the Gouy-Chapman theory that describes the electrostatic potential in the aqueous phase near the membrane. Peptide conformations and locations near the membrane, and changes in the membrane width, were sampled at random, using the Metropolis criterion, taking into account the underlying energetics. Simulations of the interactions of heptalysine and the hydrophobic-cationic peptide, Magainin2, with acidic membranes were used to calibrate the model. The calibrated model reproduced structural data and the membrane-association free energies that were measured also for other basic and hydrophobic-cationic peptides. Interestingly, amphipathic peptides, such as Magainin2, were found to adopt two main membrane-associated states. In the first, the peptide resided mostly outside the polar headgroups region. In the second, which was energetically more favorable, the peptide assumed an amphipathic-helix conformation, where its hydrophobic face was immersed in the hydrocarbon region of the membrane and the charged residues were in contact with the surface of smeared charges. This dual behavior provides a molecular interpretation of the available experimental data.
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Affiliation(s)
- Dalit Shental-Bechor
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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Veresov VG, Davidovskii AI. Monte Carlo simulations of tBid association with the mitochondrial outer membrane. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:19-33. [PMID: 17375293 DOI: 10.1007/s00249-007-0149-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 02/02/2007] [Accepted: 02/24/2007] [Indexed: 12/24/2022]
Abstract
Bid, a BH3-only pro-apoptopic member of the BCL-2 protein family, regulates cell death at the level of mitochondrial cytochrome c efflux. Bid consists of 8 alpha-helices (H1-H8, respectively) and is soluble cytosolic protein in its native state. Proteolysis of the N-terminus (encompassing H1 and H2) of Bid by caspase 8 in apoptosis yields activated "tBid" (truncated Bid), which translocates to the mitochondria and induces the efflux of cytochrome c. The release of cytochrome c from mitochondria to the cytosol constitutes a critical control point in apoptosis that is regulated by interaction of tBid protein with mitochondrial membrane. tBid displays structural homology to channel-forming bacterial toxins, such as colicins or transmembrane domain of diphtheria toxin. By analogy, it has been hypothesized that tBid would unfold and insert into the lipid bilayer of the mitochondria outer membrane (MOM) upon membrane association. However, it has been shown recently that unlike colicins and the transmembrane domain of diphtheria toxin, tBid binds to the lipid bilayer maintaining alpha-helical conformation of its helices without adopting a transmembrane orientation by them. Here, the mechanism of the association of tBid with the model membrane mimicking the mitochondrial membrane is studied by Monte Carlo simulations, taking into account the underlying energetics. A novel two-stage hierarchical simulation protocol combining coarse-grained discretization of conformational space with subsequent refinements was applied which was able to generate the protein conformation and its location in the membrane using modest computational resources. The simulations show that starting from NMR-established conformation in the solution, the protein associates with the membrane without adopting the transmembrane orientation. The configuration (conformation and location) of tBid providing the lowest free energy for the system protein/membrane/solvent has been obtained. The simulations reveal that tBid upon association with the membrane undergoes significant conformational changes primarily due to rotations within the loops between helices H4 and H5, H6 and H7, H7 and H8. It is established that in the membrane-bound state of tBid-monomer helices H3 and H5 have the locations exposed to the solution, helices H6 and H8 are partly buried and helices H4 and H7 are buried into the membrane at shallow depth. The average orientation of tBid bound to the membrane in the most stable configuration reported here is in satisfactory agreement with the evaluations obtained by indirect experimental means.
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Affiliation(s)
- Valery G Veresov
- Department of Cell Biophysics, Institute of Biophysics and Cell Engineering, Academicheskaya St. 27, Minsk 220072, Belarus.
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Echenique P, Calvo I. Explicit factorization of external coordinates in constrained statistical mechanics models. J Comput Chem 2006; 27:1748-55. [PMID: 16917856 DOI: 10.1002/jcc.20499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, the authors explicitly write the determinant of the mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule, general internal coordinates and arbitrary constraints, as a product of two functions; one depending only on the external coordinates that describe the overall translation and rotation of the system, and the other only on the internal coordinates. This work extends previous results in the literature, proving with full generality that one may integrate out the external coordinates and perform Monte Carlo simulations in the internal conformational space of macromolecules.
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Affiliation(s)
- Pablo Echenique
- Departamento de Física Teórica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
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29
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Nuara AA, Bai H, Chen N, Buller RML, Walter MR. The unique C termini of orthopoxvirus gamma interferon binding proteins are essential for ligand binding. J Virol 2006; 80:10675-82. [PMID: 16928759 PMCID: PMC1641743 DOI: 10.1128/jvi.01015-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The orthopoxviruses ectromelia virus (ECTV) and vaccinia virus (VACV) express secreted gamma interferon binding proteins (IFN-gammaBPs) with homology to the ligand binding domains of the host's IFN-gamma receptor (IFN-gammaR1). Homology between these proteins is limited to the extracellular portions of the IFN-gammaR1 and the first approximately 200 amino acids of the IFN-gammaBPs. The remaining 60 amino acids at the C termini of the IFN-gammaBPs contain a single cysteine residue shown to be important in covalent dimerization of the secreted proteins. The function of the remaining C-terminal domain (CTD) has remained elusive, yet this region is conserved within all orthopoxvirus IFN-gammaBPs. Using a series of C-terminal deletion constructs, we have determined that the CTD is essential for IFN-gamma binding despite having no predicted homology to the IFN-gammaR1. Truncation of the ECTV IFN-gammaBP by more than two amino acid residues results in a complete loss of binding activity for both murine IFN-gamma and human IFN-gamma (hIFN-gamma), as measured by surface plasmon resonance (SPR) and bioassay. Equivalent truncation of the VACV IFN-gammaBP resulted in comparable loss of hIFN-gamma binding activity by SPR. Full-length IFN-gammaBPs were observed to form higher-ordered structures larger than the previously reported dimers. Mutants that were unable to bind IFN-gamma with high affinity in SPR experiments failed to assemble into these higher-ordered structures and migrated as dimers. We conclude that the unique CTD of orthopoxvirus IFN-gammaBPs is important for the assembly of covalent homodimers as well as the assembly of higher-ordered structures essential for IFN-gamma binding.
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Affiliation(s)
- Anthony A Nuara
- Saint Louis University, Department of Molecular Microbiology and Immunology, 1402 South Grand Blvd., St. Louis, MO 63104, USA
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Abstract
The alpha-helix was the first proposed and experimentally confirmed secondary structure. The elegant simplicity of the alpha-helical structure, stabilized by hydrogen bonding between the backbone carbonyl oxygen and the peptide amide four residues away, has captivated the scientific community. In proteins, alpha-helices are also stabilized by the so-called capping interactions that occur at both the C- and the N-termini of the helix. This chapter provides a brief historical overview of the thermodynamic studies of the energetics of helix formation, and reviews recent progress in our understanding of the thermodynamics of helix formation.
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Affiliation(s)
- George I Makhatadze
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033
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