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Minute F, Hellmann N, Spinozzi F, Ortore MG, Di Muro P, Bubacco L, Beltramini M. Entrapment and characterization of functional allosteric conformers of hemocyanin in sol–gel matrices. RSC Adv 2016. [DOI: 10.1039/c5ra26377h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Entrapment of hemocyanin in sol–gel stabilizes conformations scarcely populated in solution, allowing for their structural and functional analysis.
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Affiliation(s)
- Fabrizio Minute
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Nadja Hellmann
- Institute for Molecular Biophysics
- University of Mainz
- Mainz
- Germany
| | - Francesco Spinozzi
- Department DISVA
- Marche Polytechnic University and CNISM
- I-60131 Ancona
- Italy
| | | | - Paolo Di Muro
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Luigi Bubacco
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
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2
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Kuo HT, Yang PA, Wang WR, Hsu HC, Wu CH, Ting YT, Weng MH, Kuo LH, Cheng RP. Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids. Amino Acids 2014; 46:1867-83. [DOI: 10.1007/s00726-014-1737-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/21/2014] [Indexed: 01/29/2023]
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3
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Cheng RP, Wang WR, Girinath P, Yang PA, Ahmad R, Li JH, Hart P, Kokona B, Fairman R, Kilpatrick C, Argiros A. Effect of Glutamate Side Chain Length on Intrahelical Glutamate–Lysine Ion Pairing Interactions. Biochemistry 2012; 51:7157-72. [DOI: 10.1021/bi300655z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- 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, United States
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Raheel Ahmad
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Jhe-Hao Li
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Casey Kilpatrick
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Annmarie Argiros
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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4
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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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5
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Murza A, Kubelka J. Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides. Biopolymers 2009; 91:120-31. [PMID: 18814306 DOI: 10.1002/bip.21093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adrian Murza
- Chemistry Department, University of Wyoming, Laramie, 82072, USA
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6
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Hong L. A statistical mechanical model for antiparallel β-sheet/coil equilibrium. J Chem Phys 2008; 129:225101. [DOI: 10.1063/1.3028635] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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7
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Hong L, Lei J. Statistical mechanical model for helix-sheet-coil transitions in homopolypeptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:051904. [PMID: 19113152 DOI: 10.1103/physreve.78.051904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Indexed: 05/27/2023]
Abstract
In this paper, we propose a simple statistical mechanical model to study the conformation transition between the alpha helix, beta sheet, and random coil in homopolypeptides. In our model, five parameters are introduced to obtain the partition function. There are two factors for helical propagation and initiation, which are the same as those used in the Zimm-Bragg model, and three newly introduced parameters for beta structures: the strand propagation factor for residues in beta strands and two correction factors for the initiation effect of the beta strand and beta sheet. Our model shows that the variation of these parameters may induce conformation transition from alpha helix or random coil to beta sheet. The sharpness of the transition depends on the initiation factors.
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Affiliation(s)
- Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, People's Republic of China, 100084.
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8
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Stability and Design of α-Helical Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:1-52. [DOI: 10.1016/s0079-6603(08)00601-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Abstract
Peptide helices in solution form a complex mixture of all helix, all coil or, most frequently, central helices with frayed coil ends. In order to interpret experiments on helical peptides and make theoretical predictions on helices, it is therefore essential to use a helix-coil theory that takes account of this equilibrium. The original Zimm-Bragg and Lifson-Roig helix-coil theories have been greatly extended in the last 10 years to include additional interactions. These include preferences for the N-cap, N1, N2, N3 and C-cap positions, capping motifs, helix dipoles, side chain interactions and 3(10)-helix formation. These have been applied to determine energies for these preferences from experimental data and to predict the helix contents of peptides. This review discusses these newly recognised structural features of helices and how they have been included in helix-coil models.
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Affiliation(s)
- Andrew J Doig
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK.
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Parthasarathy R, Chaturvedi S, Go K. Design of alpha-helical peptides: their role in protein folding and molecular biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1995; 64:1-54. [PMID: 8868522 DOI: 10.1016/0079-6107(95)00009-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- R Parthasarathy
- Biophysics Department, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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12
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Abstract
The folding/unfolding transition of proteins is a highly co-operative process characterized by the presence of very few or no thermodynamically stable partially folded intermediate states. The purpose of this paper is to present a thermodynamic formalism aimed at describing quantitatively the co-operative folding behavior of proteins. In order to account for this behavior, a hierarchical algorithm aimed at evaluating the folding/unfolding partition function has been developed. This formalism defines the partition function in terms of multiple levels of interacting co-operative folding units. A co-operative folding unit is defined as a protein structural element that exhibits two-state folding/unfolding behavior. At the most fundamental level are those structural elements that behave co-operatively as a result of purely local interactions. Higher-order co-operative folding units are formed through interactions between different structural elements. The hierarchical formalism utilizes the crystallographic structure of the protein as a template to generate partially folded conformations defined in terms of co-operative folding units. The Gibbs free energy of those states and their corresponding statistical weights are then computed using experimental energetic parameters determined calorimetrically. This formalism has been applied to the case of myoglobin. It is shown that the hierarchical partition function correctly predicts the presence, energetics and co-operativity of the heat and cold denaturation transitions. The major contribution to the co-operative folding behavior arises from the solvent exposure of non-polar residues located in regions complementary to those that have undergone unfolding. This entropically uncompensated and energetically unfavorable solvent exposure characterizes all partially folded states but not the unfolded state, thus minimizing the population of partially folded intermediates throughout the folding/unfolding transition.
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Affiliation(s)
- E Freire
- Department of Biology and Biocalorimetry Center, Johns Hopkins University, Baltimore, MD 21218
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