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Lomize AL, Schnitzer KA, Todd SC, Pogozheva ID. Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles. J Chem Inf Model 2021; 61:2884-2896. [PMID: 34029472 DOI: 10.1021/acs.jcim.1c00161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP 2.0 identifies locations of α-helices in the amino acid sequence, generates their three-dimensional models in planar bilayers or spherical micelles, and estimates their thermodynamic stabilities and tilt angles, depending on temperature and pH. The method was tested for 723 peptides (926 data points) experimentally studied in different environments and for 170 single-pass transmembrane (TM) proteins with available crystal structures. FMAP 2.0 detected more than 95% of experimentally observed α-helices with an average error in helix end determination of around 2, 3, 4, and 5 residues per helix for peptides in water, micelles, bilayers, and TM proteins, respectively. Helical and nonhelical residue states were predicted with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient was from 0.64 to 0.88 depending on the environment. Experimental micelle- and membrane-binding energies and tilt angles of peptides were reproduced with a root-mean-square deviation of around 2 kcal/mol and 7°, respectively. The TM and non-TM states of hydrophobic and pH-triggered α-helical peptides in various lipid bilayers were reproduced in more than 95% of cases. The FMAP 2.0 web server (https://membranome.org/fmap) is publicly available to explore the structural polymorphism of antimicrobial, cell-penetrating, fusion, and other membrane-binding peptides, which is important for understanding the mechanisms of their biological activities.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kevin A Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Spencer C Todd
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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2
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Glaser M, Bruce NJ, Han SB, Wade RC. Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics. J Phys Chem B 2021; 125:4654-4666. [PMID: 33944558 DOI: 10.1021/acs.jpcb.1c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The S100A1ct peptide, consisting of the C-terminal 20 residues of the S100A1 protein fused to an N-terminal 6-residue hydrophilic tag, has been found to exert a positive inotropic effect, resulting in improved contractile performance of failing cardiac and skeletal muscle without arrhythmic side-effects. The S100A1ct peptide thus has high potential for the treatment of acute heart failure. As a step toward understanding its molecular mechanism of action, and to provide a basis for peptidomimetic design to optimize its properties, we here describe de novo structure predictions and molecular dynamics simulations to characterize the conformational landscape of S100A1ct in aqueous environment. In S100A1, the C-terminal 20 residues form an α-helix, but de novo peptide structure predictions indicate that other conformations are also possible. Conventional molecular dynamics simulations in implicit and explicit solvent corroborated this finding. To ensure adequate sampling, we performed simulations of a tagged 10-residue segment of S100A1ct, and we carried out Gaussian accelerated molecular dynamics simulations of the peptides. These simulations showed that although the helical conformation of S100A1ct was the most energetically stable, the peptide can adopt a range of kinked conformations, suggesting that its activity may be related to its ability to act as a conformational switch.
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Affiliation(s)
- Manuel Glaser
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany
| | - Sungho Bosco Han
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Rebecca C Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany
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3
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Wu Y, Okesola BO, Xu J, Korotkin I, Berardo A, Corridori I, di Brocchetti FLP, Kanczler J, Feng J, Li W, Shi Y, Farafonov V, Wang Y, Thompson RF, Titirici MM, Nerukh D, Karabasov S, Oreffo ROC, Carlos Rodriguez-Cabello J, Vozzi G, Azevedo HS, Pugno NM, Wang W, Mata A. Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices. Nat Commun 2020; 11:1182. [PMID: 32132534 PMCID: PMC7055247 DOI: 10.1038/s41467-020-14716-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
Supramolecular chemistry offers an exciting opportunity to assemble materials with molecular precision. However, there remains an unmet need to turn molecular self-assembly into functional materials and devices. Harnessing the inherent properties of both disordered proteins and graphene oxide (GO), we report a disordered protein-GO co-assembling system that through a diffusion-reaction process and disorder-to-order transitions generates hierarchically organized materials that exhibit high stability and access to non-equilibrium on demand. We use experimental approaches and molecular dynamics simulations to describe the underlying molecular mechanism of formation and establish key rules for its design and regulation. Through rapid prototyping techniques, we demonstrate the system's capacity to be controlled with spatio-temporal precision into well-defined capillary-like fluidic microstructures with a high level of biocompatibility and, importantly, the capacity to withstand flow. Our study presents an innovative approach to transform rational supramolecular design into functional engineering with potential widespread use in microfluidic systems and organ-on-a-chip platforms.
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Affiliation(s)
- Yuanhao Wu
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
- School of Pharmacy, University of Nottingham, NG7 2RD, Nottingham, UK
- Department of Chemical and Environmental Engineering, University of Nottingham, NG7 2RD, Nottingham, UK
- Biodiscovery Institute, University of Nottingham, NG7 2RD, Nottingham, UK
| | - Babatunde O Okesola
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Jing Xu
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Ivan Korotkin
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Alice Berardo
- Laboratory of Bio-inspired, Bionic, Nano, Meta Materials & Mechanics, Università di Trento, via Mesiano, 77, I-38123, Trento, Italy
- C3A - Center Agriculture Food Environment, University of Trento/Fondazione Edmund Mach, Via Edmund Mach, 1 - 38010, San Michele all'Adige (TN), Italy
| | - Ilaria Corridori
- Laboratory of Bio-inspired, Bionic, Nano, Meta Materials & Mechanics, Università di Trento, via Mesiano, 77, I-38123, Trento, Italy
| | | | - Janos Kanczler
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Jingyu Feng
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Weiqi Li
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Yejiao Shi
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Vladimir Farafonov
- Department of Physical Chemistry, V. N. Karazin Kharkiv National University, Svobody Sq. 4, Kharkiv, 61022, Ukraine
| | - Yiqiang Wang
- United Kingdom Atomic Energy Authority, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Rebecca F Thompson
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Maria-Magdalena Titirici
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Dmitry Nerukh
- Systems Analytics Research Institute, Department of Mathematics, Aston University, Birmingham, B4 7ET, UK
| | - Sergey Karabasov
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Richard O C Oreffo
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | | | - Giovanni Vozzi
- Research Center'E. Piaggio' & Dipartimento di Ingegneria dell'Informazione, University of Pisa, Largo Lucio Lazzarino, 256126, Pisa, Italy
| | - Helena S Azevedo
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Nicola M Pugno
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
- Laboratory of Bio-inspired, Bionic, Nano, Meta Materials & Mechanics, Università di Trento, via Mesiano, 77, I-38123, Trento, Italy
- KET Labs, Edoardo Amaldi Foundation, Via del Politecnico snc, 00133, Rome, Italy
| | - Wen Wang
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Alvaro Mata
- Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, UK.
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK.
- School of Pharmacy, University of Nottingham, NG7 2RD, Nottingham, UK.
- Department of Chemical and Environmental Engineering, University of Nottingham, NG7 2RD, Nottingham, UK.
- Biodiscovery Institute, University of Nottingham, NG7 2RD, Nottingham, UK.
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Evolution and adaptation of single-pass transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:364-377. [DOI: 10.1016/j.bbamem.2017.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/29/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
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5
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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TMDOCK: An Energy-Based Method for Modeling α-Helical Dimers in Membranes. J Mol Biol 2017; 429:390-398. [DOI: 10.1016/j.jmb.2016.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/26/2016] [Accepted: 09/02/2016] [Indexed: 11/22/2022]
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7
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Lomize AL, Lomize MA, Krolicki SR, Pogozheva ID. Membranome: a database for proteome-wide analysis of single-pass membrane proteins. Nucleic Acids Res 2017; 45:D250-D255. [PMID: 27510400 PMCID: PMC5210604 DOI: 10.1093/nar/gkw712] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/31/2016] [Accepted: 08/04/2016] [Indexed: 12/29/2022] Open
Abstract
The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by providing structural information about these proteins on a genomic scale. The database currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii It presents the following data: (i) hierarchical classification of bitopic proteins into 15 functional classes, 689 structural superfamilies and 1404 families; (ii) 446 complexes of bitopic proteins with known three-dimensional (3D) structures classified into 129 families; (iii) computationally generated three-dimensional models of TM α-helices positioned in membranes; (iv) amino acid sequences, domain architecture, functional annotation and available experimental structures of bitopic proteins; (v) TM topology and intracellular localization, (vi) physical interactions between proteins from the database along with links to other resources. The database is freely accessible at http://membranome.org There is a variety of options for browsing, sorting, searching and retrieval of the content, including downloadable coordinate files of TM domains with calculated membrane boundaries.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
| | | | - Shean R Krolicki
- Department of Computational Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1065, USA
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
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8
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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9
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Madhongsa K, Pasan S, Phophetleb O, Nasompag S, Thammasirirak S, Daduang S, Taweechaisupapong S, Lomize AL, Patramanon R. Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization. PLoS Negl Trop Dis 2013; 7:e2267. [PMID: 23785532 PMCID: PMC3681726 DOI: 10.1371/journal.pntd.0002267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/01/2013] [Indexed: 01/05/2023] Open
Abstract
Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ); however, the risk of a relapse is possible. Peptide antibiotics are an alternative to classical antibiotics as they exhibit rapid action and are less likely to result in the development of resistance. The aim of this study was to determine the bactericidal activity against B. pseudomallei and examine the membrane disrupting abilities of the potent antimicrobial peptides: bactenecin, RTA3, BMAP-18 and CA-MA. All peptides exhibited >97% bactericidal activity at 20 µM, with bactenecin having slightly higher activity. Long term time-kill assays revealed a complete inhibition of cell growth at 50 µM bactenecin and CA-MA. All peptides inhibited biofilm formation comparable to CAZ, but exhibited faster kinetics (within 1 h). Bactenecin exhibited stronger binding to LPS and induced perturbation of the inner membrane of live cells. Interaction of bactenecin with model membranes resulted in changes in membrane fluidity and permeability, leading to leakage of dye across the membrane at levels two-fold greater than that of other peptides. Modeling of peptide binding on the membrane showed stable and deep insertion of bactenecin into the membrane (up to 9 Å). We propose that bactenecin is able to form dimers or large β-sheet structures in a concentration dependent manner and subsequently rapidly permeabilize the membrane, leading to cytosolic leakage and cell death in a shorter period of time compared to CAZ. Bactenecin might be considered as a potent antimicrobial agent for use against B. pseudomallei. Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy dose of antibiotics such as ceftazidime (CAZ), however, the risk of a relapse is possible. In this study we demonstrate that bactenecin, CA-MA, RTA3 and BMAP-18 are able to inhibit the growth and biofilm formation of B. pseudomallei. The strong bactericidal activity of bactenecin is attributed to its greater ability to permeabilize the membrane. Computational modeling of these peptide-membrane interactions provide support for a model in which bactenecin is able to penetrate the membrane most effectively due to its cyclical structure. The peptide, bactenecin has the potential to act as a highly effective alternative to CAZ, or as a combination therapy with CAZ in the treatment of melioidosis. Furthermore, understanding the mechanism of bactenecin may help us better design more effective peptides therapeutics of choice for melioidosis.
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Affiliation(s)
- Kanjana Madhongsa
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Supaluk Pasan
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Onanong Phophetleb
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sawinee Nasompag
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sompong Thammasirirak
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sakda Daduang
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Suwimol Taweechaisupapong
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Andrei L. Lomize
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rina Patramanon
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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Residue-specific side-chain packing determines the backbone dynamics of transmembrane model helices. Biophys J 2011; 99:2541-9. [PMID: 20959095 DOI: 10.1016/j.bpj.2010.08.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 07/06/2010] [Accepted: 08/12/2010] [Indexed: 12/28/2022] Open
Abstract
The transmembrane domains (TMDs) of membrane-fusogenic proteins contain an overabundance of β-branched residues. In a previous effort to systematically study the relation among valine content, fusogenicity, and helix dynamics, we developed model TMDs that we termed LV-peptides. The content and position of valine in LV-peptides determine their fusogenicity and backbone dynamics, as shown experimentally. Here, we analyze their conformational dynamics and the underlying molecular forces using molecular-dynamics simulations. Our study reveals that backbone dynamics is correlated with the efficiency of side-chain to side-chain van der Waals packing between consecutive turns of the helix. Leu side chains rapidly interconvert between two rotameric states, thus favoring contacts to its i±3 and i±4 neighbors. Stereochemical restraints acting on valine side chains in the α-helix force both β-substituents into an orientation where i,i±3 interactions are less favorable than i,i±4 interactions, thus inducing a local packing deficiency at VV3 motifs. We provide a quantitative molecular model to explain the relationship among chain connectivity, side-chain mobility, and backbone flexibility. We expect that this mechanism also defines the backbone flexibility of natural TMDs.
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11
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Stability and Design of α-Helical Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:1-52. [DOI: 10.1016/s0079-6603(08)00601-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
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13
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Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI. The role of hydrophobic interactions in positioning of peripheral proteins in membranes. BMC STRUCTURAL BIOLOGY 2007; 7:44. [PMID: 17603894 PMCID: PMC1934363 DOI: 10.1186/1472-6807-7-44] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 06/29/2007] [Indexed: 02/05/2023]
Abstract
BACKGROUND Three-dimensional (3D) structures of numerous peripheral membrane proteins have been determined. Biological activity, stability, and conformations of these proteins depend on their spatial positions with respect to the lipid bilayer. However, these positions are usually undetermined. RESULTS We report the first large-scale computational study of monotopic/peripheral proteins with known 3D structures. The optimal translational and rotational positions of 476 proteins are determined by minimizing energy of protein transfer from water to the lipid bilayer, which is approximated by a hydrocarbon slab with a decadiene-like polarity and interfacial regions characterized by water-permeation profiles. Predicted membrane-binding sites, protein tilt angles and membrane penetration depths are consistent with spin-labeling, chemical modification, fluorescence, NMR, mutagenesis, and other experimental studies of 53 peripheral proteins and peptides. Experimental membrane binding affinities of peripheral proteins were reproduced in cases that did not involve a helix-coil transition, specific binding of lipids, or a predominantly electrostatic association. Coordinates of all examined peripheral proteins and peptides with the calculated hydrophobic membrane boundaries, subcellular localization, topology, structural classification, and experimental references are available through the Orientations of Proteins in Membranes (OPM) database. CONCLUSION Positions of diverse peripheral proteins and peptides in the lipid bilayer can be accurately predicted using their 3D structures that represent a proper membrane-bound conformation and oligomeric state, and have membrane binding elements present. The success of the implicit solvation model suggests that hydrophobic interactions are usually sufficient to determine the spatial position of a protein in the membrane, even when electrostatic interactions or specific binding of lipids are substantial. Our results demonstrate that most peripheral proteins not only interact with the membrane surface, but penetrate through the interfacial region and reach the hydrocarbon interior, which is consistent with published experimental studies.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
| | - Mikhail A Lomize
- College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109-1065, USA
| | - Henry I Mosberg
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
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14
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Zhang W, Loughran MG, Kanna SI, Yano K, Ikebukuro K, Yokobayashi Y, Kuroda R, Karube I. Exploration of structural features of monomeric helical peptides designed with a genetic algorithm. Proteins 2003; 53:193-200. [PMID: 14517971 DOI: 10.1002/prot.10509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A genetic algorithm (GA)-based strategy to dissect the determinants of peptide folding into alpha-helix was developed. The structural information of helical peptides was obtained with respect to patterns of sequence variability. In many previously reported studies the intrinsic alpha-helical propensities of amino acids although sequence-dependent are apparently independent of the amino acid position. In this research, monomeric helical peptides selected from possible sequences produced by a GA-chemical synthesis were analyzed to identify possible influential structural features. These hexadeca-peptides were obtained after four successive generations. A total of 128 synthetic peptides were evaluated via circular dichroism (CD) measurements in aqueous solution, while the mean ellipticity at 222 nm confirmed the monomeric state of the peptides. The results presented here show that our GA-based strategy may be useful in the design of proteins with increased alpha-helix content.
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Affiliation(s)
- Wuming Zhang
- Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
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15
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Abstract
Peptide helices in solution form a complex mixture of all helix, all coil or, most frequently, central helices with frayed coil ends. In order to interpret experiments on helical peptides and make theoretical predictions on helices, it is therefore essential to use a helix-coil theory that takes account of this equilibrium. The original Zimm-Bragg and Lifson-Roig helix-coil theories have been greatly extended in the last 10 years to include additional interactions. These include preferences for the N-cap, N1, N2, N3 and C-cap positions, capping motifs, helix dipoles, side chain interactions and 3(10)-helix formation. These have been applied to determine energies for these preferences from experimental data and to predict the helix contents of peptides. This review discusses these newly recognised structural features of helices and how they have been included in helix-coil models.
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Affiliation(s)
- Andrew J Doig
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK.
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16
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Lomize AL, Reibarkh MY, Pogozheva ID. Interatomic potentials and solvation parameters from protein engineering data for buried residues. Protein Sci 2002; 11:1984-2000. [PMID: 12142453 PMCID: PMC2373680 DOI: 10.1110/ps.0307002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H-bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free-energy differences. The set of mutants included substitutions of uncharged, inflexible, water-inaccessible residues in alpha-helices and beta-sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H-bonds were smaller than in molecular mechanics and followed the "like dissolves like" rule, as expected in condensed media but not in vacuum. The depths of modified Lennard-Jones potentials were -0.34, -0.12, and -0.06 kcal/mole for similar atom types (polar-polar, aromatic-aromatic, and aliphatic-aliphatic interactions, respectively) and -0.10, -0.08, -0.06, -0.02, and nearly 0 kcal/mole for different types (sulfur-polar, sulfur-aromatic, sulfur-aliphatic, aliphatic-aromatic, and carbon-polar, respectively), whereas the depths of H-bond potentials were -1.5 to -1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, -1, -21, and -66 cal/moleA(2) for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water-protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water.
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Affiliation(s)
- Andrei L Lomize
- College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA.
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17
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Fisinger S, Serrano L, Lacroix E. Computational estimation of specific side chain interaction energies in alpha helices. Protein Sci 2001; 10:809-18. [PMID: 11274472 PMCID: PMC2373962 DOI: 10.1110/ps.34901] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We have used a structure energy-based computer program developed for protein design, Perla, to provide theoretical estimates of all specific side chain-side chain interaction energies occurring in alpha helices. The computed side chain-side chain interaction energies were used as substitutes for the corresponding values used by the helix/coil transition algorithm, AGADIR. Predictions of peptide helical contents were nearly as successful as those obtained with the originally calibrated set of parameters; a correlation to experimentally observed alpha-helical populations of 0.91 proved that our theoretical estimates are reasonably correct for amino acid pairs that are frequent in our database of peptides. Furthermore, we have determined experimentally the previously uncharacterized interaction energies for Lys-Ile, Thr-Ile, and Phe-Ile amino acid pairs at i,i + 4 positions. The experimental values compare favorably with the computed theoretical estimates. Importantly, the computed values for Thr-Ile and Phe-Ile interactions are better than the energies based on chemical similarity, whereas for Lys-Ile they are similar. Thus, computational techniques can be used to provide precise energies for amino acid pairwise interactions, a fact that supports the development of structure energy-based computational tools for structure predictions and sequence design.
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Affiliation(s)
- S Fisinger
- European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
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18
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Serrano L. The relationship between sequence and structure in elementary folding units. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:49-85. [PMID: 10751943 DOI: 10.1016/s0065-3233(00)53002-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- L Serrano
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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19
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Vijayakumar M, Qian H, Zhou HX. Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990301)34:4<497::aid-prot9>3.0.co;2-g] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Ramírez-Alvarado M, Kortemme T, Blanco FJ, Serrano L. Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorg Med Chem 1999; 7:93-103. [PMID: 10199660 DOI: 10.1016/s0968-0896(98)00215-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent knowledge about the determinants of beta-sheet formation and stability has notably been improved by the structural analysis of model peptides with beta-hairpin structure in aqueous solution. Several experimental studies have shown that the turn region residues can not only determine the stability, but also the conformation of the beta-hairpin. Specific interstrand side-chain interactions, hydrophobic and polar, have been found to be important stabilizing interactions. The knowledge acquired in the recent years from peptide systems, together with the information gathered from mutants in proteins, and the analysis of known protein structures, has led to successful design of a folded three-stranded monomeric beta-sheet structure.
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21
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Orengo C, Bray J, Hubbard T, LoConte L, Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(1999)37:3+<149::aid-prot20>3.0.co;2-h] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Lacroix E, Viguera AR, Serrano L. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 1998; 284:173-91. [PMID: 9811549 DOI: 10.1006/jmbi.1998.2145] [Citation(s) in RCA: 363] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The information about the conformational behavior of monomeric helical peptides in solution, as well as the alpha-helix stability in proteins, has been previously utilized to derive a database with the energy contributions for various interactions taking place in an alpha-helix: intrinsic helical propensities, side-chain-side-chain interactions, main-chain-main-chain hydrogen bonds, and capping effects. This database was implemented in an algorithm based on the helix/coil transition theory (AGADIR). Here, we have modified this algorithm to include previously described local motifs: hydrophobic staple, Schellman motif and Pro-capping motif, new variants of these, and newly described side-chain-side-chain interactions. Based on recent experimental data we have introduced a position dependence of the helical propensities for some of the 20 amino acid residues. A new electrostatic model that takes into consideration all electrostatic interactions up to 12 residues in distance in the helix and random-coil conformations, as well as the effect of ionic strength, has been implemented. We have synthesized and analyzed several peptides, and used data from peptides already analysed by other groups, to test the validity of our electrostatic model. The modified algorithm predicts, with an overall standard deviation value of 6.6 (maximum helix is 100%), the helical, content of 778 peptides of which 223 correspond to wild-type and modified protein fragments. To improve the prediction potential of the algorithm and to have a direct comparison with nuclear magnetic resonance data, the algorithm now predicts the conformational shift of the CalphaH protons, 13Calpha and 3JalphaN values. We have found that for those peptides correctly predicted from the point of view of circular dichroism, the prediction of the NMR parameters is very good.
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Affiliation(s)
- E Lacroix
- EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
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