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Pan Z, Mu J, Chen HF. Balanced Three-Point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins. J Chem Theory Comput 2023; 19:4837-4850. [PMID: 37452752 DOI: 10.1021/acs.jctc.3c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due to the inherent structural flexibility of IDPs, experimental methods present significant challenges for sampling their conformational information at the atomic level. Therefore, molecular dynamics (MD) simulations have emerged as the primary tools for modeling IDPs whose accuracy depend on force field and water model. To enhance the accuracy of physical modeling of IDPs, several force fields have been developed. However, current water models lack precision and underestimate the interaction between water molecules and proteins. Here, we used Monte-Carlo re-weighting method to re-parameterize a three-point water model based on OPC3 for IDPs (named OPC3-B). We benchmarked the performance of OPC3-B compared with nine different water models for 10 IDPs and three ordered proteins. The results indicate that the performance of OPC3-B is better than other water models for both IDPs and ordered proteins. At the same time, OPC3-B possess the power of transferability with other force field to simulate IDPs. This newly developed water model can be used to insight into the research of sequence-disordered-function paradigm for IDPs.
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Affiliation(s)
- Zhengsong Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Junxi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
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2
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Khechinashvili NN, Kondratyev MS, Polozov RV. Thermodynamics of globular protein native structure. J Biomol Struct Dyn 2022; 41:3218-3221. [PMID: 35345984 DOI: 10.1080/07391102.2022.2046637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The temperature dependence of the partial heat capacity of the native protein structure in an aqueous solution has been analyzed. It is shown that the strictly linear temperature dependence is due to the contributions of the vibrational and conformational components, which indicates volume consistensy and the absence of conformational transitions up to the main two-state transition. The two-level structural and functional organization of the protein three-dimensional structure are considered in relation to the energy and conformational entropy properties in accordance with the principles of the organization of the protein macromolecule.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Maxim S Kondratyev
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Robert V Polozov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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3
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Yang MJ, Kim J, Lee Y, Lee W, Park CJ. NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. Int J Mol Sci 2022; 23:ijms23063099. [PMID: 35328522 PMCID: PMC8954794 DOI: 10.3390/ijms23063099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
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4
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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5
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Mu J, Pan Z, Chen HF. Balanced Solvent Model for Intrinsically Disordered and Ordered Proteins. J Chem Inf Model 2021; 61:5141-5151. [PMID: 34546059 DOI: 10.1021/acs.jcim.1c00407] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) have no fixed three-dimensional (3D) structures under physiological conditions, with the content being about 51% in human proteomics. IDPs are associated with many human diseases, such as cancer, diabetes, and neurodegenerative diseases. Because IDPs do not crystallize and have diverse conformers, traditional experimental methods such as crystallization and NMR can hardly capture their conformation ensemble and just provide average structural characters of IDPs. Therefore, molecular dynamics (MD) simulations become a valuable complement to the experimental data. However, the accuracy of molecular dynamics simulation for IDPs depends on the combination of force fields and solvent models. Recently, we released an environment-specific force field (ESFF1) for IDPs, which can well reproduce the local structural properties (such as J-coupling and secondary chemical shifts). However, there is still a large deviation for the radius of gyration (Rg). Therefore, a solvent model combined with ESFF1 is necessary to capture the local and global characters for IDPs and ordered proteins. Here, we investigated the underestimation or overestimation of the solvent interaction for four solvent models (TIP3P, TIP4P-Ew, TIP4P-D, OPC) under ESFF1 and found the important ε parameter of the solvent model to play a key role in scaling Rg. A near-linear relationship between the simulation Rg and the ε parameter was used to develop the new solvent model, named TIP4P-B. The results indicate that the simulated Rg with TIP4P-B is in better agreement with the experimental observations than the other four solvent models. Simultaneously, TIP4P-B can also maintain the advantages of the ESFF1 force field for the local structural properties. Additionally, TIP4P-B can successfully sample the conformation of ordered proteins. These findings confirm that TIP4P-B is a balanced solvent model and can improve sampling Rg performance for folded proteins and IDPs.
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Affiliation(s)
- Junxi Mu
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhengsong Pan
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,MD Program, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai 200235, China
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6
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Qiu Y, Shan W, Zhang H. Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions. J Chem Inf Model 2021; 61:3571-3582. [PMID: 34185520 DOI: 10.1021/acs.jcim.1c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Classical protein force fields were reported with too weak protein-water interactions relative to protein-protein interactions, leading to more compact structures and artificial protein aggregation. Here we investigated the impacts of scaled Lennard-Jones (LJ) interactions on the hydration of amino acids and the simulation of folded and intrinsically disordered proteins (IDPs). The obtained optimal scaling parameters reproduce accurately hydration free energies of neutral amino acid side chain analogues and do not affect the compactness and structural stability of folded proteins significantly. The scaling leads to less compact IDPs and varies from case to case. Strengthening the interactions between protein and water oxygen or hydrogen atoms by increasing the interacting LJ well depth (ε) appears more effective than weakening protein-protein interactions by reducing the interacting dispersion coefficients (C6). We demonstrate that weakening water-water interactions is a solution as well to obtaining more favorable protein-water interactions in an indirect way, although modern force fields like Amber ff19SB and a99SB-disp tend to use water models with strong water-water interactions. This is likely a compromise between strong protein-protein interactions and strong water-water interactions. Independent optimization of protein force fields and water models is therefore needed to make both interactions more close to reality, leading to good accuracy without bias or scaling.
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Affiliation(s)
- Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Wenjie Shan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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7
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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8
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Overbeck JH, Kremer W, Sprangers R. A suite of 19F based relaxation dispersion experiments to assess biomolecular motions. JOURNAL OF BIOMOLECULAR NMR 2020; 74:753-766. [PMID: 32997265 PMCID: PMC7701166 DOI: 10.1007/s10858-020-00348-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/18/2020] [Indexed: 05/08/2023]
Abstract
Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1ρ and off-resonance R1ρ RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.
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Affiliation(s)
- Jan H Overbeck
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Werner Kremer
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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9
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Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. Malar J 2020; 19:382. [PMID: 33109193 PMCID: PMC7592540 DOI: 10.1186/s12936-020-03448-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.
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10
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von König K, Kachel N, Kalbitzer HR, Kremer W. RNA and DNA Binding Epitopes of the Cold Shock Protein TmCsp from the Hyperthermophile Thermotoga maritima. Protein J 2020; 39:487-500. [PMID: 33094361 PMCID: PMC7704496 DOI: 10.1007/s10930-020-09929-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
Prokaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At “physiological” growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) μM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises β-strands 1 and 2, the loop β1–β2 as well as the loops connecting β3 with β4 and β4 with β5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.
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Affiliation(s)
- Konstanze von König
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany
| | - Norman Kachel
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany.
| | - Werner Kremer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany.
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11
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Rahman MU, Rehman AU, Liu H, Chen HF. Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins. J Chem Inf Model 2020; 60:4912-4923. [PMID: 32816485 DOI: 10.1021/acs.jcim.0c00762] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics (MD) simulations of six upgraded empirical force fields were compared and evaluated with short peptides, intrinsically disordered proteins, and folded proteins using trajectories of 1, 1.5, 5, or 10 μs (five replicates of 200 ns, 300 ns, 1 μs, or 2 μs) for each system. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. Here, the MD simulations were done in an explicit solvent with RS-peptide, HEWL19, HIV-rev, β amyloid (Aβ)-40, Aβ-42, phosphodiesterase-γ, CspTm, and ubiquitin using ff99IDPs, ff14IDPs, ff14IDPSFF, ff03w, CHARMM36m, and CHARMM22* force fields. The IDP ensembles generated by six all-atom empirical force fields were compared against NMR data. Despite using identical starting structures and simulation parameters, ensembles obtained with different force fields exhibit significant differences in NMR RMDs, secondary structure contents, and global properties such as the radius of gyration. The intrinsically disordered protein (IDP)-specific force fields could substantially reproduce the experimental observables in force field comparison: they have the lowest error in chemical shifts and J-couplings for short peptides/proteins, reasonably well for large IDPs and reasonably well with the radius of gyration. A high population of disorderness was observed in the IDP-specific force field for the IDP ensemble with a fraction of β sheets for β-amyloids. CHARMM22* performs better for many observables; however, it still has a preference toward the helicity for short peptides. The results of β-amyloid 42 starting from two different initial structures (Aβ421Z0Q and Aβ42model) were also compared with DSSP and NMR data. The results obtained with IDP-specific force fields within 2 μs simulation time are similar, even though starting from different structures. The current force fields perform equally well for folded proteins. The results of currently developed or modified force fields for IDPs are capable of enlightening the overall performance of the force field for disordered as well as folded proteins, thereby contributing to force field development.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai 200235, China
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12
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Reinartz I, Weiel M, Schug A. FRET Dyes Significantly Affect SAXS Intensities of Proteins. Isr J Chem 2020. [DOI: 10.1002/ijch.202000007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ines Reinartz
- Institute for Automation and Applied InformaticsKarlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- HIDSS4Health – Helmholtz Information and Data Science School for Health Karlsruhe/Heidelberg Germany
| | - Marie Weiel
- Department of PhysicsKarlsruhe Institute of Technology Wolfgang-Gaede-Str. 1 76131 Karlsruhe Germany
- Steinbuch Centre for ComputingKarlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Alexander Schug
- Institute for Advanced Simulation Jülich Supercomputing Center Wilhelm-Johnen-Straße 52428 Jülich Germany
- Faculty of BiologyUniversity of Duisburg-Essen Germany
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13
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Budkina KS, Zlobin NE, Kononova SV, Ovchinnikov LP, Babakov AV. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. BIOCHEMISTRY (MOSCOW) 2020; 85:S1-S19. [DOI: 10.1134/s0006297920140011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Ferreira PHB, Freitas FC, McCully ME, Slade GG, de Oliveira RJ. The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. J Chem Inf Model 2020; 60:546-561. [PMID: 31910002 DOI: 10.1021/acs.jcim.9b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding which aspects contribute to the thermostability of proteins is a challenge that has persisted for decades, and it is of great relevance for protein engineering. Several types of interactions can influence the thermostability of a protein. Among them, the electrostatic interactions have been a target of particular attention. Aiming to explore how this type of interaction can affect protein thermostability, this paper investigated four homologous cold shock proteins from psychrophilic, mesophilic, thermophilic, and hyperthermophilic organisms using a set of theoretical methodologies. It is well-known that electrostatics as well as hydrophobicity are key-elements for the stabilization of these proteins. Therefore, both interactions were initially analyzed in the native structure of each protein. Electrostatic interactions present in the native structures were calculated with the Tanford-Kirkwood model with solvent accessibility, and the amount of hydrophobic surface area buried upon folding was estimated by measuring both folded and extended structures. On the basis of Energy Landscape Theory, the local frustration and the simplified alpha-carbon structure-based model were modeled with a Debye-Hückel potential to take into account the electrostatics and the effects of an implicit solvent. Thermodynamic data for the structure-based model simulations were collected and analyzed using the Weighted Histogram Analysis and Stochastic Diffusion methods. Kinetic quantities including folding times, transition path times, folding routes, and Φ values were also obtained. As a result, we found that the methods are able to qualitatively infer that electrostatic interactions play an important role on the stabilization of the most stable thermophilic cold shock proteins, showing agreement with the experimental data.
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Affiliation(s)
- Paulo Henrique Borges Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Michelle E McCully
- Department of Biology , Santa Clara University , Santa Clara , California 95050 , United States
| | - Gabriel Gouvêa Slade
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , Minas Gerais 38064200 , Brazil
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15
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Freitas FC, Lima AN, Contessoto VDG, Whitford PC, Oliveira RJD. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. J Chem Phys 2019; 151:114106. [DOI: 10.1063/1.5113499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Angelica Nakagawa Lima
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Vinícius de Godoi Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
- Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, SP, Brazil
| | - Paul C. Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
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16
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Lee Y, Kwak C, Jeong KW, Durai P, Ryu KS, Kim EH, Cheong C, Ahn HC, Kim HJ, Kim Y. Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein. Biochemistry 2018; 57:3625-3640. [PMID: 29737840 DOI: 10.1021/acs.biochem.8b00144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Although Cp-Csp shares sequence homology, common folding patterns, and motifs, including a five β-stranded barrel, with its thermophilic counterparts, its thermostability (37 °C) was markedly lower than those of other Csps. Cp-Csp binds heptathymidine with an affinity of 10-7 M, thereby increasing its thermostability to 50 °C. Nuclear magnetic resonance spectroscopic analysis of the Cp-Csp structure and backbone dynamics revealed a flexible structure with only one salt bridge and 10 residues in the hydrophobic cavity. Notably, Cp-Csp contains Tyr51 instead of the conserved Phe in the hydrophobic core, and its phenolic hydroxyl group projects toward the surface. The Y51F mutation increased the stability of hydrophobic packing and may have allowed for the formation of a K3-E21 salt bridge, thereby increasing its thermostability to 43 °C. Cp-Csp exhibited conformational exchanges in its ribonucleoprotein motifs 1 and 2 (754 and 642 s-1), and heptathymidine binding markedly decreased these motions. Cp-Csp lacks salt bridges and has longer flexible loops and a less compact hydrophobic cavity resulting from Tyr51 compared to mesophilic and thermophilic Csps. These might explain the low thermostability of Cp-Csp. The conformational flexibility of Cp-Csp facilitates its accommodation of nucleic acids at low temperatures in polar oceans and its function as an RNA chaperone for cold adaptation.
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Affiliation(s)
- Yeongjoon Lee
- Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea
| | - Chulhee Kwak
- Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea
| | - Ki-Woong Jeong
- Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea
| | - Prasannavenkatesh Durai
- Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance , KBSI , Chungbuk 28119 , Republic of Korea
| | - Eun-Hee Kim
- Division of Magnetic Resonance , KBSI , Chungbuk 28119 , Republic of Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance , KBSI , Chungbuk 28119 , Republic of Korea
| | - Hee-Chul Ahn
- College of Pharmacy , Dongguk University , Goyang , Gyeonggi-do 410-820 , Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry , Pukyong National University , Busan 48547 , Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea
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17
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Reinartz I, Sinner C, Nettels D, Stucki-Buchli B, Stockmar F, Panek PT, Jacob CR, Nienhaus GU, Schuler B, Schug A. Simulation of FRET dyes allows quantitative comparison against experimental data. J Chem Phys 2018; 148:123321. [DOI: 10.1063/1.5010434] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ines Reinartz
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Claude Sinner
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Florian Stockmar
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Pawel T. Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
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18
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Caruso IP, Panwalkar V, Coronado MA, Dingley AJ, Cornélio ML, Willbold D, Arni RK, Eberle RJ. Structure and interaction of Corynebacterium pseudotuberculosis cold shock protein A with Y-box single-stranded DNA fragment. FEBS J 2017; 285:372-390. [PMID: 29197185 DOI: 10.1111/febs.14350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/07/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection in livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from Cp (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box ssDNA motif is presented. The Cp-CspA structure contains five β-strands making up a β-barrel fold with 11 hydrophobic core residues and two salt bridges that confers it with a melting temperature of ~ 54 °C that is similar to mesophilic Bs-CspB. Chemical shift perturbations analysis revealed that residues in the nucleic acid-binding motifs (RNP 1 and 2) and loop 3 are involved in binding to the Y-box fragment either by direct interaction or by conformational rearrangements remote from the binding region. Fluorescence quenching experiments of Cp-CspA showed that the dissociation constants for Y-box ssDNA binding is nanomolar and the binding affinity decreased as the temperature increased, indicating that the interaction is enthalpically driven and the hydrogen bonds and van der Waals forces are important contributions for complex stabilization. The Y31 of Cp-CspA is a particular occurrence among Csps from mesophilic bacteria that provide a possible explanation for the higher binding affinity to ssDNA than that observed for Bs-CspB. Anisotropy measurements indicated that the reduction in molecular mobility of Cp-CspA upon Y-box binding is characterized by a cooperative process. DATABASE Resonance assignment and structural data are available in the Biological Magnetic Resonance Data Bank and Protein Data Bank under accession number 26802 and 5O6F, respectively.
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Affiliation(s)
- Icaro P Caruso
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vineet Panwalkar
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Monika A Coronado
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Andrew J Dingley
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Marinônio L Cornélio
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir K Arni
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Raphael J Eberle
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
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19
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Abstract
Inspired by Somero's corresponding state principle that relates protein enhanced thermal stability with mechanical rigidity, we deployed state of the art computational techniques (based on atomistic steered molecular dynamics and Hamiltonian-replica exchange simulations) to study the in silico realization of mechanical and thermal unfolding of two homologous Csp proteins that have evolved to thrive in different thermal environments. By complementing recent single-molecule experiments, we unambiguously show that, for these homologues whose structures are very similar, the increased thermal resistance of the thermophilic variant is not associated with an increased mechanical stability. Our approach provides microscopic insights that are otherwise inaccessible to experimental techniques, and explains why the protein weak spots for thermal and mechanical denaturation are distinct.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
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20
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Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. RNA binding and chaperone activity of the E. coli cold-shock protein CspA. Nucleic Acids Res 2017; 45:4255-4268. [PMID: 28126922 PMCID: PMC5397153 DOI: 10.1093/nar/gkx044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/17/2017] [Indexed: 11/14/2022] Open
Abstract
Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.
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Affiliation(s)
- Enrico Rennella
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Tomáš Sára
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Michael Juen
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Wunderlich
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Lionel Imbert
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Zsofia Solyom
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Katharina Weinhäupl
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Robert Konrat
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
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21
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Carvajal AI, Vallejos G, Komives EA, Castro-Fernández V, Leonardo DA, Garratt RC, Ramírez-Sarmiento CA, Babul J. Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics. FEBS J 2017; 284:1882-1896. [PMID: 28457014 DOI: 10.1111/febs.14093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/09/2017] [Accepted: 04/26/2017] [Indexed: 01/22/2023]
Abstract
Cold shock proteins (Csp) constitute a family of ubiquitous small proteins that act as RNA-chaperones to avoid cold-induced termination of translation. All members contain two subdomains composed of 2 and 3 β-strands, respectively, which are connected by a hinge loop and fold into a β-barrel. Bacillus caldolyticus Csp (BcCsp) is one of the most studied members of the family in terms of its folding, function, and structure. This protein has been described as a monomer in solution, although a recent crystal structure showed dimerization via domain swapping (DS). In contrast, other cold shock proteins of the same fold are known to dimerize in a nonswapped arrangement. Hypothesizing that reducing the size of the hinge loop may promote swapping as in several other DS proteins with different folds we deleted two residues from these region (BcCsp∆36-37), leading to a protein in monomer-dimer equilibrium with similar folding stability to that of the wild-type. Strikingly, the crystal structure of BcCsp∆36-37 revealed a nonswapped dimer with its interface located at the nucleic acid-binding surface, showing that the deletion led to structural consequences far from the perturbation site. Concomitantly, circular dichroism experiments on BcCsp∆36-37 demonstrated that binding of the oligonucleotide hexathymidine disrupts the dimer. Additionally, HDXMS shows a protective effect on the protein structure upon dimerization, where the resulting interactions between ligand-binding surfaces in the dimer reduced the extent of exchange throughout the whole protein. Our work provides evidence of the complex interplay between conformational dynamics, deletions, and oligomerization within the Csp protein family. DATABASES Structural data are available in the Protein Data Bank under accession number 5JX4.
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Affiliation(s)
- Alonso I Carvajal
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gabriel Vallejos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Diego A Leonardo
- Instituto de Física de São Carlos, Universidade de São Paulo, Brazil
| | - Richard C Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, Brazil
| | - César A Ramírez-Sarmiento
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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22
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Thirumuruganandham SP, Gómez EA, Lakshmanan S, Hamblin MR. Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study. IEEE TRANSACTIONS ON TERAHERTZ SCIENCE AND TECHNOLOGY 2017; 7:131-143. [PMID: 30881732 PMCID: PMC6419770 DOI: 10.1109/tthz.2016.2637380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.
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Affiliation(s)
| | - Edgar A Gómez
- Programa de Física, Universidad del Quindío, Armenia, Colombia
| | - Shanmugamurthy Lakshmanan
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael R Hamblin
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
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23
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de Sancho D, Best RB. Reconciling Intermediates in Mechanical Unfolding Experiments with Two-State Protein Folding in Bulk. J Phys Chem Lett 2016; 7:3798-3803. [PMID: 27626458 PMCID: PMC5597958 DOI: 10.1021/acs.jpclett.6b01722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Most experimentally well-characterized single domain proteins of less than 100 residues have been found to be two-state folders. That is, only two distinct populations can explain both equilibrium and kinetic measurements. Results from single molecule force spectroscopy, where a protein is unfolded by applying a mechanical pulling force to its ends, have largely confirmed this description for proteins found to be two-state in ensemble experiments. Recently, however, stable intermediates have been reported in mechanical unfolding experiments on a cold-shock protein previously found to be a prototypical two-state folder. Here, we tackle this discrepancy using free energy landscapes and Markov state models derived from coarse-grained molecular simulations. We show that protein folding intermediates can be selectively stabilized by the pulling force and that the populations of these intermediates vary in a force-dependent manner. Our model qualitatively captures the experimental results and suggests a possible origin of the apparent discrepancy.
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Affiliation(s)
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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24
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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25
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Su JG, Han XM, Zhao SX, Hou YX, Li XY, Qi LS, Wang JH. Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model. J Mol Model 2016; 22:91. [DOI: 10.1007/s00894-016-2958-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
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26
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Zerze GH, Best RB, Mittal J. Modest influence of FRET chromophores on the properties of unfolded proteins. Biophys J 2015; 107:1654-60. [PMID: 25296318 DOI: 10.1016/j.bpj.2014.07.071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 05/10/2014] [Accepted: 07/11/2014] [Indexed: 11/27/2022] Open
Abstract
Single-molecule Förster resonance energy transfer (FRET) experiments are often used to study the properties of unfolded and intrinsically disordered proteins. Because of their large extinction coefficients and quantum yields, synthetic heteroaromatic chromophores covalently linked to the protein are often used as donor and acceptor fluorophores. A key issue in the interpretation of such experiments is the extent to which the properties of the unfolded chain may be affected by the presence of these chromophores. In this article, we investigate this question using all-atom explicit solvent replica exchange molecular dynamics simulations of three different unfolded or intrinsically disordered proteins. We find that the secondary structure and long-range contacts are largely the same in the presence or absence of the fluorophores, and that the dimensions of the chain with and without chromophores are similar. This suggests that, at least in the cases studied, extrinsic fluorophores have little effect on the structural properties of unfolded or disordered proteins. We also find that the critical FRET orientational factor κ(2), has an average value and equilibrium distribution very close to that expected for isotropic orientations, which supports one of the assumptions frequently made when interpreting FRET efficiency in terms of distances.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania.
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27
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Walczewska-Szewc K, Corry B. Accounting for dye diffusion and orientation when relating FRET measurements to distances: three simple computational methods. Phys Chem Chem Phys 2015; 16:12317-26. [PMID: 24824374 DOI: 10.1039/c4cp01222d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Förster resonance energy transfer (FRET) allows in principal for the structural changes of biological systems to be revealed by monitoring distributions and distance fluctuations between parts of individual molecules. However, because flexible probes usually have to be attached to the macromolecule to conduct these experiments, they suffer from uncertainty in probe positions and orientations. One of the way to address this issue is to use molecular dynamics simulations to explicitly model the likely positions of the probes, but, this is still not widely accessible because of the large computational effort required. Here we compare three simpler methods that can potentially replace MD simulations in FRET data interpretation. In the first, the volume accessible for dye movement is calculated using a fast, geometrical algorithm. The next method, adapted from the analysis of electron paramagnetic studies, utilises a library of rotamers describing probe conformations. The last method uses preliminary MD simulations of fluorescent dyes in solution, to identify all conformational states of dyes and overlays this on the macromolecular system. A comparison of these methods in the simple system of dye-labelled polyproline, shows that in the case of lack of interaction between the dye and host, all give results comparable with MD simulations but require much less time. Differences between these three methods and their ability to compete with MD simulations in the analysis of real experiment are demonstrated and discussed using the examples of cold shock protein and leucine transporter systems.
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28
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Piana S, Donchev AG, Robustelli P, Shaw DE. Water dispersion interactions strongly influence simulated structural properties of disordered protein states. J Phys Chem B 2015; 119:5113-23. [PMID: 25764013 DOI: 10.1021/jp508971m] [Citation(s) in RCA: 550] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many proteins can be partially or completely disordered under physiological conditions. Structural characterization of these disordered states using experimental methods can be challenging, since they are composed of a structurally heterogeneous ensemble of conformations rather than a single dominant conformation. Molecular dynamics (MD) simulations should in principle provide an ideal tool for elucidating the composition and behavior of disordered states at an atomic level of detail. Unfortunately, MD simulations using current physics-based models tend to produce disordered-state ensembles that are structurally too compact relative to experiments. We find that the water models typically used in MD simulations significantly underestimate London dispersion interactions, and speculate that this may be a possible reason for these erroneous results. To test this hypothesis, we create a new water model, TIP4P-D, that approximately corrects for these deficiencies in modeling water dispersion interactions while maintaining compatibility with existing physics-based models. We show that simulations of solvated proteins using this new water model typically result in disordered states that are substantially more expanded and in better agreement with experiment. These results represent a significant step toward extending the range of applicability of MD simulations to include the study of (partially or fully) disordered protein states.
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Affiliation(s)
- Stefano Piana
- †D. E. Shaw Research, New York, New York 10036, United States
| | | | - Paul Robustelli
- †D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- †D. E. Shaw Research, New York, New York 10036, United States.,‡Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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29
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Life in extreme environments: single molecule force spectroscopy as a tool to explore proteins from extremophilic organisms. Biochem Soc Trans 2015; 43:179-85. [DOI: 10.1042/bst20140274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Extremophiles are organisms which survive and thrive in extreme environments. The proteins from extremophilic single-celled organisms have received considerable attention as they are structurally stable and functionally active under extreme physical and chemical conditions. In this short article, we provide an introduction to extremophiles, the structural adaptations of proteins from extremophilic organisms and the exploitation of these proteins in industrial applications. We provide a review of recent developments which have utilized single molecule force spectroscopy to mechanically manipulate proteins from extremophilic organisms and the information which has been gained about their stability, flexibility and underlying energy landscapes.
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30
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Jin B, Jeong KW, Kim Y. Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus. Biochem Biophys Res Commun 2014; 451:402-7. [PMID: 25101648 DOI: 10.1016/j.bbrc.2014.07.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 11/15/2022]
Abstract
The thermophilic bacterium Thermus aquaticus is a well-known source of Taq polymerase. Here, we studied the structure and dynamics of the T. aquaticus cold-shock protein (Ta-Csp) to better understand its thermostability using NMR spectroscopy. We found that Ta-Csp has a five-stranded β-barrel structure with five salt bridges which are important for more rigid structure and a higher melting temperature (76 °C) of Ta-Csp compared to mesophilic and psychrophilic Csps. Microsecond to millisecond time scale exchange processes occur only at the β1-β2 surface region of the nucleic acid binding site with an average conformational exchange rate constant of 674 s(-1). The results imply that thermophilic Ta-Csp has a more rigid structure and may not need high structural flexibility to accommodate nucleic acids upon cold shock compared to its mesophile and psychrophile counterparts.
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Affiliation(s)
- Bonghwan Jin
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea
| | - Ki-Woong Jeong
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 143-701, South Korea.
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31
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Echeverria I, Makarov DE, Papoian GA. Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins. J Am Chem Soc 2014; 136:8708-13. [DOI: 10.1021/ja503069k] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ignacia Echeverria
- Department
of Chemistry and Biochemistry and Institute for Physical Science and
Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Dmitrii E. Makarov
- Department
of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Garegin A. Papoian
- Department
of Chemistry and Biochemistry and Institute for Physical Science and
Technology, University of Maryland, College Park, Maryland 20742, United States
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32
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Lee J, Jeong KW, Jin B, Ryu KS, Kim EH, Ahn JH, Kim Y. Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium. Biochemistry 2013; 52:2492-504. [PMID: 23506337 DOI: 10.1021/bi301641b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cold-shock proteins (Csps), proteins expressed when the ambient temperature drops below the growth-supporting temperature, bind to single-stranded nucleic acids and act as RNA chaperones to regulate translation. Listeria monocytogenes is a psychrophilic food-borne pathogen that is problematic for the food industry. Structures of Csps from psychrophilic bacteria have not yet been studied. Despite dramatic differences in the thermostability of Csps of various thermophilic microorganisms, these proteins share a high degree of primary sequence homology and a high degree of three-dimensional structural similarity. Here, we investigated the structural and dynamic features as well as the thermostability of L. monocytogenes CspA (Lm-CspA). Lm-CspA has a five-stranded β-barrel structure with hydrophobic core packing and two salt bridges. When heptathymidine (dT(7)) binds, values for the heteronuclear nuclear Overhauser effect and order parameters of residues in surface loop regions near nucleic acid binding sites increase dramatically. Moreover, Carr-Purcell-Meiboom-Gill experiments showed that slow motions observed for the nucleic acid binding residues K7, W8, F15, F27, and R56 disappeared in Lm-CspA-dT(7). Lm-CspA is less thermostable than mesophilic and thermophilic Csps, with a lower melting temperature (40 °C). The structural flexibility that accompanies longer surface loops and less hydrophobic core packing and a number of salt bridges and unfavorable electrostatic repulsion are likely key factors in the low thermostability of Lm-CspA. This implies that the large conformational flexibility of psychrophilic Lm-CspA, which more easily accommodates nucleic acids at low temperature, is required for RNA chaperone function under cold-shock conditions and for the cold adaptation of L. monocytogenes.
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Affiliation(s)
- Juho Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, South Korea
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33
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Hoffmann T, Tych KM, Brockwell DJ, Dougan L. Single-molecule force spectroscopy identifies a small cold shock protein as being mechanically robust. J Phys Chem B 2013; 117:1819-26. [PMID: 23293964 DOI: 10.1021/jp310442s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful approach to examine the stability and dynamics of single proteins. We have completed force extension experiments on the small cold shock protein B from Thermotoga maritima, using a specially constructed chimeric polyprotein. The protein's simple topology, which is distinct from the mechanically well-characterized β-grasp and immunoglobulin (Ig)-like folds, in addition to the wide range of structural homologues resulting from its ancient origin, provides an attractive model protein for single-molecule force spectroscopy studies. We have determined that the protein has mechanical stability, unfolding at greater than 70 pN at a pulling velocity of 100 nm s(-1). We reveal features of the unfolding energy landscape by measuring the dependence of the mechanical stability on pulling velocity, in combination with Monte Carlo simulations. We show that the cold shock protein has mechanically robust, yet malleable, features that may be important in providing the protein with stability and flexibility to function over a range of environmental conditions. These results provide insights into the relationship between the secondary structure and topology of a protein and its mechanical strength. This lays the foundation for the investigation of the effects of changes in environmental conditions on the mechanical and dynamic properties of cold shock proteins.
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Affiliation(s)
- Toni Hoffmann
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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34
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Gerarden KP, Fuchs AM, Koch JM, Mueller MM, Graupner DR, O'Rorke JT, Frost CD, Heinen HA, Lackner ER, Schoeller SJ, House PG, Peterson FC, Veldkamp CT. Solution structure of the cold-shock-like protein from Rickettsia rickettsii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1284-8. [PMID: 23143233 PMCID: PMC3515365 DOI: 10.1107/s174430911203881x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/10/2012] [Indexed: 11/25/2022]
Abstract
The solution structure of the cold-shock-like protein from R. rickettsii, the causative agent of Rocky Mountain spotted fever, is reported. Rocky Mountain spotted fever is caused by Rickettsia rickettsii infection. R. rickettsii can be transmitted to mammals, including humans, through the bite of an infected hard-bodied tick of the family Ixodidae. Since the R. rickettsii genome contains only one cold-shock-like protein and given the essential nature of cold-shock proteins in other bacteria, the structure of the cold-shock-like protein from R. rickettsii was investigated. With the exception of a short α-helix found between β-strands 3 and 4, the solution structure of the R. rickettsii cold-shock-like protein has the typical Greek-key five-stranded β-barrel structure found in most cold-shock domains. Additionally, the R. rickettsii cold-shock-like protein, with a ΔG of unfolding of 18.4 kJ mol−1, has a similar stability when compared with other bacterial cold-shock proteins.
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Affiliation(s)
- Kyle P Gerarden
- Department of Chemistry, University of Wisconsin-Whitewater, 800 West Main Street, Whitewater, WI 53190, USA
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35
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Lee JH, Jeong KW, Kim YM. Purification and Structural Characterization of Cold Shock Protein from Listeria monocytogenes. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.8.2508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Durdenko EV, Saburova EA. A special role of phosphate in the stability of lactate dehydrogenase against destruction by a polyelectrolyte. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s1068162012040061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Xu W, Lai Z, Oliveira RJ, Leite VBP, Wang J. Configuration-dependent diffusion dynamics of downhill and two-state protein folding. J Phys Chem B 2012; 116:5152-9. [PMID: 22497604 DOI: 10.1021/jp212132v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Configuration-dependent diffusion (CDD) is important for protein folding kinetics with small thermodynamic barriers. CDD can be even more crucial in downhill folding without thermodynamic barriers. We explored the CDD of a downhill protein (BBL), and a two-state protein (CI2). The hidden kinetic barriers due to CDD were revealed. The increased ~1 k(B)T kinetic barrier is in line with experimental value based on other fast folding proteins. Compared to that of CI2, the effective free-energy profile of BBL is found to be significantly influenced by CDD, and the kinetics are totally determined by diffusion. These findings are consistent with both earlier bulk and single-molecule fluorescence measurements. In addition, we found the temperature dependence of CDD. We also found that the ratio of folding transition temperature against optimal kinetic folding temperature can provide both a quantitative measure for the underlying landscape topography and an indicator for the possible appearance of downhill folding. Our study can help for a better understanding of the role of diffusion in protein folding dynamics.
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Affiliation(s)
- Weixin Xu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
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38
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Tanaka T, Mega R, Kim K, Shinkai A, Masui R, Kuramitsu S, Nakagawa N. A non-cold-inducible cold shock protein homolog mainly contributes to translational control under optimal growth conditions. FEBS J 2012; 279:1014-29. [PMID: 22251463 DOI: 10.1111/j.1742-4658.2012.08492.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) include both cold-induced and non-cold-induced proteins, contrary to their name. Cold-induced Csps are well studied; they function in cold acclimation by controlling transcription and translation. Some Csps have been reported to contribute to other cellular processes. However, the functions of non-cold-induced Csps under optimal growth conditions remain unknown. To elucidate these functions, we used transcriptome and proteome analyses as comprehensive approaches and have compared the outputs of wild-type and non-cold-induced Csp-deletion mutant cells. As a model organism, we selected Thermus thermophilus HB8 because it has only two csp genes (ttcsp1 and ttcsp2); ttCsp1 is the only non-cold-induced Csp. Surprisingly, the amount of transcripts and proteins upon deletion of the ttcsp1 gene was quite different. DNA microarray analysis revealed that the deletion of ttcsp1 did not affect the amount of transcripts, although the ttcsp1 gene was constantly expressed in the wild-type cell. Nonetheless, proteomic analysis revealed that the expression levels of many proteins were significantly altered when ttcsp1 was deleted. These results suggest that ttCsp1 functions in translation independent of transcription. Furthermore, ttCsp1 is involved in both the stimulation and inhibition of translation of specific proteins. Here, we have determined the crystal structure of ttCsp1 at 1.65 Å. This is the first report to present the structure of a non-cold-inducible cold shock protein. We also report the nucleotide binding affinity of ttCsp1. Finally, we discuss the functions of non-cold-induced Csps and propose how they modulate the levels of specific proteins to suit the prevailing environmental conditions.
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Affiliation(s)
- Toshiko Tanaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Japan
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39
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Sachs R, Max KE, Heinemann U, Balbach J. RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. RNA (NEW YORK, N.Y.) 2012; 18:65-76. [PMID: 22128343 PMCID: PMC3261745 DOI: 10.1261/rna.02809212] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 08/29/2011] [Indexed: 05/26/2023]
Abstract
Bacterial cold shock proteins (CSPs) regulate the cellular response to temperature downshift. Their general principle of function involves RNA chaperoning and transcriptional antitermination. Here we present two crystal structures of cold shock protein B from Bacillus subtilis (Bs-CspB) in complex with either a hexanucleotide (5'-UUUUUU-3') or heptanucleotide (5'-GUCUUUA-3') single-stranded RNA (ssRNA). Hydrogen bonds and stacking interactions between RNA bases and aromatic sidechains characterize individual binding subsites. Additional binding subsites which are not occupied by the ligand in the crystal structure were revealed by NMR spectroscopy in solution on Bs-CspB·RNA complexes. Binding studies demonstrate that Bs-CspB associates with ssDNA as well as ssRNA with moderate sequence specificity. Varying affinities of oligonucleotides are reflected mainly in changes of the dissociation rates. The generally lower binding affinity of ssRNA compared to its ssDNA analog is attributed solely to the substitution of thymine by uracil bases in RNA.
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Affiliation(s)
- Rolf Sachs
- Fachgruppe Biophysik Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Klaas E.A. Max
- Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, 13125 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jochen Balbach
- Fachgruppe Biophysik Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
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40
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Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol 2011; 283:60-70. [PMID: 21635900 DOI: 10.1016/j.jtbi.2011.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 05/17/2011] [Accepted: 05/18/2011] [Indexed: 01/15/2023]
Abstract
This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties--specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the "fuzzy oil drop" model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback-Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group - specifically, cold shock proteins - is shown to agree with the proposed model.
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Affiliation(s)
- I Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530 Krakow, Poland.
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41
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Mojib N, Andersen DT, Bej AK. Structure and function of a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica. FEMS Microbiol Lett 2011; 319:106-14. [PMID: 21426380 DOI: 10.1111/j.1574-6968.2011.02269.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A cold shock domain (CSD)-containing protein, CspD, of molecular mass ~7.28 kDa in a psychrotolerant Antarctic Janthinobacterium sp. Ant5-2 (ATCC BAA-2154) exhibited constitutive expression at 37, 22, 15, 4 and -1°C. The cspD gene encoding the CspD protein of Ant5-2 was cloned, sequenced and analyzed. The deduced protein sequence was highly similar to the conserved domains of the cold shock proteins (Csps) from bacteria belonging to the class Betaproteobacteria. Its expression was both time- and growth phase-dependent and increased when exposed to 37°C and UV radiation (UVC, dose: 1.8 and 2.8 mJ cm(-2)). The results from the electrophoretic mobility shift and subcellular localization study confirmed its single-stranded DNA-binding property. In silico analysis of the deduced tertiary structure of CspD from Ant5-2 showed a highly stable domain-swapped dimer, forming two similar monomeric Csp folds. This study established an overall framework of the structure, function and phylogenetic analysis of CspD from an Antarctic Janthinobacterium sp. Ant5-2, which may facilitate and stimulate the study of CSD fold proteins in the class Betaproteobacteria.
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Affiliation(s)
- Nazia Mojib
- Department of Biology, University of Alabama at Birmingham, AL 35294-1170, USA
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42
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D’Auria G, Esposito C, Falcigno L, Calvanese L, Iaccarino E, Ruggiero A, Pedone C, Pedone E, Berisio R. Dynamical properties of cold shock protein A from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2010; 402:693-8. [DOI: 10.1016/j.bbrc.2010.10.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
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43
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Oliveira RJ, Whitford PC, Chahine J, Wang J, Onuchic JN, Leite VBP. The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J 2010; 99:600-8. [PMID: 20643080 DOI: 10.1016/j.bpj.2010.04.041] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 04/06/2010] [Accepted: 04/14/2010] [Indexed: 11/17/2022] Open
Abstract
We present a method for calculating the configurational-dependent diffusion coefficient of a globular protein as a function of the global folding process. Using a coarse-grained structure-based model, we determined the diffusion coefficient, in reaction coordinate space, as a function of the fraction of native contacts formed Q for the cold shock protein (TmCSP). We find nonmonotonic behavior for the diffusion coefficient, with high values for the folded and unfolded ensembles and a lower range of values in the transition state ensemble. We also characterized the folding landscape associated with an energetically frustrated variant of the model. We find that a low-level of frustration can actually stabilize the native ensemble and increase the associated diffusion coefficient. These findings can be understood from a mechanistic standpoint, in that the transition state ensemble has a more homogeneous structural content when frustration is present. Additionally, these findings are consistent with earlier calculations based on lattice models of protein folding and more recent single-molecule fluorescence measurements.
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Affiliation(s)
- Ronaldo J Oliveira
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
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44
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Oliveira RJ, Whitford PC, Chahine J, Leite VBP, Wang J. Coordinate and time-dependent diffusion dynamics in protein folding. Methods 2010; 52:91-8. [PMID: 20438841 DOI: 10.1016/j.ymeth.2010.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/23/2010] [Accepted: 04/28/2010] [Indexed: 11/25/2022] Open
Abstract
We developed both analytical and simulation methods to explore the diffusion dynamics in protein folding. We found the diffusion as a quantitative measure of escape from local traps along the protein folding funnel with chosen reaction coordinates has two remarkable effects on kinetics. At a fixed coordinate, local escape time depends on the distribution of barriers around it, therefore the diffusion is often time distributed. On the other hand, the environments (local escape barriers) change along the coordinates, therefore diffusion is coordinate dependent. The effects of time-dependent diffusion on folding can lead to non-exponential kinetics and non-Poisson statistics of folding time distribution. The effects of coordinate dependent diffusion on folding can lead to the change of the kinetic barrier height as well as the position of the corresponding transition state and therefore modify the folding kinetic rates as well as the kinetic routes. Our analytical models for folding are based on a generalized Fokker-Planck diffusion equation with diffusion coefficient both dependent on coordinate and time. Our simulation for folding are based on structure-based folding models with a specific fast folding protein CspTm studied experimentally on diffusion and folding with single molecules. The coordinate and time-dependent diffusion are especially important to be considered in fast folding and single molecule studies, when there is a small or no free energy barrier and kinetics is controlled by diffusion while underlying statistics of kinetics become important. Including the coordinate dependence of diffusion will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory will also have to be quantitatively modified. Complex kinetics with multiple time scales may allow us not only to explore the folding kinetics but also probe the local landscape and barrier height distribution with single-molecule experiments.
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Affiliation(s)
- Ronaldo J Oliveira
- Departamento de Física - Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, Brazil
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MOTONO C, GROMIHA MM. Dynamic and Structural Analysis of Hyperthermophilic Cold Shock Protein Stability. KOBUNSHI RONBUNSHU 2010. [DOI: 10.1295/koron.67.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chie MOTONO
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
| | - M. Michael GROMIHA
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
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Abstract
Large population sizes, rapid growth and 3.8 billion years of evolution firmly establish microorganisms as a major source of the planet's biological and genetic diversity. However, up to 99% of the microorganisms in a given environment cannot be cultured. Culture-independent methods that directly access the genetic potential of an environmental sample can unveil new proteins with diverse functions, but the sequencing of random DNA can generate enormous amounts of extraneous data. Integrons are recombination systems that accumulate open reading frames (gene cassettes), many of which code for functional proteins with enormous adaptive potential. Some integrons harbor hundreds of gene cassettes and evidence suggests that the gene cassette pool may be limitless in size. Accessing this genetic pool has been hampered since sequence-based techniques, such as hybridization or PCR, often recover only partial genes or a small subset of those present in the sample. Here, a three-plasmid genetic strategy for the sequence-independent recovery of gene cassettes from genomic libraries is described and its use by retrieving functional gene cassettes from the chromosomal integron of Vibrio vulnificus ATCC 27562 is demonstrated. By manipulating the natural activity of integrons, we can gain access to the caches of functional genes amassed by these structures.
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Affiliation(s)
- Dean A Rowe-Magnus
- Division of Clinical Integrative Biology, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, S1-26A, Toronto, Ontario M4N 3N5, Canada.
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47
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Thermal stability of proteins does not correlate with the energy of intramolecular interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1830-4. [DOI: 10.1016/j.bbapap.2008.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 07/07/2008] [Accepted: 07/09/2008] [Indexed: 11/20/2022]
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Motono C, Gromiha MM, Kumar S. Thermodynamic and kinetic determinants ofThermotoga maritimacold shock protein stability: A structural and dynamic analysis. Proteins 2008; 71:655-69. [DOI: 10.1002/prot.21729] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ren J, Nettleship JE, Sainsbury S, Saunders NJ, Owens RJ. Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:247-51. [PMID: 18391418 DOI: 10.1107/s1744309108005411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 02/26/2008] [Indexed: 11/11/2022]
Abstract
The structure of the cold-shock domain protein from Neisseria meningitidis has been solved to 2.6 A resolution and shown to comprise a dimer formed by the exchange of two beta-strands between protein monomers. The overall fold of the monomer closely resembles those of other bacterial cold-shock proteins. The neisserial protein behaved as a monomer in solution and was shown to bind to a hexathymidine oligonucleotide with a stoichiometry of 1:1 and a K(d) of 1.25 microM.
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Affiliation(s)
- Jingshan Ren
- The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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50
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Kim MJ, Lee YK, Lee HK, Im H. Characterization of cold-shock protein A of Antarctic Streptomyces sp. AA8321. Protein J 2007; 26:51-9. [PMID: 17203395 DOI: 10.1007/s10930-006-9044-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polar organisms should have mechanisms to survive the extremely cold environment. Four genes encoding cold-shock proteins, which are small, cold-induced bacterial proteins, have been cloned from the Antarctic bacterium Streptomyces sp. AA8321. Since the specific functions of any polar bacterial or Streptomyces cold-shock proteins have not yet been determined, we examined the role of cold-shock protein A from Streptomyces sp. AA8321 (CspA(St)). Gel filtration chromatography showed that purified CspA(St) exists as a homodimer under physiological conditions, and gel shift assays showed that it binds to single-stranded, but not double-stranded, DNA. Overexpression of CspA(St) in Escherichia coli severely impaired the ability of the host cells to form colonies, and the cells developed an elongated morphology. Incorporation of a deoxynucleoside analogue, 5-bromo-2'-deoxyuridine, into newly synthesized DNA was also drastically diminished in CspA(St)-overexpressing cells. These results suggest that CspA(St) play a role in inhibition of DNA replication during cold-adaptation.
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Affiliation(s)
- Min-Jung Kim
- Department of Molecular Biology, Sejong University, 98 Gunjadong, Kwangjin-gu, Seoul, 143-747, Korea
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