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Aguilar MI, Yarovsky I. Quest for New Generation Biocompatible Materials: Tailoring β-Peptide Structure and Interactions via Synergy of Experiments and Modelling. J Mol Biol 2024:168646. [PMID: 38848868 DOI: 10.1016/j.jmb.2024.168646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials.
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Affiliation(s)
- Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
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2
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Christofferson AJ, Al-Garawi ZS, Todorova N, Turner J, Del Borgo MP, Serpell LC, Aguilar MI, Yarovsky I. Identifying the Coiled-Coil Triple Helix Structure of β-Peptide Nanofibers at Atomic Resolution. ACS NANO 2018; 12:9101-9109. [PMID: 30157375 DOI: 10.1021/acsnano.8b03131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β3-Peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone, and we reported fibers derived from the self-assembly of β3-peptides that adopt 14-helical structures. β3-Peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. To develop structure-based criteria for the design of β3-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β3-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β3[LIA] in water and used to inform and validate the model structure. Models with 3-fold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macroscale fibers derived from β3-peptide-based materials provide valuable insight into the effects of the geometric placement of the side chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology.
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Affiliation(s)
| | - Zahraa S Al-Garawi
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
- Chemistry Department , Mustansiriyah University , Baghdad Iraq
| | - Nevena Todorova
- School of Engineering , RMIT University , Melbourne , Victoria 3001 , Australia
| | - Jack Turner
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Melbourne , Victoria 3800 , Australia
| | - Louise C Serpell
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Melbourne , Victoria 3800 , Australia
| | - Irene Yarovsky
- School of Engineering , RMIT University , Melbourne , Victoria 3001 , Australia
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3
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validation of Molecular Simulation: An Overview of Issues. Angew Chem Int Ed Engl 2017; 57:884-902. [PMID: 28682472 DOI: 10.1002/anie.201702945] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/14/2022]
Abstract
Computer simulation of molecular systems enables structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp , 2) the accuracy of the function Q(rN ) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN ) to the configuration rN , 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, UAB, 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, 08010, Barcelona, Spain
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Lorna J Smith
- Department of Chemistry, Inorganic Chemistry, Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wilfred F. van Gunsteren
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine; Universitat Autònoma de Barcelona; Spanien
- Catalan Institution for Research and Advanced Studies, ICREA; Barcelona Spanien
| | - Niels Hansen
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik; Universität Stuttgart; Deutschland
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences; University of Queensland; St. Lucia Australien
| | - Chris Oostenbrink
- Institut für Molekulare Modellierung und Simulation; Universität für Bodenkultur Wien; Österreich
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Lorna J. Smith
- Inorganic Chemistry Laboratory; Department of Chemistry; University of Oxford; Großbritannien
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5
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Smith LJ, Athill R, van Gunsteren WF, Hansen N. Interpretation of Seemingly Contradictory Data: Low NMR S 2 Order Parameters Observed in Helices and High NMR S 2 Order Parameters in Disordered Loops of the Protein hGH at Low pH. Chemistry 2017; 23:9585-9591. [PMID: 28503764 DOI: 10.1002/chem.201700896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/16/2022]
Abstract
At low pH, human growth hormone (hGH) adopts a partially folded state, in which the native helices are maintained, but the long loop regions and side-chain packing become disordered. Some of the S2 order parameters for backbone N-H vectors derived from NMR relaxation measurements on hGH at low pH initially seem contradictory. Three isolated residues (15, 20, and 171) in helices A and D exhibit low order parameter values (<0.5) indicating flexibility, whereas residue 143 in the centre of a long flexible loop region has a high order parameter (0.82). Using S2 order parameter restraining MD simulations, this paradox has been resolved. Low S2 values in helices are due to the presence of a mixture of 310 -helical and α-helical hydrogen bonds. High S2 values in relatively disordered parts of a protein may be due to fluctuating networks of hydrogen bonds between the backbone and the side chains, which restrict the motion of N-H bond vectors.
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Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Roya Athill
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | | | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany
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6
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Zhang C, Peng H, Li W, Liu L, Puttick S, Reid J, Bernardi S, Searles DJ, Zhang A, Whittaker AK. Conformation Transitions of Thermoresponsive Dendronized Polymers across the Lower Critical Solution Temperature. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng Zhang
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Hui Peng
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Wen Li
- Department
of Polymer Materials, Shanghai University, Shangda Street 99, Mailbox 152, Shanghai 200444, China
| | - Lianxiao Liu
- Department
of Polymer Materials, Shanghai University, Shangda Street 99, Mailbox 152, Shanghai 200444, China
| | - Simon Puttick
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, Qld 4072, Australia
| | | | | | | | - Afang Zhang
- Department
of Polymer Materials, Shanghai University, Shangda Street 99, Mailbox 152, Shanghai 200444, China
| | - Andrew K. Whittaker
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, Qld 4072, Australia
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7
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Liu C, Ponder JW, Marshall GR. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence. Proteins 2014; 82:3043-61. [PMID: 25116421 PMCID: PMC4206583 DOI: 10.1002/prot.24665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 02/03/2023]
Abstract
Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.
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Affiliation(s)
- Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, 63130
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8
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Choutko A, van Gunsteren WF. Conformational Preferences of aβ-Octapeptide as Function of Solvent and Force-Field Parameters. Helv Chim Acta 2013. [DOI: 10.1002/hlca.201200173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Wang D, Freitag F, Gattin Z, Haberkern H, Jaun B, Siwko M, Vyas R, van Gunsteren WF, Dolenc J. Validation of the GROMOS 54A7 Force Field Regarding Mixedα/β-Peptide Molecules. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200534] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Baldauf C, Hofmann HJ. Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200436] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA. Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput 2012; 8:3452-3462. [PMID: 23144597 PMCID: PMC3491577 DOI: 10.1021/ct300076y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the rapidly evolving disease of HIV drug resistance readily emerges, nullifying the effectiveness of therapy. Drug resistance has been extensively studied in HIV-1 protease where resistance occurs when the balance between enzyme inhibition and substrate recognition and turn-over is perturbed to favor catalytic activity. Mutations which confer drug resistance can impact the dynamics and structure of both the bound and unbound forms of the enzyme. Flap+ is a multi-drug-resistant variant of HIV-1 protease with a combination of mutations at the edge of the active site, within the active site, and in the flaps (L10I, G48V, I54V, V82A). The impact of these mutations on the dynamics in the unliganded form in comparison with the wild-type protease was elucidated with Molecular Dynamic simulations and NMR relaxation experiments. The comparative analyses from both methods concur in showing that the enzyme's dynamics are impacted by the drug resistance mutations in Flap+ protease. These alterations in the enzyme dynamics, particularly within the flaps, likely modulate the balance between substrate turn-over and drug binding, thereby conferring drug resistance.
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Affiliation(s)
- Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Wazo Myint
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
- Co-Corresponding authors: Celia A. Schiffer Phone: (508) 856-8008. Rieko Ishima Phone: (412) 648-9056
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Co-Corresponding authors: Celia A. Schiffer Phone: (508) 856-8008. Rieko Ishima Phone: (412) 648-9056
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12
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Allison JR. Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data. Biophys Rev 2012; 4:189-203. [PMID: 28510078 DOI: 10.1007/s12551-012-0087-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022] Open
Abstract
The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties.
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Affiliation(s)
- Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural Sciences, Massey University Albany, Albany Highway, Auckland, 0632, New Zealand.
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13
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Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J 2012; 102:315-24. [PMID: 22339868 DOI: 10.1016/j.bpj.2011.12.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/12/2011] [Accepted: 12/01/2011] [Indexed: 12/21/2022] Open
Abstract
The aggregation of amyloid beta (Aβ) peptides plays an important role in the development of Alzheimer's disease. Despite extensive effort, it has been difficult to characterize the secondary and tertiary structure of the Aβ monomer, the starting point for aggregation, due to its hydrophobicity and high aggregation propensity. Here, we employ extensive molecular dynamics simulations with atomistic protein and water models to determine structural ensembles for Aβ(42), Aβ(40), and Aβ(42)-E22K (the Italian mutant) monomers in solution. Sampling of a total of >700 microseconds in all-atom detail with explicit solvent enables us to observe the effects of peptide length and a pathogenic mutation on the disordered Aβ monomer structural ensemble. Aβ(42) and Aβ(40) have crudely similar characteristics but reducing the peptide length from 42 to 40 residues reduces β-hairpin formation near the C-terminus. The pathogenic Italian E22K mutation induces helix formation in the region of residues 20-24. This structural alteration may increase helix-helix interactions between monomers, resulting in altered mechanism and kinetics of Aβ oligomerization.
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Affiliation(s)
- Yu-Shan Lin
- Department of Chemistry, Stanford University, Stanford, California, USA
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14
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Kunz APE, Lin Z, van Gunsteren WF. Test of a method for sampling the internal degrees of freedom of a flexible solute molecule based on adiabatic decoupling and temperature or force scaling. Mol Phys 2012. [DOI: 10.1080/00268976.2011.650716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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15
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Wood GPF, Rothlisberger U. Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts. J Chem Theory Comput 2011; 7:1552-63. [PMID: 26610144 DOI: 10.1021/ct200156e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The distinct conformational dependence of chemical shifts caused by α-helices and β-sheets renders NMR chemical shift analysis a powerful tool for the structural determination of proteins. However, the time scale of NMR experiments can make a secondary structure assignment of highly flexible peptides or proteins, which may be converting between conformational substates, problematic. For instance the amyloid-β monomer, according to NMR chemical shifts, adopts a predominately random coil structure in aqueous solution (with <3% α-helical content). Molecular dynamics simulations, on the other hand, suggest that α-helical content can be significant (10-25%). In this paper, we explore the possible reasons for this discrepancy and show that the different results from experiments and theory are not necessarily mutually exclusive but may reflect a general problem of secondary structure assignment of conformationally flexible biomolecules.
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Affiliation(s)
- Geoffrey P F Wood
- Laboratory of Computational Chemistry and Biochemistry, BCH 4107 EPF Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, BCH 4107 EPF Lausanne, CH-1015 Lausanne, Switzerland
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16
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Lin Z, Schmid N, van Gunsteren WF. The effect of using a polarizable solvent model upon the folding equilibrium of different β-peptides. Mol Phys 2011. [DOI: 10.1080/00268976.2010.532163] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids. J Comput Chem 2010; 31:2063-77. [PMID: 20175215 DOI: 10.1002/jcc.21493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All-atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic beta-amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using beta(3)-homo-Alanine (beta(3)-hAla) diamide in water with SCC-DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the beta(3)-hAla diamide in water. The MM model is further applied to a beta-hepta-peptide in methanol solution. The calculated NOE values and (3)J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non-natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of beta amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that beta-amino-acid based random copolymers can develop a high degree of amphiphilicity without regular three-dimensional structure.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706, USA
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18
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Wang D, Friedmann M, Gattin Z, Jaun B, van Gunsteren W. The Propensity of α-Aminoisobutyric Acid (=2-Methylalanine; Aib) to Induce Helical Secondary Structure in an α-Heptapeptide: A Computational Study. Helv Chim Acta 2010. [DOI: 10.1002/hlca.200900420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Lin Z, Liu H, van Gunsteren WF. Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution. J Comput Chem 2010; 31:2419-27. [PMID: 20652985 DOI: 10.1002/jcc.21534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force-field parameters. Here, we use the one-step perturbation technique to predict the change of the free enthalpy of folding of a beta-peptide in methanol solution due to changing a variety of force-field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut-off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction-field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom-positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one-step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one-step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force-field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude.
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Affiliation(s)
- Zhixiong Lin
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH 8093, Zurich, Switzerland
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20
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Dolenc J, Missimer JH, Steinmetz MO, van Gunsteren WF. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1. JOURNAL OF BIOMOLECULAR NMR 2010; 47:221-235. [PMID: 20524044 DOI: 10.1007/s10858-010-9425-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 04/21/2010] [Indexed: 05/29/2023]
Abstract
The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 phi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and (3)J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and (3)J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.
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Affiliation(s)
- Jozica Dolenc
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093, Zürich, Switzerland
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21
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Meier K, Gunsteren WFV. Cyclic β-Helical/β-Hairpin d,l-α-Peptide: Study of Its Folding Properties and Structure Refinement Using Molecular Dynamics. J Phys Chem A 2010; 114:1852-9. [DOI: 10.1021/jp906218f] [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)
- Katharina Meier
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich ETH, 8093 Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich ETH, 8093 Zürich, Switzerland
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22
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Wang D, Jaun B, van Gunsteren WF. Folding and Unfolding of Two Mixed α/β Peptides. Chembiochem 2009; 10:2032-41. [DOI: 10.1002/cbic.200900125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Katarzyńska J, Mazur A, Bilska M, Adamek E, Zimecki M, Jankowski S, Zabrocki J. Synthesis and immunosuppressive activity of new cyclolinopeptide A analogs modified with beta-prolines. J Pept Sci 2009; 14:1283-94. [PMID: 18821729 DOI: 10.1002/psc.1069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Immune response suppressors are used in the medical praxis to prevent graft rejection after organ transplantation and in the therapy of some autoimmune diseases. As a continuation of our previous work searching for new, effective suppressors devoid of toxicity, we present the synthesis, conformational analysis, and biological activity of nonapeptides 1-6, analogs of naturally existing immunomodulatory peptide CLA. New CLA analogs were modified with (S)-beta(2)-iso-proline 7 or (S)-beta(3)-homo-proline 8, respectively. The conformational influence of the beta-iso-proline and beta-homo-proline building blocks was analyzed by NMR spectroscopy. Peptides 1-6 exist as a mixture of four isomers due to cis/trans isomerization of the Xxx-Pro peptide bond. The major isomers of peptides 1, 3, and 4 contain all peptide bonds of the trans geometry. The geometry of the proline-proline bond of the second populated isomer of peptides 3 and 4 is cis. The proline-proline peptide bond is cis for the major isomers of peptides 2, 5, and 6. The peptides were tested for their ability to suppress the proliferative response of mouse splenocytes to T- and B-cell mitogens and the secondary humoral immune response to sheep erythrocytes in vitro in parallel with a reference drug-cyclosporine A. The immunoregulatory actions of the peptides depended on the position and content of proline isomers and were, with some exceptions, strongly inhibitory at the highest dose tested (100 microg/ml). In addition, the peptides were practically devoid of toxicity at that dose. In conclusion, the replacement of Pro by beta-Pro may be useful for fine-tuning CLA immunosuppressive potency and undesirable toxicity.
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Affiliation(s)
- Joanna Katarzyńska
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Zeromskiego 116, 90-924 Łódź, Poland
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Isaksson J, Nyström S, Derbyshire D, Wallberg H, Agback T, Kovacs H, Bertini I, Giachetti A, Luchinat C. Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. J Med Chem 2009; 52:1712-22. [DOI: 10.1021/jm801388q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johan Isaksson
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Susanne Nyström
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Dean Derbyshire
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Hans Wallberg
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Tatiana Agback
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Helena Kovacs
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Ivano Bertini
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Andrea Giachetti
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
| | - Claudio Luchinat
- Medivir AB, PO Box 1086, SE-141 22 Huddinge, Sweden, Bruker BioSpin AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, Department of Agricultural Biotechnology, University of Florence, Via Maragliano 75−77, 50144 Florence, Italy, ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino,
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25
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Molecular dynamics simulation of antimicrobial peptide arenicin-2: β-Hairpin stabilization by noncovalent interactions. Biopolymers 2009; 92:143-55. [DOI: 10.1002/bip.21149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Wu YD, Han W, Wang DP, Gao Y, Zhao YL. Theoretical analysis of secondary structures of beta-peptides. Acc Chem Res 2008; 41:1418-27. [PMID: 18828608 DOI: 10.1021/ar800070b] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Unlike alpha-amino acids, peptides formed from beta-amino acids (beta-peptides) display stability toward enzymatic degradation and may form turns and helices with as few as four residues. Because both the C alpha and C beta of the beta-amino acid may bear substituents, a large number of beta-amino acids can be synthesized. Beta-peptides form various well-defined secondary structures, including 14-helix, 12-helix, 10/12-helix, 10-helix, 8-helix, turn structures, sheets, and hairpins. For all of these reasons, beta-amino acids have been increasingly used as building blocks for molecular design and pharmaceutical applications. To explain the conformational features of beta-peptides, several quantum mechanics and molecular dynamics studies that rationalize the observed conformational features have been reported. However, a systematic account that unifies various factors critical to the conformational features is still lacking. In this Account, we present a detailed analysis of the conformational features of various beta-peptides. We start by studying the basic local conformational features of beta-peptides using di- and tripeptide models. Then, various secondary structures of unsubstituted beta-peptides with differing numbers of residues are investigated using a repeating unit approach to derive the intrinsic backbone conformational features. We find that the 10/12-helix is intrinsically most stable for the beta-peptide backbone. The 14-helix, 12-helix, and 10-helix structures have similar stabilities for beta-peptide backbones of four to six residues. The substituent effects on the stabilities of beta-peptide secondary structures are then analyzed. Combined with the substituent effect and the intrinsic backbone preferences, all experimental observations of secondary structure formation can be understood. For example, the 10/12-helix is favored for like-beta(2)/beta(3)-peptides, unlike-beta(3)/beta(3)-peptides, and beta(3)/beta-hGly-peptides because these substitution patterns do not cause steric problems for the 10/12-helix. Beta(3)-peptides, beta(2)-peptides, and beta (2,3)-peptides favor the 14-helix because the substituents in these peptides benefit the 14-helix the most but significantly destabilize the 10/12-helix. Because the 10/12-helix is intrinsically favored and has two favorable positions in each residue for substituents, many more hybrid beta-peptides are predicted to exist in this secondary structure, which suggests the need for further experiments. These results are valuable for determining the best use of these building blocks in the design of well-structured molecules with desirable chemical functions.
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Affiliation(s)
- Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Han
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - De-Ping Wang
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yi Gao
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yi-Lei Zhao
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
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27
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Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue. J Phys Chem B 2008; 112:5439-48. [PMID: 18402479 DOI: 10.1021/jp077601y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-atom molecular mechanical (MM) force field parameters are developed for a cyclic beta-amino acid, amino-cyclo-pentane-carboxylic acid (ACPC), using a multi-objective evolutionary algorithm. The MM model is benchmarked using several short, ACPC-containing alpha/beta-peptides in water and methanol with SCC-DFTB (self consistent charge-density functional tight binding)/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the tetra-alpha/beta-peptide in water. For the octa-alpha/beta-peptide in methanol, the MM and SCC-DFTB/MM simulations predict the 11- and 14/15-helical form as the more stable conformation, respectively; however, the two helical forms are very close in energy (2-4 kcal/mol) at both theoretical levels, which is also the conclusion from recent NMR experiments. As the first application, the MM model is applied to an alpha/beta-pentadeca-peptide in water with both explicit and implicit solvent models. The stability of the peptide is sensitive to the starting configuration in the explicit solvent simulations due to their limited length ( approximately 10-40 ns). Multiple ( approximately 20 x 20 ns) implicit solvent simulations consistently show that the 14/15-helix is the predominant conformation of this peptide, although substantially different conformations are also accessible. The calculated nuclear Overhauser effect (NOE) values averaged over different trajectories are consistent with experimental data, which emphasizes the importance of considering conformational heterogeneity in such comparisons for highly dynamical peptides.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Theoretical Chemistry Institute, The BACTER Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wiconsin 53706, USA
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28
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Kaur K, Sprules T, Soliman W, Beleid R, Ahmed S. Right-handed 14-Helix in β3-Peptides from L-Aspartic Acid Monomers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:658-65. [DOI: 10.1016/j.bbapap.2008.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 12/19/2007] [Accepted: 01/08/2008] [Indexed: 11/17/2022]
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29
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van Gunsteren WF, Dolenc J, Mark AE. Molecular simulation as an aid to experimentalists. Curr Opin Struct Biol 2008; 18:149-53. [PMID: 18280138 DOI: 10.1016/j.sbi.2007.12.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/19/2007] [Accepted: 12/21/2007] [Indexed: 11/26/2022]
Abstract
Computer-based molecular simulation techniques are increasingly used to interpret experimental data on biomolecular systems at an atomic level. Direct comparison between experiment and simulation is, however, seldom straightforward. The available experimental data are limited in scope and generally correspond to averages over both time and space. A critical analysis of the various factors that may influence the apparent degree of agreement between the results of simulations and experimentally measured quantities is presented and illustrated using examples from recent literature.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH-8093 Zurich, Switzerland.
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30
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Goodman CM, Choi S, Shandler S, DeGrado WF. Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol 2007; 3:252-62. [PMID: 17438550 PMCID: PMC3810020 DOI: 10.1038/nchembio876] [Citation(s) in RCA: 759] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and function. Foldamers also provide templates for presenting complex arrays of functional groups in virtually unlimited geometrical patterns, thereby presenting attractive opportunities for the design of molecules that bind in a sequence- and structure-specific manner to oligosaccharides, nucleic acids, membranes and proteins. We summarize recent advances and highlight the future applications and challenges of this rapidly expanding field.
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Affiliation(s)
- Catherine M Goodman
- Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, USA
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31
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Baumketner A, Shea JE. The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent. J Mol Biol 2007; 366:275-85. [PMID: 17166516 DOI: 10.1016/j.jmb.2006.11.015] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 10/29/2006] [Accepted: 11/03/2006] [Indexed: 11/28/2022]
Abstract
The conformational states sampled by the Alzheimer amyloid beta (10-35) (Abeta 10-35) peptide were probed using replica-exchange molecular dynamics (REMD) simulations in explicit solvent. The Abeta 10-35 peptide is a fragment of the full-length Abeta 40/42 peptide that possesses many of the amyloidogenic properties of its full-length counterpart. Under physiological temperature and pressure, our simulations reveal that the Abeta 10-35 peptide does not possess a single unique folded state. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is dominated by random coil and bend structures with insignificant presence of an alpha-helical or beta-sheet structure. The 3D structure of Abeta 10-35 is seen to be defined by a salt bridge formed between the side-chains of K28 and D23. This salt bridge is also observed in Abeta fibrils and our simulations suggest that monomeric conformations of Abeta 10-35 contain pre-folded structural motifs that promote rapid aggregation of this peptide.
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Affiliation(s)
- Andrij Baumketner
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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32
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Trzesniak D, Jaun B, Mathad RI, van Gunsteren WF. Simulation of an all-β3-icosapeptide containing the 20 proteinogenic side chains: Effect of temperature, pH, counterions, solvent, and force field on helix stability. Biopolymers 2006; 83:636-45. [PMID: 16967513 DOI: 10.1002/bip.20601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Simulations of various beta-peptides have in the last years clarified several issues concerning peptide folding equilibria and interpretation of experimental data, especially from NMR and CD spectroscopy. These simulations involved different temperatures, pH-values, ionic strengths, solvents, and force-field parameters, but a variation of these factors for one beta-peptide has not yet been done. To investigate the influence of varying these factors, we analyze the helix stability of an all-beta3-icosapeptide bearing all 20 proteinogenic amino acid side chains, which is experimentally observed to fold into a 3(14)-helix in methanol but not in water. Structural aspects, such as hydrogen-bonded rings and salt bridges, are discussed and a comparison with NMR primary (NOE distance bounds and 3J-values) and secondary (NMR derived model structures) data is made. We further investigate the reasons for the 3(14)-helix stability/instability in methanol/water. Of all factors studied, the presence of counterions seems to be the one inducing most significant effects in the simulations.
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Affiliation(s)
- Daniel Trzesniak
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, CH-8093 Zürich, Switzerland
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35
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Abstract
The principal secondary structural motifs adopted by peptides assembled from beta-amino acid units are discussed: the 14-, 12-, 10-, 12/10-, and 8-helices, as well as the hairpin turn, extended structures, stacks, and sheets. Features that promote a particular folding propensity are outlined and illustrated by structures determined in solution (NMR) and in the solid-state (x-ray). The N-C(beta)-C(alpha)-CO dihedral angles from molecular dynamics simulations, which are indicative of a particular secondary structure, are presented. A brief description of a helix and a turn of gamma-peptides is also given.
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Affiliation(s)
- Dieter Seebach
- Laboratorium für Organische Chemie der Eidgenössischen Technischen Hochschule Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.
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