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Abstract
The formation of amyloid fibrils is a complex phenomenon that remains poorly understood at the atomic scale. Herein, we perform extended unbiased all-atom simulations in explicit solvent of a short amphipathic peptide to shed light on the three mechanisms accounting for fibril formation, namely, nucleation via primary and secondary mechanisms, and fibril growth. We find that primary nucleation takes place via the formation of an intermediate state made of two laminated β-sheets oriented perpendicular to each other. The amyloid fibril spine subsequently emerges from the rotation of these β-sheets to account for peptides that are parallel to each other and perpendicular to the main axis of the fibril. Growth of this spine, in turn, takes place via a dock-and-lock mechanism. We find that peptides dock onto the fibril tip either from bulk solution or after diffusing on the fibril surface. The latter docking pathway contributes significantly to populate the fibril tip with peptides. We also find that side chain interactions drive the motion of peptides in the lock phase during growth, enabling them to adopt the structure imposed by the fibril tip with atomic fidelity. Conversely, the docked peptide becomes trapped in a local free energy minimum when docked-conformations are sampled randomly. Our simulations also highlight the role played by nonpolar fibril surface patches in catalyzing and orienting the formation of small cross-β structures. More broadly, our simulations provide important new insights into the pathways and interactions accounting for primary and secondary nucleation as well as the growth of amyloid fibrils.
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Affiliation(s)
- Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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2
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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3
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Jalali S, Yang Y, Mahmoudinobar F, Singh SM, Nilsson BL, Dias C. Using all-atom simulations in explicit solvent to study aggregation of amphipathic peptides into amyloid-like fibrils. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Helmick H, Turasan H, Yildirim M, Bhunia A, Liceaga A, Kokini JL. Cold Denaturation of Proteins: Where Bioinformatics Meets Thermodynamics to Offer a Mechanistic Understanding: Pea Protein As a Case Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6339-6350. [PMID: 34029090 DOI: 10.1021/acs.jafc.0c06558] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein structure can be altered with heat, but models which predict denaturation show that globular proteins also spontaneously unfold at low temperatures through cold denaturation. By an analysis of the primary structure of pea protein using bioinformatic modeling, a mechanism of pea protein cold denaturation is proposed. Pea protein is then fractionated into partially purified legumin and vicilin components, suspended in ethanol, and subjected to low temperatures (-10 to -20 °C). The structural characterizations of the purified fractions are conducted through FTIR, ζ potential, dynamic light scattering, and oil binding, and these are compared to the results of commercial protein isolates. The observed structural changes suggest that pea protein undergoes changes in structure as the result of low-temperature treatments, which could lead to innovative industrial processing techniques for functionalization by low-temperature processing.
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Affiliation(s)
- Harrison Helmick
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
| | - Hazal Turasan
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
| | - Merve Yildirim
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
| | - Arun Bhunia
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
| | - Andrea Liceaga
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
| | - Jozef L Kokini
- Purdue University Food Science Department, 745 Agriculture Mall Drive West Lafayette, Indiana 47907, United States
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5
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Computational studies of protein aggregation mediated by amyloid: Fibril elongation and secondary nucleation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:461-504. [DOI: 10.1016/bs.pmbts.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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6
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Manandhar A, Chakraborty K, Tang PK, Kang M, Zhang P, Cui H, Loverde SM. Rational Coarse-Grained Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes. J Phys Chem B 2019; 123:10582-10593. [DOI: 10.1021/acs.jpcb.9b07417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Kaushik Chakraborty
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Phu K. Tang
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Myungshim Kang
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Pengcheng Zhang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
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7
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Su Z, Dias CL. Individual and combined effects of urea and trimethylamine N-oxide (TMAO) on protein structures. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Ilie IM, Nayar D, den Otter WK, van der Vegt NFA, Briels WJ. Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:3298-3310. [PMID: 29715424 DOI: 10.1021/acs.jctc.8b00183] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in solution have a propensity toward attaining non-β conformations, indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in solution, while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein, and enables the parametrization of coarse grained models.
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Affiliation(s)
- Ioana M Ilie
- Computational Chemical Physics, Faculty of Science and Technology , University of Twente , 7500 AE Enschede , the Netherlands.,MESA+ Institute for Nanotechnology , 7500 AE Enschede , the Netherlands.,Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
| | - Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces , Technische Universität Darmstadt , 64287 Darmstadt , Germany
| | - Wouter K den Otter
- Computational Chemical Physics, Faculty of Science and Technology , University of Twente , 7500 AE Enschede , the Netherlands.,MESA+ Institute for Nanotechnology , 7500 AE Enschede , the Netherlands.,Multi Scale Mechanics, Faculty of Engineering Technology , University of Twente , 7500 AE Enschede , the Netherlands
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces , Technische Universität Darmstadt , 64287 Darmstadt , Germany
| | - Wim J Briels
- Computational Chemical Physics, Faculty of Science and Technology , University of Twente , 7500 AE Enschede , the Netherlands.,Forschungszentrum Jülich , ICS-3 , D-52428 Jülich , Germany
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9
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10
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Schwierz N, Frost CV, Geissler PL, Zacharias M. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc 2016; 138:527-39. [PMID: 26694883 DOI: 10.1021/jacs.5b08717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.
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Affiliation(s)
- Nadine Schwierz
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Christina V Frost
- Physik Department, Technische Universität München , 85748 Garching, Germany
| | - Phillip L Geissler
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Martin Zacharias
- Physik Department, Technische Universität München , 85748 Garching, Germany
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11
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Rao Jampani S, Mahmoudinobar F, Su Z, Dias CL. Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties. Proteins 2015; 83:1963-72. [PMID: 26264694 DOI: 10.1002/prot.24875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/22/2015] [Accepted: 08/02/2015] [Indexed: 11/10/2022]
Abstract
Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21.
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Affiliation(s)
- Srinivasa Rao Jampani
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
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12
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Higo J, Dasgupta B, Mashimo T, Kasahara K, Fukunishi Y, Nakamura H. Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J Comput Chem 2015; 36:1489-501. [DOI: 10.1002/jcc.23948] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Bhaskar Dasgupta
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next Generation Natural Products Chemistry; 2-3-26 Aomi Koto-Ku Tokyo 135-0064 Japan
- Information, Mathematical Science and Bioinformatics Co., Ltd.; 4-21-1, Higashiikebukuro Toshima-ku Tokyo 170-0013 Japan
| | - Kota Kasahara
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST); 2-3-26 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
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13
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Rašković B, Popović M, Ostojić S, Anđelković B, Tešević V, Polović N. Fourier transform infrared spectroscopy provides an evidence of papain denaturation and aggregation during cold storage. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:238-246. [PMID: 26051646 DOI: 10.1016/j.saa.2015.05.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
Papain is a cysteine protease with wide substrate specificity and many applications. Despite its widespread applications, cold stability of papain has never been studied. Here, we used differential spectroscopy to monitor thermal denaturation process. Papain was the most stabile from 45 °C to 60 °C with ΔG°321 of 13.9±0.3 kJ/mol and Tm value of 84±1 °C. After cold storage, papain lost parts of its native secondary structures elements which gave an increase of 40% of intermolecular β-sheet content (band maximum detected at frequency of 1621 cm(-1) in Fourier transform infrared (FT-IR) spectrum) indicating the presence of secondary structures necessary for aggregation. The presence of protein aggregates after cold storage was also proven by analytical size exclusion chromatography. After six freeze-thaw cycles around 75% of starting enzyme activity of papain was lost due to cold denaturation and aggregation of unfolded protein. Autoproteolysis of papain did not cause significant loss of the protein activity. Upon the cold storage, papain underwent structural rearrangements and aggregation that correspond to other cold denatured proteins, rather than autoproteolysis which could have the commercial importance for the growing polypeptide based industry.
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Affiliation(s)
- Brankica Rašković
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Milica Popović
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Sanja Ostojić
- Institute of General and Physical Chemistry, Studentski trg 12, 11000 Belgrade, Serbia
| | - Boban Anđelković
- Department of Organic Chemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Vele Tešević
- Department of Organic Chemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Natalija Polović
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia.
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14
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Mahmoudinobar F, Dias CL, Zangi R. Role of side-chain interactions on the formation of α-helices in model peptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032710. [PMID: 25871147 DOI: 10.1103/physreve.91.032710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Indexed: 06/04/2023]
Abstract
The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.
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Affiliation(s)
- Farbod Mahmoudinobar
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Ronen Zangi
- Department of Organic Chemistry I and POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
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