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Nasedkin A, Davidsson J, Niemi AJ, Peng X. Solution x-ray scattering and structure formation in protein dynamics. Phys Rev E 2018; 96:062405. [PMID: 29347365 DOI: 10.1103/physreve.96.062405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 11/07/2022]
Abstract
We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jan Davidsson
- Department of Chemistry, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden
| | - Antti J Niemi
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Nordita, Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,Department of Physics and Astronomy, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.,School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China.,Laboratory of Physics of Living Matter, School of Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia¶
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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Liu J, Dai J, He J, Niemi AJ, Ilieva N. Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example. Phys Rev E 2017; 95:032406. [PMID: 28415220 DOI: 10.1103/physreve.95.032406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 01/08/2023]
Abstract
We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the Cα backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the Cα profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal α helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.
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Affiliation(s)
- Jiaojiao Liu
- School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jin Dai
- School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jianfeng He
- School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Antti J Niemi
- School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China.,Nordita, Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,Department of Physics and Astronomy, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.,Physics of Living Matter, School of Biomedicine, Far Eastern Federal University, Vladivostok 690950, Russia
| | - Nevena Ilieva
- Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, 25A, Acad. G. Bonchev Str., Sofia 1113, Bulgaria
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Peng X, Sieradzan AK, Niemi AJ. Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach. Phys Rev E 2016; 94:062405. [PMID: 28085346 DOI: 10.1103/physreve.94.062405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 11/07/2022]
Abstract
The Landau-Ginzburg-Wilson paradigm is applied to model the low-temperature crystallographic Cα backbone structure of sperm whale myoglobin. The Glauber protocol is employed to simulate its response to an increase in ambient temperature. The myoglobin is found to unfold from its native state by a succession of α-helical intermediates, fully in line with the observed folding and unfolding patterns in denaturation experiments. In particular, a molten globule intermediate is identified with experimentally correct attributes. A detailed, experimentally testable contact map is constructed to characterize the specifics of the unfolding pathway, including the formation of long-range interactions. The results reveal how the unfolding process of a protein is driven by the interplay between, and a successive melting of, its modular secondary structure components.
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Affiliation(s)
- Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Antti J Niemi
- Department of Physics and Astronomy, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.,Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081, People's Republic of China
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