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Bhargav P, Mukherjee A. AlphaMut: A Deep Reinforcement Learning Model to Suggest Helix-Disrupting Mutations. J Chem Theory Comput 2025; 21:463-473. [PMID: 39702999 DOI: 10.1021/acs.jctc.4c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Helices are important secondary structural motifs within proteins and are pivotal in numerous physiological processes. While amino acids (AA) such as alanine and leucine are known to promote helix formation, proline and glycine disfavor it. Helical structure formation, however, also depends on its environment, and hence, prior prediction of a mutational effect on a helical structure is difficult. Here, we employ a reinforcement learning algorithm to develop a predictive model for helix-disrupting mutations. We start with a model to disrupt helices independent of their protein environment. Our results show that only a few mutations lead to a drastic disruption of the target helix. We further extend our approach to helices in proteins and validate the results using rigorous free energy calculations. Our strategy identifies amino acids crucial for maintaining structural integrity and predicts key mutations that could alter protein structure. Through our work, we present a new use case for reinforcement learning in protein structure disruption.
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Affiliation(s)
- Prathith Bhargav
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
- Department of Data Science, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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2
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Škrbić T, Maritan A, Giacometti A, Banavar JR. Local sequence-structure relationships in proteins. Protein Sci 2021; 30:818-829. [PMID: 33511717 PMCID: PMC7980514 DOI: 10.1002/pro.4032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/11/2022]
Abstract
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to address these questions, we represent the local structure of each Cα atom of a protein by just two angles, θ and μ, and we analyze a set of more than 4,000 protein structures from the PDB. We use a hierarchical clustering scheme to divide the 20 amino acids into six distinct groups based on their similarity to each other in fitting local structural space. We present the results of a detailed analysis of patterns of amino acid specificity in adopting local structural conformations and show that the sequence-structure correlation is not very strong compared with a random assignment of sequence to structure. Yet, our analysis may be useful to determine an effective scoring rubric for quantifying the match of an amino acid to its putative local structure.
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Affiliation(s)
- Tatjana Škrbić
- Department of Physics and Institute for Fundamental ScienceUniversity of OregonEugeneOregonUSA
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari VeneziaVenezia MestreItaly
| | - Amos Maritan
- Dipartimento di Fisica e AstronomiaUniversità di Padova and INFNPadovaItaly
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari VeneziaVenezia MestreItaly
| | - Jayanth R. Banavar
- Department of Physics and Institute for Fundamental ScienceUniversity of OregonEugeneOregonUSA
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3
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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4
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Cramer JM, Pohlmann D, Gomez F, Mark L, Kornegay B, Hall C, Siraliev-Perez E, Walavalkar NM, Sperlazza MJ, Bilinovich S, Prokop JW, Hill AL, Williams Jr. DC. Methylation specific targeting of a chromatin remodeling complex from sponges to humans. Sci Rep 2017; 7:40674. [PMID: 28094816 PMCID: PMC5240623 DOI: 10.1038/srep40674] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/09/2016] [Indexed: 12/31/2022] Open
Abstract
DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.
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Affiliation(s)
- Jason M. Cramer
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - Deborah Pohlmann
- Department of Biology, University of Richmond, Richmond, VA, USA
| | - Fernando Gomez
- Department of Biology, University of Richmond, Richmond, VA, USA
| | - Leslie Mark
- Department of Biology, University of Richmond, Richmond, VA, USA
| | | | - Chelsea Hall
- Department of Biology, University of Richmond, Richmond, VA, USA
| | - Edhriz Siraliev-Perez
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ninad M. Walavalkar
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M. Jeannette Sperlazza
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - April L. Hill
- Department of Biology, University of Richmond, Richmond, VA, USA
| | - David C. Williams Jr.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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5
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Yakimov A, Afanaseva A, Khodorkovskiy M, Petukhov M. Design of Stable α-Helical Peptides and Thermostable Proteins in Biotechnology and Biomedicine. Acta Naturae 2016; 8:70-81. [PMID: 28050268 PMCID: PMC5199208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 11/24/2022] Open
Abstract
α-Helices are the most frequently occurring elements of the secondary structure in water-soluble globular proteins. Their increased conformational stability is among the main reasons for the high thermal stability of proteins in thermophilic bacteria. In addition, α-helices are often involved in protein interactions with other proteins, nucleic acids, and the lipids of cell membranes. That is why the highly stable α-helical peptides used as highly active and specific inhibitors of protein-protein and other interactions have recently found more applications in medicine. Several different approaches have been developed in recent years to improve the conformational stability of α-helical peptides and thermostable proteins, which will be discussed in this review. We also discuss the methods for improving the permeability of peptides and proteins across cellular membranes and their resistance to intracellular protease activity. Special attention is given to the SEQOPT method (http://mml.spbstu.ru/services/seqopt/), which is used to design conformationally stable short α-helices.
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Affiliation(s)
- A.P. Yakimov
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg 195251 , Russia
- Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, Orlova Roscha, 1, Gatchina, 188300, Russia
| | - A.S. Afanaseva
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg 195251 , Russia
- Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, Orlova Roscha, 1, Gatchina, 188300, Russia
| | - M.A. Khodorkovskiy
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg 195251 , Russia
| | - M.G. Petukhov
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg 195251 , Russia
- Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, Orlova Roscha, 1, Gatchina, 188300, Russia
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6
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Apicella A, Marascio M, Colangelo V, Soncini M, Gautieri A, Plummer CJG. Molecular dynamics simulations of the intrinsically disordered protein amelogenin. J Biomol Struct Dyn 2016; 35:1813-1823. [PMID: 27366858 DOI: 10.1080/07391102.2016.1196151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amelogenin refers to a class of intrinsically disordered proteins that are the major constituents of enamel matrix derivative (EMD), an extract of porcine fetal teeth used in regenerative periodontal therapy. Modifications in molecular conformation induced by external stresses, such as changes in temperature or pH, are known to reduce the effectiveness of EMD. However, detailed descriptions of the conformational behavior of native amelogenin are lacking in the open literature. In the present work, a molecular model for the secondary and tertiary structure of the full-length major porcine amelogenin P173 was constructed from its primary sequence by replica exchange molecular dynamics (REMD) simulations. The REMD results for isolated amelogenin molecules at different temperatures were shown to be consistent with the available spectroscopic data. They therefore represent an important first step toward the simulation of the intra- and intermolecular interactions that mediate self-organization in amelogenin and its behavior in the presence of other EMD components under conditions representative of its therapeutic application.
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Affiliation(s)
- Alessandra Apicella
- a Laboratoire de Technologie des Composites et Polymères (LTC) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12, CH-1015 Lausanne , Switzerland
| | - Matteo Marascio
- a Laboratoire de Technologie des Composites et Polymères (LTC) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12, CH-1015 Lausanne , Switzerland.,b Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Piazza Leonardo da Vinci 32, 20133 Milan , Italy
| | - Vincenzo Colangelo
- b Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Piazza Leonardo da Vinci 32, 20133 Milan , Italy
| | - Monica Soncini
- b Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Piazza Leonardo da Vinci 32, 20133 Milan , Italy
| | - Alfonso Gautieri
- b Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Piazza Leonardo da Vinci 32, 20133 Milan , Italy
| | - Christopher J G Plummer
- a Laboratoire de Technologie des Composites et Polymères (LTC) , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12, CH-1015 Lausanne , Switzerland
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7
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Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
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Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
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8
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Molecular dynamics simulation and experimental verification of the interaction between cyclin T1 and HIV-1 Tat proteins. PLoS One 2015; 10:e0119451. [PMID: 25781978 PMCID: PMC4363469 DOI: 10.1371/journal.pone.0119451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
The viral encoded Tat protein is essential for the transcriptional activation of HIV proviral DNA. Interaction of Tat with a cellular transcription elongation factor P-TEFb containing CycT1 is critically required for its action. In this study, we performed MD simulation using the 3D data for wild-type and 4CycT1mutants3D data. We found that the dynamic structural change of CycT1 H2’ helix is indispensable for its activity for the Tat action. Moreover, we detected flexible structural changes of the Tat-recognition cavity in the WT CycT1 comprising of ten AAs that are in contact with Tat. These structural fluctuations in WT were lost in the CycT1 mutants. We also found the critical importance of the hydrogen bond network involving H1, H1’ and H2 helices of CycT1. Since similar AA substitutions of the Tat-CycT1 chimera retained the Tat-supporting activity, these interactions are considered primarily involved in interaction with Tat. These findings described in this paper should provide vital information for the development of effective anti-Tat compound.
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9
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Elbaum MB, Zondlo NJ. OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification. Biochemistry 2014; 53:2242-60. [PMID: 24641765 PMCID: PMC4004263 DOI: 10.1021/bi500117c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
OGlcNAcylation
and phosphorylation are the major competing intracellular
post-translational modifications of serine and threonine residues.
The structural effects of both post-translational modifications on
serine and threonine were examined within Baldwin model α-helical
peptides (Ac-AKAAAAKAAAAKAAGY-NH2 or Ac-YGAKAAAAKAAAAKAA-NH2). At the N-terminus of an α-helix, both phosphorylation
and OGlcNAcylation stabilized the α-helix relative to the free
hydroxyls, with a larger induced structure for phosphorylation than
for OGlcNAcylation, for the dianionic phosphate than for the monoanionic
phosphate, and for modifications on threonine than for modifications
on serine. Both phosphoserine and phosphothreonine resulted in peptides
more α-helical than alanine at the N-terminus, with dianionic
phosphothreonine the most α-helix-stabilizing residue here.
In contrast, in the interior of the α-helix, both post-translational
modifications were destabilizing with respect to the α-helix,
with the greatest destabilization seen for threonine OGlcNAcylation
at residue 5 and threonine phosphorylation at residue 10, with peptides
containing either post-translational modification existing as random
coils. At the C-terminus, both OGlcNAcylation and phosphorylation
were destabilizing with respect to the α-helix, though the induced
structural changes were less than in the interior of the α-helix.
In general, the structural effects of modifications on threonine were
greater than the effects on serine, because of both the lower α-helical
propensity of Thr and the more defined induced structures upon modification
of threonine than serine, suggesting threonine residues are particularly
important loci for structural effects of post-translational modifications.
The effects of serine and threonine post-translational modifications
are analogous to the effects of proline on α-helices, with the
effects of phosphothreonine being greater than those of proline throughout
the α-helix. These results provide a basis for understanding
the context-dependent structural effects of these competing protein
post-translational modifications.
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Affiliation(s)
- Michael B Elbaum
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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10
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Abstract
Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization.
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11
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Abstract
A new peptidomimetic is proposed, resulting from substitution of the C═O carbonyl group by a B-F bond at the amide linkage. The effects of such chemical alteration are theoretically investigated through comparative calculations on dimethyl-fluoro-aminoborane H(3)C-BF-NH-CH(3) and N-methylacetamide H(3)C-CO-NH-CH(3), the simplest model of a peptide linkage. While little difference is found regarding size, electronic structure, and plaque rigidity, substantial distinctions are, however, observed between the polarities and association energies of the two compounds, with a B-F···H-N hydrogen bond estimated to be about one-third as strong as the natural C═O···H-N one. The conformational maps of the corresponding dipeptide models exhibit similarities and distinctions, which partly account for helical oligomer properties. Although capable of a high level of organization, the chains made of fluoro-aminoborane units show overall less structuration and more plasticity than their peptidic counterparts. Contrasts with fluorine-containing peptidomimetic 2-fluoro-2-butene are further underlined.
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Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantiques (CNRS, UMR-5626), IRSAMC, Université Paul-Sabatier, 31062 Toulouse Cedex, France
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12
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The structure of the ends of α-helices in globular proteins: Effect of additional hydrogen bonds and implications for helix formation. Proteins 2011; 79:1010-9. [DOI: 10.1002/prot.22942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/29/2010] [Accepted: 11/05/2010] [Indexed: 11/07/2022]
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13
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Cheng RP, Girinath P, Suzuki Y, Kuo HT, Hsu HC, Wang WR, Yang PA, Gullickson D, Wu CH, Koyack MJ, Chiu HP, Weng YJ, Hart P, Kokona B, Fairman R, Lin TE, Barrett O. Positional Effects on Helical Ala-Based Peptides. Biochemistry 2010; 49:9372-84. [DOI: 10.1021/bi101156j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Prashant Girinath
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yuta Suzuki
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Chun Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Donald Gullickson
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Cheng-Hsun Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Marc J. Koyack
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yi-Jen Weng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Tzu-En Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Olivia Barrett
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
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Bhattacharjee N, Biswas P. Position-specific propensities of amino acids in the β-strand. BMC STRUCTURAL BIOLOGY 2010; 10:29. [PMID: 20920153 PMCID: PMC2955036 DOI: 10.1186/1472-6807-10-29] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/28/2010] [Indexed: 11/23/2022]
Abstract
Background Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated. Results The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands. Conclusions The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.
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15
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Surzhik MA, Churkina SV, Shmidt AE, Shvetsov AV, Kozhina TN, Firsov DL, Firsov LM, Petukhov MG. The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810020134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Thorvaldsen S, Ytterstad E. Environmental adaptation of proteins: regression models with simple physicochemical properties. Comput Biol Chem 2009; 33:351-6. [PMID: 19679511 DOI: 10.1016/j.compbiolchem.2009.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/01/2009] [Indexed: 10/20/2022]
Abstract
Bio-sequences from ortholog proteins are well suited for statistical inference when the sequences can be divided into ordinal groups based on known environmental features or traits of the host organisms. In this paper two new regression models are described for extracting proteomic trends of extreme environments. The approach is based on physicochemical properties of the amino acids, and may also utilise stratification of the data. We are especially looking for connections of temperature adaptation between the organism and its molecular level. To show the applicability of the methods, we present analyses of genomic data from proteobacteria orders, where we examine the cold adaptation of membrane proteins, intracellular proteins, and the enzyme endonuclease I. Our results confirm earlier findings that redistribution of charge and increase of surface hydrophobicity might be some of the most important signatures for cold adaptation.
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Affiliation(s)
- Steinar Thorvaldsen
- Department of Mathematics and Statistics, Faculty of Science, University of Tromsø, 9037 Tromsø, Norway.
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17
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Petukhov M, Tatsu Y, Tamaki K, Murase S, Uekawa H, Yoshikawa S, Serrano L, Yumoto N. Design of stable alpha-helices using global sequence optimization. J Pept Sci 2009; 15:359-65. [PMID: 19222027 DOI: 10.1002/psc.1122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The rational design of peptide and protein helices is not only of practical importance for protein engineering but also is a useful approach in attempts to improve our understanding of protein folding. Recent modifications of theoretical models of helix-coil transitions allow accurate predictions of the helix stability of monomeric peptides in water and provide new possibilities for protein design. We report here a new method for the design of alpha-helices in peptides and proteins using AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides and the tunneling algorithm of global optimization of multidimensional functions for optimization of amino acid sequences. CD measurements of helical content of peptides with optimized sequences indicate that the helical potential of protein amino acids is high enough to allow formation of stable alpha-helices in peptides as short as of 10 residues in length. The results show the maximum achievable helix content (HC) of short peptides with fully optimized sequences at 5 degrees C is expected to be approximately 70-75%. Under certain conditions the method can be a powerful practical tool for protein engineering. Unlike traditional approaches that are often used to increase protein stability by adding a few favorable interactions to the protein structure, this method deals with all possible sequences of protein helices and selects the best one from them.
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Affiliation(s)
- Michael Petukhov
- Petersburg Institute of Nuclear Physics, the Russian Academy of Sciences, 188300, Gatchina, Russia.
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18
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Fonseca NA, Camacho R, Magalhães AL. Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins 2008; 70:188-96. [PMID: 17654550 DOI: 10.1002/prot.21525] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A systematic survey was carried out in an unbiased sample of 815 protein chains with a maximum of 20% homology selected from the Protein Data Bank, whose structures were solved at a resolution higher than 1.6 A and with a R-factor lower than 25%. A set of 5556 subsequences with alpha-helix or 3(10)-helix motifs was extracted from the protein chains considered. Global and local propensities were then calculated for all possible amino acid pairs of the type (i, i + 1), (i, i + 2), (i, i + 3), and (i, i + 4), starting at the relevant helical positions N1, N2, N3, C3, C2, C1, and N-int (interior positions), and also at the first nonhelical positions in both termini of the helices, namely, N-cap and C-cap. The statistical analysis of the propensity values has shown that pairing is significantly dependent on the type of the amino acids and on the position of the pair. A few sequences of three and four amino acids were selected and their high prevalence in helices is outlined in this work. The Glu-Lys-Tyr-Pro sequence shows a peculiar distribution in proteins, which may suggest a relevant structural role in alpha-helices when Pro is located at the C-cap position. A bioinformatics tool was developed, which updates automatically and periodically the results and makes them available in a web site.
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Affiliation(s)
- Nuno A Fonseca
- IBMC and LIACC, R. Campo Alegre, 1021/1055, 4169-007 Porto, Portugal
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19
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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: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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20
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López-Llano J, Campos LA, Sancho J. Alpha-helix stabilization by alanine relative to glycine: roles of polar and apolar solvent exposures and of backbone entropy. Proteins 2006; 64:769-78. [PMID: 16755589 DOI: 10.1002/prot.21041] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The energetics of alpha-helix formation are fairly well understood and the helix content of a given amino acid sequence can be calculated with reasonable accuracy from helix-coil transition theories that assign to the different residues specific effects on helix stability. In internal helical positions, alanine is regarded as the most stabilizing residue, whereas glycine, after proline, is the more destabilizing. The difference in stabilization afforded by alanine and glycine has been explained by invoking various physical reasons, including the hydrophobic effect and the entropy of folding. Herein, the contribution of these two effects and that of hydrophilic area burial is evaluated by analyzing Ala and Gly mutants implemented in three helices of apoflavodoxin. These data, combined with available data for similar mutations in other proteins (22 Ala/Gly mutations in alpha-helices have been considered), allow estimation of the difference in backbone entropy between alanine and glycine and evaluation of its contribution and that of apolar and polar area burial to the helical stabilization typically associated to Gly-->Ala substitutions. Alanine consistently stabilizes the helical conformation relative to glycine because it buries more apolar area upon folding and because its backbone entropy is lower. However, the relative contribution of polar area burial (which is shown to be destabilizing) and of backbone entropy critically depends on the approximation used to model the structure of the denatured state. In this respect, the excised-peptide model of the unfolded state, proposed by Creamer and coworkers (1995), predicts a major contribution of polar area burial, which is in good agreement with recent quantitations of the relative enthalpic contribution of Ala and Gly residues to alpha-helix formation.
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Affiliation(s)
- J López-Llano
- Departamento de Bioquímica y Biología Molecular y Celular & Biocomputation and Complex Systems Physics Institute BIFI, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
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21
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López-Llano J, Campos LA, Bueno M, Sancho J. Equilibrium Φ-Analysis of a Molten Globule: The 1-149 Apoflavodoxin Fragment. J Mol Biol 2006; 356:354-66. [PMID: 16364364 DOI: 10.1016/j.jmb.2005.10.086] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 10/27/2005] [Accepted: 10/28/2005] [Indexed: 11/19/2022]
Abstract
The apoflavodoxin fragment comprising residues 1-149 that can be obtained by chemical cleavage of the C-terminal alpha-helix of the full-length protein is known to populate a molten globule conformation that displays a cooperative behaviour and experiences two-state urea and thermal denaturation. Here, we have used a recombinant form of this fragment to investigate molten globule energetics and to derive structural information by equilibrium Phi-analysis. We have characterized 15 mutant fragments designed to probe the persistence of native interactions in the molten globule and compared their conformational stability to that of the equivalent full-length apoflavodoxin mutants. According to our data, most of the mutations analysed modify the stability of the molten globule fragment following the trend observed when the same mutations are implemented in the full-length protein. However, the changes in stability observed in the molten globule are much smaller and the Phi-values calculated are (with a single exception) below 0.4. This is consistent with an overall and significant debilitation of the native structure. Nevertheless, the fact that the molten globule fragment can be stabilised using as a guide the native structure of the full-length protein (by increasing helix propensity, optimising charge interactions and filling small cavities) suggests that the overall structure of the molten globule is still quite close to native, in spite of the lowered stability observed.
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Affiliation(s)
- J López-Llano
- Dep. Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Biocomputation and Complex Systems Physics Institute-BIFI, University of Zaragoza, Spain
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22
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Wieczorek R, Dannenberg JJ. The Energetic and Structural Effects of Single Amino Acid Substitutions upon Capped α-Helical Peptides Containing 17 Amino Acid Residues. An ONIOM DFT/AM1 Study. J Am Chem Soc 2005; 127:17216-23. [PMID: 16332068 DOI: 10.1021/ja052689j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluate the effect of the amino acid mutations of glycine, leucine, valine, phenylalanine, serine, and proline for the 10th alanine in the capped peptide, acetly(Ala)(17)NH(2), upon the energies of the alpha-helices and beta-strands using ONIOM DFT/AM1 molecular orbital calculations. The relative stabilities of the alpha-helix (to the beta-strand) derive from the differences between the effects upon not only the helix but the strand as well. Thus, Ala --> Pro significantly destabilizes both but destabilizes the alpha-helix more, while Ala --> Gly stabilizes both but stabilizes the beta-strand more. The theoretical results are discussed in the context of the known experimental reports. We suggest that the solvation of the unfolded state drives the helix/coil equilibrium in solution.
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Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA
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23
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Regis WCB, Fattori J, Santoro MM, Jamin M, Ramos CHI. On the difference in stability between horse and sperm whale myoglobins. Arch Biochem Biophys 2005; 436:168-77. [PMID: 15752722 DOI: 10.1016/j.abb.2005.01.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 01/19/2005] [Indexed: 11/16/2022]
Abstract
The work in the literature on apomyoglobin is almost equally divided between horse and sperm whale myoglobins. The two proteins share high homology, show similar folding behavior, and it is often assumed that all folding phenomena found with one protein will also be found with the other. We report data at equilibrium showing that horse myoglobin was 2.1 kcal/mol less stable than sperm whale myoglobin at pH 5.0, and aggregated at high concentrations as measured by gel filtration and analytical ultracentrifugation experiments. The higher stability of sperm whale myoglobin was identified for both apo and holo forms, and was independent of pH from 5 to 8 and of the presence of sodium chloride. We also show that the substitution of sperm whale myoglobin residues Ala15 and Ala74 to Gly, the residues found at positions 15 and 74 in horse myoglobin, decreased the stability by 1.0 kcal/mol, indicating that helix propensity is an important component of the explanation for the difference in stability between the two proteins.
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Affiliation(s)
- Wiliam C B Regis
- Centro de Biologia Molecular Estrutural, Laboratório Nacional de Luz Síncrotron, P.O. Box 6192, ZIP Code 13084971, Campinas SP, Brazil
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24
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Iqbalsyah TM, Doig AJ. Pairwise Coupling in an Arg-Phe-Met Triplet Stabilizes α-Helical Peptide via Shared Rotamer Preferences. J Am Chem Soc 2005; 127:5002-3. [PMID: 15810818 DOI: 10.1021/ja043446e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrophobic Arg-Phe and Phe-Met side chain interactions stabilize the alpha-helix by -0.29 and -0.59 kcal/mol, respectively, when placed i, i + 4 in an alanine-based peptide. When both interactions are present simultaneously, however, they stabilize the helix by an additional -0.75 kcal/mol, nearly as much as the sum of its parts. We attribute this coupling to a shared rotamer preference, as the central Phe is t in both bonds. The energetic cost of restricting the Phe residue into a t conformation is only paid once in the triplet, rather than twice when the interactions are separate. Coupling is thus demonstrated to have large effects on protein stability.
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Affiliation(s)
- Teuku M Iqbalsyah
- Faculty of Life Sciences, Jackson's Mill, The University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, UK
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25
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Ho BK, Thomas A, Brasseur R. Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. Protein Sci 2004; 12:2508-22. [PMID: 14573863 PMCID: PMC2366959 DOI: 10.1110/ps.03235203] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
What determines the shape of the allowed regions in the Ramachandran plot? Although Ramachandran explained these regions in terms of 1-4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the alphaR, alphaL, and beta-strand regions are diagonal. The alphaR-region also varies along the alpha-helix where it is constrained at the center and the amino terminus but diffuse at the carboxyl terminus. By analyzing a high-resolution database of protein structures, we find that certain 1-4 hard-sphere repulsions in the standard steric map of Ramachandran do not affect the statistical distributions. By ignoring these steric clashes (NH(i+1) and O(i-1)C), we identify a revised set of steric clashes (CbetaO, O(i-1)N(i+1), CbetaN(i+1), O(i-1)Cbeta, and O(i-1)O) that produce a better match with the data. We also find that the strictly forbidden region in the Ramachandran plot is excluded by multiple steric clashes, whereas the outlier region is excluded by only one significant steric clash. However, steric clashes alone do not account for the diagonal regions. Using electrostatics to analyze the conformational dependence of specific interatomic interactions, we find that the diagonal shape of the alphaR and alphaL-regions also depends on the optimization of the NH(i+1) and O(i-1)C interactions, and the diagonal beta-strand region is due to the alignment of the CO and NH dipoles. Finally, we reproduce the variation of the Ramachandran plot along the alpha-helix in a simple model that uses only H-bonding constraints. This allows us to rationalize the difference between the amino terminus and the carboxyl terminus of the alpha-helix in terms of backbone entropy.
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Affiliation(s)
- Bosco K Ho
- Centre de Biophysique Moléculaire Numérique (CBMN), B-5030 Gembloux, Belgium.
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26
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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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27
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Ermolenko DN, Richardson JM, Makhatadze GI. Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. Protein Sci 2003; 12:1169-76. [PMID: 12761387 PMCID: PMC2323897 DOI: 10.1110/ps.0304303] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2003] [Revised: 03/20/2003] [Accepted: 03/20/2003] [Indexed: 10/27/2022]
Abstract
It was established previously that helical propensities of different amino acid residues in the middle of alpha-helix in peptides and in proteins are very similar. The statistical analysis of the protein helices from the known three-dimensional structures shows no difference in the frequency of noncharged residues in the middle and at the C terminus. Yet, experimental studies show distinctive differences for the helical propensities of noncharged residues in the middle and in the C terminus in model peptides. Is this a general effect, and is it applicable to protein helices or is it specific to the model alanine-based peptides? To answer this question, the effects of substitutions at positions 28 (middle residue) and 32 (C2 position at the C terminus) of the alpha-helix of ubiquitin on the stability of this protein are measured by using differential scanning calorimetry. The two data sets produce similar values for intrinsic helix propensity, leading to a conclusion that noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. This conclusion is further supported with an excellent correlation between the helix propensity scale obtained for the two positions in ubiquitin with the experimental helix propensity scale established previously and with the statistical distribution of the residues in protein helices.
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Affiliation(s)
- Dmitri N Ermolenko
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
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28
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Andrew CD, Bhattacharjee S, Kokkoni N, Hirst JD, Jones GR, Doig AJ. Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism. J Am Chem Soc 2002; 124:12706-14. [PMID: 12392418 DOI: 10.1021/ja027629h] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.
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Affiliation(s)
- Charles D Andrew
- Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, UK
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29
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Butterfield SM, Patel PR, Waters ML. Contribution of aromatic interactions to alpha-helix stability. J Am Chem Soc 2002; 124:9751-5. [PMID: 12175233 DOI: 10.1021/ja026668q] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of natural and unnatural i, i + 4 aromatic side chain-side chain interactions on alpha-helix stability was determined in Ala-Lys host peptides by circular dichroism (CD). All interactions investigated provided some stability to the helix; however, phenylalanine-phenylalanine (F-F) and phenylalanine-pentafluorophenylalanine (F-f5F) interactions resulted in the greatest enhancement in helicity, doubling the helical content over i, i + 5 control peptides at internal positions. Quantification of these interactions using AGADIR multistate helix-coil algorithm revealed that the F-F and F-f5F interaction energies are equivalent at internal positions in the sequence (deltaGF-F = deltaGF-f5F = -0.27 kcal/mol), despite the differences in their expected geometries. As the strength of a face-to-face stacked phenyl-pentafluorophenyl interaction should surpass an edge-to-face or offset-stacked phenyl-phenyl interaction, we believe this result reflects the inability of the side chains in F-f5F to attain a fully stacked geometry within the context of an alpha-helix. Positioning the interactions at the C-terminus led to much stronger interactions (deltaGF-F = -0.8 kcal/mol; deltaGF-f5F = -0.55 kcal/mol) likely because of favorable chi(1) rotameric preferences for aromatic residues at C-capping regions of alpha-helices, suggesting that aromatic side chain-side chain interactions are an effective alpha-helix C-capping method.
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Affiliation(s)
- Sara M Butterfield
- Department of Chemistry, UNC Chapel Hill, Venable and Kenan Laboratories, CB 3290, Chapel Hill, North Carolina 27599, USA
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