1
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Khoroshunova YV, Morozov DA, Kuznetsov DA, Rybalova TV, Glazachev YI, Bagryanskaya EG, Kirilyuk IA. Synthesis and Properties of (1 R( S),5 R( S),7 R( S),8 R( S))-1,8-Bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl: Reduction-Resistant Spin Labels with High Spin Relaxation Times. Int J Mol Sci 2023; 24:11498. [PMID: 37511257 PMCID: PMC10380268 DOI: 10.3390/ijms241411498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Site-directed spin labeling followed by investigation using Electron Paramagnetic Resonance spectroscopy is a rapidly expanding powerful biophysical technique to study structure, local dynamics and functions of biomolecules using pulsed EPR techniques and nitroxides are the most widely used spin labels. Modern trends of this method include measurements directly inside a living cell, as well as measurements without deep freezing (below 70 K), which provide information that is more consistent with the behavior of the molecules under study in natural conditions. Such studies require nitroxides, which are resistant to the action of biogenic reductants and have high spin relaxation (dephasing) times, Tm. (1R(S),5R(S),7R(S),8R(S))-1,8-bis(hydroxymethyl)-6-azadispiro[4.1.4.2]tridecane-6-oxyl is a unique nitroxide that combines these features. We have developed a convenient method for the synthesis of this radical and studied the ways of its functionalization. Promising spin labels have been obtained, the parameters of their spin relaxation T1 and Tm have been measured, and the kinetics of reduction with ascorbate have been studied.
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Affiliation(s)
- Yulia V Khoroshunova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Denis A Morozov
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Danil A Kuznetsov
- Department of Physics, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Tatyana V Rybalova
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Yurii I Glazachev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3, 630090 Novosibirsk, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
| | - Igor A Kirilyuk
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia
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Si W, Xie Y, Dong J, Wang C, Zhang F, Yue J, Jian S, Wei J, Liu S, Wang L, Zhang H. AMPK activation enhances neutrophil's fungicidal activity in vitro and improves the clinical outcome of Fusarium solani keratitis in vivo. Curr Eye Res 2022; 47:1131-1143. [PMID: 35575029 DOI: 10.1080/02713683.2022.2078494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | | | | | | | - Juan Yue
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
| | - Shoujun Jian
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
| | - Jingjing Wei
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
| | - Susu Liu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
| | - Liya Wang
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
| | - Hongmin Zhang
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, Henan Key Laboratory for Ophthalmology and Visual Science, 450003, China.
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3
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The cell as a bag of RNA. Trends Genet 2021; 37:1064-1068. [PMID: 34462156 DOI: 10.1016/j.tig.2021.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
Genomic sequencing has provided insight into the genetic characterization of many organisms, and we are now seeing sequencing technologies turned towards phenotypic characterization of cells, tissues, and whole organisms. In particular, single-cell transcriptomic techniques are revolutionizing certain aspects of cell biology and enabling fundamental discoveries about cellular diversity, cell state, and cell type identity. I argue here that much of this progress depends on abstracting one's view of the cell to regard it as a 'bag of RNA'.
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Abstract
The hydrogen ion concentration ([H+]) in intracellular cytoplasmic fluid (ICF) must be maintained in a narrow range in all species for normal protein functions. Thus, mechanisms regulating ICF are of fundamental biological importance. Studies on the regulation of ICF [H+] have been hampered by use of pH notation, failure to consider the roles played by differences in the concentration of strong ions (strong ion difference, SID), the conservation of mass, the principle of electrical neutrality, and that [H+] and bicarbonate ions [HCO3-] are dependent variables. This argument is based on the late Peter Stewart's physical-chemical analysis of [H+] regulation reported in this journal nearly forty years ago (Stewart. 1983. Can. J. Physiol. Pharmacol. 61: 1444-1461. Doi:10.1139/y83-207). We start by outlining the principles of Stewart's analysis and then provide a general understanding of its significance for regulation of ICF [H+]. The system may initially appear complex, but it becomes evident that changes in SID dominate regulation of [H+]. The primary strong ions are Na+, K+, and Cl-, and a few organic strong anions. The second independent variable, partial pressure of carbon dioxide (PCO2), can easily be assessed. The third independent variable, the activity of intracellular weak acids ([Atot]), is much more complex but largely plays a modifying role. Attention to these principles will potentially provide new insights into ICF pH regulation.
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Affiliation(s)
- Sheldon Magder
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
| | - Alexandr Magder
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
| | - Gordan Samoukovic
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
- Department of Critical Care, McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
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5
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Breindel L, Yu J, Burz DS, Shekhtman A. Intact ribosomes drive the formation of protein quinary structure. PLoS One 2020; 15:e0232015. [PMID: 32330166 PMCID: PMC7182177 DOI: 10.1371/journal.pone.0232015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 01/19/2023] Open
Abstract
Transient, site-specific, or so-called quinary, interactions are omnipresent in live cells and modulate protein stability and activity. Quinary intreactions are readily detected by in-cell NMR spectroscopy as severe broadening of the NMR signals. Intact ribosome particles were shown to be necessary for the interactions that give rise to the NMR protein signal broadening observed in cell lysates and sufficient to mimic quinary interactions present in the crowded cytosol. Recovery of target protein NMR spectra that were broadened in lysates, in vitro and in the presence of purified ribosomes was achieved by RNase A digestion only after the structure of the ribosome was destabilized by removing magnesium ions from the system. Identifying intact ribosomal particles as the major protein-binding component of quinary interactions and consequent spectral peak broadening will facilitate quantitative characterization of macromolecular crowding effects in live cells and streamline models of metabolic activity.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - Jianchao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - David S. Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
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6
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Widder P, Schuck J, Summerer D, Drescher M. Combining site-directed spin labeling in vivo and in-cell EPR distance determination. Phys Chem Chem Phys 2020; 22:4875-4879. [DOI: 10.1039/c9cp05584c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Non-canonical amino acid incorporation via amber stop codon suppression and in vivo site-directed spin labeling allow in-cell EPR distance determination in E. coli.
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Affiliation(s)
- Pia Widder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Julian Schuck
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
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7
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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8
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Breindel L, Burz DS, Shekhtman A. Interaction proteomics by using in-cell NMR spectroscopy. J Proteomics 2019; 191:202-211. [PMID: 29427760 PMCID: PMC6082733 DOI: 10.1016/j.jprot.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/31/2018] [Accepted: 02/04/2018] [Indexed: 12/17/2022]
Abstract
A synopsis of in-cell NMR spectroscopic approaches to study interaction proteomics in prokaryotic and eukaryotic cells is presented. We describe the use of in-cell NMR spectroscopy to resolve high resolution protein structures, discuss methodologies for determining and analyzing high and low affinity protein-target structural interactions, including intrinsically disordered proteins, and detail important functional interactions that result from these interactions. SIGNIFICANCE: The ultimate goal of structural and biochemical research is to understand how macromolecular interactions give rise to and regulate biological activity in living cells. The challenge is formidable due to the complexity that arises not only from the number of proteins (genes) expressed by the organism, but also from the combinatorial interactions between them. Despite ongoing efforts to decipher the complex nature of protein interactions, new methods for structurally characterizing protein complexes are needed to fully understand molecular networks. With the onset of in-cell NMR spectroscopy, molecular structures and interactions can be studied under physiological conditions shedding light on the structural underpinning of biological activity.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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9
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Ribeiro S, Ebbinghaus S, Marcos JC. Protein folding and quinary interactions: creating cellular organisation through functional disorder. FEBS Lett 2018; 592:3040-3053. [DOI: 10.1002/1873-3468.13211] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/16/2018] [Accepted: 07/29/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Sara Ribeiro
- Centre of Chemistry University of Minho Braga Portugal
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry Technical University Braunschweig Germany
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10
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Xu C, Bouvier G, Bardiaux B, Nilges M, Malliavin T, Lisser A. Ordering Protein Contact Matrices. Comput Struct Biotechnol J 2018; 16:140-156. [PMID: 29632657 PMCID: PMC5889711 DOI: 10.1016/j.csbj.2018.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 11/29/2022] Open
Abstract
Numerous biophysical approaches provide information about residues spatial proximity in proteins. However, correct assignment of the protein fold from this proximity information is not straightforward if the spatially close protein residues are not assigned to residues in the primary sequence. Here, we propose an algorithm to assign such residue numbers by ordering the columns and lines of the raw protein contact matrix directly obtained from proximity information between unassigned amino acids. The ordering problem is formatted as the search of a trail within a graph connecting protein residues through the nonzero contact values. The algorithm performs in two steps: (i) finding the longest trail of the graph using an original dynamic programming algorithm, (ii) clustering the individual ordered matrices using a self-organizing map (SOM) approach. The combination of the dynamic programming and self-organizing map approaches constitutes a quite innovative point of the present work. The algorithm was validated on a set of about 900 proteins, representative of the sizes and proportions of secondary structures observed in the Protein Data Bank. The algorithm was revealed to be efficient for noise levels up to 40%, obtaining average gaps of about 20% at maximum between ordered and initial matrices. The proposed approach paves the ways toward a method of fold prediction from noisy proximity information, as TM scores larger than 0.5 have been obtained for ten randomly chosen proteins, in the case of a noise level of 10%. The methods has been also validated on two experimental cases, on which it performed satisfactorily.
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Affiliation(s)
- Chuan Xu
- Laboratoire de Recherche en Informatique, Université Paris-Sud and CNRS UMR8623, France
| | - Guillaume Bouvier
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, France
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, France
| | - Benjamin Bardiaux
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, France
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, France
| | - Michael Nilges
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, France
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, France
| | - Thérèse Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, France
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, France
| | - Abdel Lisser
- Laboratoire de Recherche en Informatique, Université Paris-Sud and CNRS UMR8623, France
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11
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Lippens G, Cahoreau E, Millard P, Charlier C, Lopez J, Hanoulle X, Portais JC. In-cell NMR: from metabolites to macromolecules. Analyst 2018; 143:620-629. [PMID: 29333554 DOI: 10.1039/c7an01635b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.
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Affiliation(s)
- G Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - E Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - P Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - C Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - J Lopez
- CERMN, Seccion Quimica, Departemento de Ciencias, Pontificia Universidad Catolica del Peru, Lima 32, Peru
| | - X Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), University of Lille, CNRS UMR8576, Lille, France
| | - J C Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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12
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Kyne C, Crowley PB. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm. Biochemistry 2017; 56:5026-5032. [DOI: 10.1021/acs.biochem.7b00731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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13
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Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
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14
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Cohen RD, Pielak GJ. A cell is more than the sum of its (dilute) parts: A brief history of quinary structure. Protein Sci 2017; 26:403-413. [PMID: 27977883 PMCID: PMC5326556 DOI: 10.1002/pro.3092] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
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15
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Emergence of Life on Earth: A Physicochemical Jigsaw Puzzle. J Mol Evol 2016; 84:1-7. [PMID: 27995274 DOI: 10.1007/s00239-016-9775-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
Abstract
We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces. (4) Some microspaces persist and retain memory from past cycles, and others re-dissolve and re-disperse back into the Earth's chemical reservoir. (5) Proto-metabolites and proto-biopolymers coevolve with and within persisting microspaces, where (6) Macromolecular crowding and other non-covalent molecular forces govern the evolution of hydrophilic, hydrophobic, and charged molecular surfaces. (7) The matrices of microspaces evolve into proto-biofilms of progenotes with rudimentary but evolving replication, transcription, and translation, enclosed in unstable cell envelopes. (8) Stabilization of cell envelopes 'crystallizes' bacteria-like genetics and metabolism with low horizontal gene transfer-life 'as we know it.' These factors and processes constitute the 'working pieces' of the jigsaw puzzle of life's emergence. They extend the concept of progenotes as the first proto-cellular life, connected backward in time to the cycling chemistries of the Earth-Moon planetary system, and forward to the ancient cell cycle of first bacteria-like organisms. Supra-macromolecular models of 'compartments first' are preferred: they facilitate macromolecular crowding-a key abiotic/biotic transition toward living states. Evolutionary models of metabolism or genetics 'first' could not have evolved in unconfined and uncrowded environments because of the diffusional drift to disorder mandated by the second law of thermodynamics.
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16
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Majumder S, DeMott CM, Reverdatto S, Burz DS, Shekhtman A. Total Cellular RNA Modulates Protein Activity. Biochemistry 2016; 55:4568-73. [PMID: 27456029 DOI: 10.1021/acs.biochem.6b00330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA constitutes up to 20% of a cell's dry weight, corresponding to ∼20 mg/mL. This high concentration of RNA facilitates low-affinity protein-RNA quinary interactions, which may play an important role in facilitating and regulating biological processes. In the yeast Pichia pastoris, the level of ubiquitin-RNA colocalization increases when cells are grown in the presence of dextrose and methanol instead of methanol as the sole carbon source. Total RNA isolated from cells grown in methanol increases β-galactosidase activity relative to that seen with RNA isolated from cells grown in the presence of dextrose and methanol. Because the total cellular RNA content changes with growth medium, protein-RNA quinary interactions can alter in-cell protein biochemistry and may play an important role in cell adaptation, critical to many physiological and pathological states.
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Affiliation(s)
- Subhabrata Majumder
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany , 1400 Washington Avenue, Albany, New York 12222, United States
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