• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4832241)   Today's Articles (5688)
For: Petukhov M, Uegaki K, Yumoto N, Serrano L. Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus. Protein Sci 2002;11:766-77. [PMID: 11910021 PMCID: PMC2373540 DOI: 10.1110/ps.2610102] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Number Cited by Other Article(s)
1
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]
2
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]
3
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]
4
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
5
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
6
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]
7
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]
8
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
9
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]
10
De novo design of stable α-helices. Methods Mol Biol 2014;1216:1-14. [PMID: 25213408 DOI: 10.1007/978-1-4939-1486-9_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
11
Mathieu S, Trinquier G. The -BF-NH- link as a peptide-bond surrogate. J Phys Chem B 2012;116:8863-72. [PMID: 22794798 DOI: 10.1021/jp304150p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
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]
13
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]
14
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]
15
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]
16
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]
17
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]
18
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]
19
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]
20
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]
21
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]
22
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]
23
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]
24
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]
25
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]
26
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]
27
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]
28
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]
29
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]
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA