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Yeritsyan K, Valant M, Badasyan A. Processing helix–coil transition data: Account of chain length and solvent effects. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.982644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Numerous nanobiotechnologies include manipulations of short polypeptide chains. The conformational properties of these polypeptides are studied in vitro by circular dichroism and time-resolved infrared spectroscopy. To find out the interaction parameters, the measured temperature dependence of normalized helicity degree needs to be further processed by fitting to a model. Using recent advances in the Hamiltonian formulation of the classical Zimm and Bragg model, we explicitly include chain length and solvent effects in the theoretical description. The expression for the helicity degree we suggest successfully fits the experimental data and provides hydrogen bonding energies and nucleation parameter values within the standards in the field.
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins. Commun Chem 2021; 4:57. [PMID: 36697562 PMCID: PMC9814862 DOI: 10.1038/s42004-021-00499-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.
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Mansouri AL, Grese LN, Rowe EL, Pino JC, Chennubhotla SC, Ramanathan A, O'Neill HM, Berthelier V, Stanley CB. Folding propensity of intrinsically disordered proteins by osmotic stress. MOLECULAR BIOSYSTEMS 2016; 12:3695-3701. [PMID: 27752679 PMCID: PMC5363718 DOI: 10.1039/c6mb00512h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain α-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. By focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.
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Affiliation(s)
- Amanda L Mansouri
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA
| | - Laura N Grese
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Erica L Rowe
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - James C Pino
- Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Ramanathan
- Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh M O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Valerie Berthelier
- Department of Medicine, Graduate School of Medicine, University of Tennessee, Health Science Center, Knoxville, TN, USA
| | - Christopher B Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Ginzburg VV, Sammler RL, Huang W, Larson RG. Anisotropic self-assembly and gelation in aqueous methylcellulose-theory and modeling. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/polb.24065] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Valeriy V. Ginzburg
- The Dow Chemical Company, Core R&D, Materials Science; Midland Michigan 48674
| | - Robert L. Sammler
- The Dow Chemical Company, Core R&D, Materials Science; Midland Michigan 48674
| | - Wenjun Huang
- Department of Chemical Engineering; University of Michigan; Ann Arbor Michigan 48109
| | - Ronald G. Larson
- Department of Chemical Engineering; University of Michigan; Ann Arbor Michigan 48109
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Torosyan MA, Karapetian AT. Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters. J Biomol Struct Dyn 2016; 34:1377-82. [PMID: 26239502 DOI: 10.1080/07391102.2015.1079557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.
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Affiliation(s)
- Poghos O Vardevanyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Ara P Antonyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Marine A Parsadanyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Margarita A Torosyan
- b Department of Physics and Electric Engineering , National University of Architecture and Construction , Yerevan 0009 , Armenia
| | - Armen T Karapetian
- b Department of Physics and Electric Engineering , National University of Architecture and Construction , Yerevan 0009 , Armenia
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DeForte S, Reddy KD, Uversky VN. Quarterly intrinsic disorder digest (January-February-March, 2014). INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1153395. [PMID: 28232896 DOI: 10.1080/21690707.2016.1153395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Badasyan A, Mamasakhlisov YS, Podgornik R, Parsegian VA. Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins. J Chem Phys 2015; 143:014102. [DOI: 10.1063/1.4923292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Artem Badasyan
- Materials Research Laboratory, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia
| | - Yevgeni Sh. Mamasakhlisov
- Department of Molecular Physics, Yerevan State University, A. Manougian St. 1, 0025 Yerevan, Armenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA
| | - V. Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA
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Grigoryan ZA, Karapetyan AT. 142 The cold melting effect of complexes DNA with two different ligands using different binding mechanisms. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sapir L, Harries D. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions. J Chem Theory Comput 2015; 11:3478-90. [DOI: 10.1021/acs.jctc.5b00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Asatryan AV, Tonoyan SA, Mirtavoosi S, Mamasakhlisov YS, Morozov VF. 192 The helix-coil transition in two-component solvent in the frames of GMPC. Ligands effects on the characteristics of the transition. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Karapetian AT, Grigoryan ZA, Mamasakhlisov YS, Minasyants MV, Vardevanyan PO. Theoretical treatment of helix–coil transition of complexes DNA with two different ligands having different binding parameters. J Biomol Struct Dyn 2015; 34:201-5. [DOI: 10.1080/07391102.2015.1010584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Budkov YA, Kolesnikov AL, Georgi N, Kiselev MG. A statistical theory of cosolvent-induced coil-globule transitions in dilute polymer solution. J Chem Phys 2014; 141:014902. [DOI: 10.1063/1.4884958] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu. A. Budkov
- Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
| | - A. L. Kolesnikov
- Ivanovo State University, Ivanovo, Russia
- Institut für Nichtklassische Chemie e.V., Universitat Leipzig, Leipzig, Germany
| | - N. Georgi
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - M. G. Kiselev
- Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
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