1
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Klukowski P, Damberger FF, Allain FHT, Iwai H, Kadavath H, Ramelot TA, Montelione GT, Riek R, Güntert P. The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis. Sci Data 2024; 11:30. [PMID: 38177162 PMCID: PMC10767026 DOI: 10.1038/s41597-023-02879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
Multidimensional NMR spectra are the basis for studying proteins by NMR spectroscopy and crucial for the development and evaluation of methods for biomolecular NMR data analysis. Nevertheless, in contrast to derived data such as chemical shift assignments in the BMRB and protein structures in the PDB databases, this primary data is in general not publicly archived. To change this unsatisfactory situation, we present a standardized set of solution NMR data comprising 1329 2-4-dimensional NMR spectra and associated reference (chemical shift assignments, structures) and derived (peak lists, restraints for structure calculation, etc.) annotations. With the 100-protein NMR spectra dataset that was originally compiled for the development of the ARTINA deep learning-based spectra analysis method, 100 protein structures can be reproduced from their original experimental data. The 100-protein NMR spectra dataset is expected to help the development of computational methods for NMR spectroscopy, in particular machine learning approaches, and enable consistent and objective comparisons of these methods.
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Affiliation(s)
- Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Fred F Damberger
- Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Hideo Iwai
- Institute of Biotechnology, University of Helsinki, 00100, Helsinki, Finland
| | | | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
- Institute of Biophysical Chemistry, Goethe University, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, 192-0397, Tokyo, Japan.
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2
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Braun V, Ratliff AC, Celia H, Buchanan SK. Energization of Outer Membrane Transport by the ExbB ExbD Molecular Motor. J Bacteriol 2023; 205:e0003523. [PMID: 37219427 PMCID: PMC10294619 DOI: 10.1128/jb.00035-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The outer membranes (OM) of Gram-negative bacteria contain a class of proteins (TBDTs) that require energy for the import of nutrients and to serve as receptors for phages and protein toxins. Energy is derived from the proton motif force (pmf) of the cytoplasmic membrane (CM) through the action of three proteins, namely, TonB, ExbB, and ExbD, which are located in the CM and extend into the periplasm. The leaky phenotype of exbB exbD mutants is caused by partial complementation by homologous tolQ tolR. TonB, ExbB, and ExbD are genuine components of an energy transmission system from the CM into the OM. Mutant analyses, cross-linking experiments, and most recently X-ray and cryo-EM determinations were undertaken to arrive at a model that describes the energy transfer from the CM into the OM. These results are discussed in this paper. ExbB forms a pentamer with a pore inside, in which an ExbD dimer resides. This complex harvests the energy of the pmf and transmits it to TonB. TonB interacts with the TBDT at the TonB box, which triggers a conformational change in the TBDT that releases bound nutrients and opens the pore, through which nutrients pass into the periplasm. The structurally altered TBDT also changes the interactions of its periplasmic signaling domain with anti-sigma factors, with the consequence being that the sigma factors initiate transcription.
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Affiliation(s)
- Volkmar Braun
- Max-Planck-Institute for Biology, Department of Protein Evolution, Tübingen, Germany
| | - Anna C. Ratliff
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
| | - Herve Celia
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Maryland, Bethesda, USA
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3
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Hu L, Zhao L, Zhuang Z, Wang X, Fu Q, Huang H, Lin L, Huang L, Qin Y, Zhang J, Yan Q. The Effect of tonB Gene on the Virulence of Pseudomonas plecoglossicida and the Immune Response of Epinephelus coioides. Front Microbiol 2021; 12:720967. [PMID: 34484162 PMCID: PMC8415555 DOI: 10.3389/fmicb.2021.720967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/21/2021] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas plecoglossicida is the causative agent of "visceral white spot disease" in cultured fish and has resulted in serious economic losses. tonB gene plays a crucial role in the uptake of nutrients from the outer membranes in Gram-negative bacteria. The previous results of our lab showed that the expression of tonB gene of P. plecoglossicida was significantly upregulated in the spleens of infected Epinephelus coioides. To explore the effect of tonB gene on the virulence of P. plecoglossicida and the immune response of E. coioides, tonB gene of P. plecoglossicida was knocked down by RNAi; and the differences between the wild-type strain and the tonB-RNAi strain of P. plecoglossicida were investigated. The results showed that all of the four mutants of P. plecoglossicida exhibited significant decreases in mRNA of tonB gene, and the best knockdown efficiency was 94.0%; the survival rate of E. coioides infected with the tonB-RNAi strain was 20% higher than of the counterpart infected with the wild strain of P. plecoglossicida. Meanwhile, the E. coioides infected with the tonB-RNAi strain of P. plecoglossicida carried less pathogens in the spleen and less white spots on the surface of the spleen; compared with the wild-type strain, the motility, chemotaxis, adhesion, and biofilm formation of the tonB-RNAi strain were significantly attenuated; the transcriptome data of E. coioides infected with the tonB-RNAi strain were different from the counterpart infected with the wild strain of P. plecoglossicida; the antigen processing and presentation pathway and the complement and coagulation cascade pathway were the most enriched immune pathways. The results indicated that tonB was a virulence gene of P. plecoglossicida; tonB gene was involved in the regulation of motility, chemotaxis, adhesion, and biofilm formation; tonB gene affected the immune response of E. coioides to P. plecoglossicida infection.
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Affiliation(s)
- Lingfei Hu
- Fisheries College, Jimei University, Xiamen, China
| | - Lingmin Zhao
- Fisheries College, Jimei University, Xiamen, China
| | - Zhixia Zhuang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Xiaoru Wang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Qi Fu
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Huabin Huang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Lili Lin
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Lixing Huang
- Fisheries College, Jimei University, Xiamen, China
| | - Yingxue Qin
- Fisheries College, Jimei University, Xiamen, China
| | - Jiaonan Zhang
- Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, China
| | - Qingpi Yan
- Fisheries College, Jimei University, Xiamen, China.,College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China.,Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, China
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4
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Morin CD, Déziel E, Gauthier J, Levesque RC, Lau GW. An Organ System-Based Synopsis of Pseudomonas aeruginosa Virulence. Virulence 2021; 12:1469-1507. [PMID: 34180343 PMCID: PMC8237970 DOI: 10.1080/21505594.2021.1926408] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Driven in part by its metabolic versatility, high intrinsic antibiotic resistance, and a large repertoire of virulence factors, Pseudomonas aeruginosa is expertly adapted to thrive in a wide variety of environments, and in the process, making it a notorious opportunistic pathogen. Apart from the extensively studied chronic infection in the lungs of people with cystic fibrosis (CF), P. aeruginosa also causes multiple serious infections encompassing essentially all organs of the human body, among others, lung infection in patients with chronic obstructive pulmonary disease, primary ciliary dyskinesia and ventilator-associated pneumonia; bacteremia and sepsis; soft tissue infection in burns, open wounds and postsurgery patients; urinary tract infection; diabetic foot ulcers; chronic suppurative otitis media and otitis externa; and keratitis associated with extended contact lens use. Although well characterized in the context of CF, pathogenic processes mediated by various P. aeruginosa virulence factors in other organ systems remain poorly understood. In this review, we use an organ system-based approach to provide a synopsis of disease mechanisms exerted by P. aeruginosa virulence determinants that contribute to its success as a versatile pathogen.
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Affiliation(s)
- Charles D Morin
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Jeff Gauthier
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Roger C Levesque
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, US
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5
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Virtanen SI, Kiirikki AM, Mikula KM, Iwaï H, Ollila OHS. Heterogeneous dynamics in partially disordered proteins. Phys Chem Chem Phys 2021; 22:21185-21196. [PMID: 32929427 DOI: 10.1039/d0cp03473h] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance of disordered protein regions is increasingly recognized in biology, but their characterization remains challenging due to the lack of suitable experimental and theoretical methods. NMR experiments can detect multiple timescale dynamics and structural details of disordered protein regions, but their detailed interpretation is often difficult. Here we combine protein backbone 15N spin relaxation data with molecular dynamics (MD) simulations to detect not only heterogeneous dynamics of large partially disordered proteins but also their conformational ensembles. We observed that the rotational dynamics of folded regions in partially disordered proteins is dominated by similar rigid body rotation as in globular proteins, thereby being largely independent of flexible disordered linkers. Disordered regions, on the other hand, exhibit complex rotational motions with multiple timescales below ∼30 ns which are difficult to detect from experimental data alone, but can be captured by MD simulations. Combining MD simulations and backbone 15N spin relaxation data, measured applying segmental isotopic labeling with salt-inducible split intein, we resolved the conformational ensemble and dynamics of partially disordered periplasmic domain of TonB protein from Helicobacter pylori containing 250 residues. To demonstrate the universality of our approach, it was applied also to the partially disordered region of chicken Engrailed 2. Our results pave the way in understanding how TonB transfers energy from inner membrane to the outer membrane receptors in Gram-negative bacteria, as well as the function of other proteins with disordered domains.
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Affiliation(s)
- Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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6
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Ciragan A, Backlund SM, Mikula KM, Beyer HM, Samuli Ollila OH, Iwaï H. NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein. Front Chem 2020; 8:136. [PMID: 32266203 PMCID: PMC7098700 DOI: 10.3389/fchem.2020.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 11/22/2022] Open
Abstract
The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
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Affiliation(s)
- Annika Ciragan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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7
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Hoffmann F, Mulder FAA, Schäfer LV. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. J Chem Phys 2020; 152:084102. [DOI: 10.1063/1.5135379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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8
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Celia H, Noinaj N, Buchanan SK. Structure and Stoichiometry of the Ton Molecular Motor. Int J Mol Sci 2020; 21:E375. [PMID: 31936081 PMCID: PMC7014051 DOI: 10.3390/ijms21020375] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
The Ton complex is a molecular motor that uses the proton gradient at the inner membrane of Gram-negative bacteria to generate force and movement, which are transmitted to transporters at the outer membrane, allowing the entry of nutrients into the periplasmic space. Despite decades of investigation and the recent flurry of structures being reported by X-ray crystallography and cryoEM, the mode of action of the Ton molecular motor has remained elusive, and the precise stoichiometry of its subunits is still a matter of debate. This review summarizes the latest findings on the Ton system by presenting the recently reported structures and related reports on the stoichiometry of the fully assembled complex.
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Affiliation(s)
- Herve Celia
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA;
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA;
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA;
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9
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Fujita M, Mori K, Hara H, Hishiyama S, Kamimura N, Masai E. A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound. Commun Biol 2019; 2:432. [PMID: 31799434 PMCID: PMC6874591 DOI: 10.1038/s42003-019-0676-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
TonB-dependent receptors (TBDRs) mediate substrate-specific transport across the outer membrane, utilizing energy derived from the proton motive force transmitted from the TonB-ExbB-ExbD complex located in the inner membrane (TonB system). Although a number of TonB systems involved in the uptake of siderophores, vitamin B12 and saccharides have been identified, their involvement in the uptake and catabolism of aromatic compounds was previously unknown. Here, we show that the outer membrane transport of a biphenyl compound derived from lignin is mediated by the TonB system in a Gram-negative bacterium capable of degrading lignin-derived aromatic compounds, Sphingobium sp. strain SYK-6. Furthermore, we found that overexpression of the corresponding TBDR gene enhanced the uptake of this biphenyl compound, contributing to the improved rate of platform chemical production. Our results will provide an important basis for establishing engineered strains optimized for use in lignin valorisation.
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Affiliation(s)
- Masaya Fujita
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Kosuke Mori
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Hirofumi Hara
- 2Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Kuala Lumpur, Malaysia
| | - Shojiro Hishiyama
- 3Forestry and Forest Products Research Institute, Tsukuba, Ibaraki Japan
| | - Naofumi Kamimura
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
| | - Eiji Masai
- 1Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata Japan
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10
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Ollila OHS, Heikkinen HA, Iwaï H. Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations. J Phys Chem B 2018; 122:6559-6569. [PMID: 29812937 PMCID: PMC6150695 DOI: 10.1021/acs.jpcb.8b02250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Conformational
fluctuations and rotational tumbling of proteins
can be experimentally accessed with nuclear spin relaxation experiments.
However, interpretation of molecular dynamics from the experimental
data is often complicated, especially for molecules with anisotropic
shape. Here, we apply classical molecular dynamics simulations to
interpret the conformational fluctuations and rotational tumbling
of proteins with arbitrarily anisotropic shape. The direct calculation
of spin relaxation times from simulation data did not reproduce the
experimental data. This was successfully corrected by scaling the
overall rotational diffusion coefficients around the protein inertia
axes with a constant factor. The achieved good agreement with experiments
allowed the interpretation of the internal and overall dynamics of
proteins with significantly anisotropic shape. The overall rotational
diffusion was found to be Brownian, having only a short subdiffusive
region below 0.12 ns. The presented methodology can be applied to
interpret rotational dynamics and conformation fluctuations of proteins
with arbitrary anisotropic shape. However, a water model with more
realistic dynamical properties is probably required for intrinsically
disordered proteins.
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Affiliation(s)
- O H Samuli Ollila
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology , University of Helsinki , 00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , 117 20 Prague 6 , Czech Republic
| | - Harri A Heikkinen
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology , University of Helsinki , 00014 Helsinki , Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology , University of Helsinki , 00014 Helsinki , Finland
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