1
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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2
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Rivas G, Minton A. Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo. Annu Rev Biochem 2022; 91:321-351. [PMID: 35287477 DOI: 10.1146/annurev-biochem-040320-104151] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain;
| | - Allen Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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3
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Gruber T, Lewitzky M, Machner L, Weininger U, Feller SM, Balbach J. Macromolecular crowding induces a binding competent transient structure in intrinsically disordered Gab1. J Mol Biol 2021; 434:167407. [PMID: 34929201 DOI: 10.1016/j.jmb.2021.167407] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 10/19/2022]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of proteins which lack tertiary structure elements. Their dynamic properties can depend on reversible post-translational modifications and the complex cellular milieu, which provides a crowded environment. Both influences the thermodynamic stability and folding of globular proteins as well as the conformational plasticity of IDPs. Here we investigate the intrinsically disordered C-terminal region (amino acids 613-694) of human Grb2-associated binding protein 1 (Gab1), which binds to the disease-relevant Src homolog region2 (SH2) domain-containing protein tyrosine phosphatase SHP2 (PTPN11). This binding is mediated by phosphorylation at Tyr 627 and Tyr 659 in Gab1. We characterize induced structure in Gab1613-694 and binding to SHP2 by NMR, CD and ITC under non-crowding and crowding conditions, employing chemical and biological crowding agents and compare the results of the non-phosphorylated and tyrosine phosphorylated C-terminal Gab1 fragment. Our results show that under crowding conditions pre-structured motifs in two distinct regions of Gab1 are formed whereas phosphorylation has no impact on the dynamics and IDP character. These structured regions are identical to the binding regions towards SHP2. Therefore, biological crowders could induce some SHP2 binding capacity. Our results therefore indicate that high concentrations of macromolecules stabilize the preformed or excited binding state in the C-terminal Gab1 region and foster the binding to the SH2 tandem motif of SHP2, even in the absence of tyrosine phosphorylation.
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Affiliation(s)
- Tobias Gruber
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Marc Lewitzky
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Lisa Machner
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany.
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Technical Biochemistry e.V. and Center for Structure and Dynamics of Proteins, Martin-Luther-University of Halle-Wittenberg, Germany.
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4
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Hasanbasri Z, Singewald K, Gluth TD, Driesschaert B, Saxena S. Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell. J Phys Chem B 2021; 125:5265-5274. [PMID: 33983738 DOI: 10.1021/acs.jpcb.1c02371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitive in-cell distance measurements in proteins using pulsed-electron spin resonance (ESR) require reduction-resistant and cleavage-resistant spin labels. Among the reduction-resistant moieties, the hydrophilic trityl core known as OX063 is promising due to its long phase-memory relaxation time (Tm). This property leads to a sufficiently intense ESR signal for reliable distance measurements. Furthermore, the Tm of OX063 remains sufficiently long at higher temperatures, opening the possibility for measurements at temperatures above 50 K. In this work, we synthesized deuterated OX063 with a maleimide linker (mOX063-d24). We show that the combination of the hydrophilicity of the label and the maleimide linker enables high protein labeling that is cleavage-resistant in-cells. Distance measurements performed at 150 K using this label are more sensitive than the measurements at 80 K. The sensitivity gain is due to the significantly short longitudinal relaxation time (T1) at higher temperatures, which enables more data collection per unit of time. In addition to in vitro experiments, we perform distance measurements in Xenopus laevis oocytes. Interestingly, the Tm of mOX063-d24 is sufficiently long even in the crowded environment of the cell, leading to signals of appreciable intensity. Overall, mOX063-d24 provides highly sensitive distance measurements both in vitro and in-cells.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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5
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Studying protein folding in health and disease using biophysical approaches. Emerg Top Life Sci 2021; 5:29-38. [PMID: 33660767 PMCID: PMC8138949 DOI: 10.1042/etls20200317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022]
Abstract
Protein folding is crucial for normal physiology including development and healthy aging, and failure of this process is related to the pathology of diseases including neurodegeneration and cancer. Early thermodynamic and kinetic studies based on the unfolding and refolding equilibrium of individual proteins in the test tube have provided insight into the fundamental principles of protein folding, although the problem of predicting how any given protein will fold remains unsolved. Protein folding within cells is a more complex issue than folding of purified protein in isolation, due to the complex interactions within the cellular environment, including post-translational modifications of proteins, the presence of macromolecular crowding in cells, and variations in the cellular environment, for example in cancer versus normal cells. Development of biophysical approaches including fluorescence resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) techniques and cellular manipulations including microinjection and insertion of noncanonical amino acids has allowed the study of protein folding in living cells. Furthermore, biophysical techniques such as single-molecule fluorescence spectroscopy and optical tweezers allows studies of simplified systems at the single molecular level. Combining in-cell techniques with the powerful detail that can be achieved from single-molecule studies allows the effects of different cellular components including molecular chaperones to be monitored, providing us with comprehensive understanding of the protein folding process. The application of biophysical techniques to the study of protein folding is arming us with knowledge that is fundamental to the battle against cancer and other diseases related to protein conformation or protein–protein interactions.
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6
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Pittas T, Zuo W, Boersma AJ. Engineering crowding sensitivity into protein linkers. Methods Enzymol 2020; 647:51-81. [PMID: 33482994 DOI: 10.1016/bs.mie.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intracellular environment contains a high concentration of biomacromolecules that present steric barriers and ample surface area for weak chemical interactions. Consequently, these forces influence protein conformations and protein self-assembly, with an outcome that depends on the sum of the effects resulting from crowding. Linkers are disordered domains that lack tertiary structure, and this flexible nature would render them susceptible to compression or extension under crowded conditions, compared to the equilibrium conformation in a dilute buffer. The change in distance between the linked proteins can become essential where it attenuates protein activity. In this chapter, we first discuss the experimental findings in vitro and in the cell on how linkers and other relevant macromolecules are affected by crowding. We focus on the dependence on the linker's size, flexibility, and the intra- and intermolecular interactions. Although the experimental data on the systematic variation of proteins in a buffer and cells is limited, extrapolating the available insights allows us to propose a protocol on how to engineer the directionality of crowding effects in the linker. Finally, we describe a straightforward experimental protocol on the determination of crowding sensitivity in a buffer and cell.
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Affiliation(s)
- Theodoros Pittas
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Weiyan Zuo
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany.
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7
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In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy. Proc Natl Acad Sci U S A 2020; 117:20566-20575. [PMID: 32788347 DOI: 10.1073/pnas.2005779117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The complexity of the cellular medium can affect proteins' properties, and, therefore, in-cell characterization of proteins is essential. We explored the stability and conformation of the first baculoviral IAP repeat (BIR) domain of X chromosome-linked inhibitor of apoptosis (XIAP), BIR1, as a model for a homodimer protein in human HeLa cells. We employed double electron-electron resonance (DEER) spectroscopy and labeling with redox stable and rigid Gd3+ spin labels at three representative protein residues, C12 (flexible region), E22C, and N28C (part of helical residues 26 to 31) in the N-terminal region. In contrast to predictions by excluded-volume crowding theory, the dimer-monomer dissociation constant K D was markedly higher in cells than in solution and dilute cell lysate. As expected, this increase was partially recapitulated under conditions of high salt concentrations, given that conserved salt bridges at the dimer interface are critically required for association. Unexpectedly, however, also the addition of the crowding agent Ficoll destabilized the dimer while the addition of bovine serum albumin (BSA) and lysozyme, often used to represent interaction with charged macromolecules, had no effect. Our results highlight the potential of DEER for in-cell study of proteins as well as the complexities of the effects of the cellular milieu on protein structures and stability.
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8
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Klishin AA, van Anders G. When does entropy promote local organization? SOFT MATTER 2020; 16:6523-6531. [PMID: 32597444 DOI: 10.1039/c9sm02540e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crowded soft-matter and biological systems organize locally into preferred motifs. Locally-organized motifs in soft systems can, paradoxically, arise from a drive to maximize overall system entropy. Entropy-driven local order has been directly confirmed in model, synthetic colloidal systems, however similar patterns of organization occur in crowded biological systems ranging from the contents of a cell to collections of cells. In biological settings, and in soft matter more broadly, it is unclear whether entropy generically promotes or inhibits local organization. Resolving this is difficult because entropic effects are intrinsically collective, complicating efforts to isolate them. Here, we employ minimal models that artificially restrict system entropy to show that entropy drives systems toward local organization, even when the model system entropy is below reasonable physical bounds. By establishing this bound, our results suggest that entropy generically promotes local organization in crowded soft and biological systems of rigid objects.
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Affiliation(s)
- Andrei A Klishin
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
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9
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Gasic AG, Cheung MS. A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure. J Phys Chem B 2020; 124:1619-1627. [DOI: 10.1021/acs.jpcb.9b10734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrei G. Gasic
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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10
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Ahmed SM, Johar D, Ali MM, El-Badri N. Insights into the Role of DNA Methylation and Protein Misfolding in Diabetes Mellitus. Endocr Metab Immune Disord Drug Targets 2019; 19:744-753. [DOI: 10.2174/1871530319666190305131813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/25/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022]
Abstract
Background:
Diabetes mellitus is a metabolic disorder that is characterized by impaired
glucose tolerance resulting from defects in insulin secretion, insulin action, or both. Epigenetic modifications,
which are defined as inherited changes in gene expression that occur without changes in gene
sequence, are involved in the etiology of diabetes.
Methods:
In this review, we focused on the role of DNA methylation and protein misfolding and their
contribution to the development of both type 1 and type 2 diabetes mellitus.
Results:
Changes in DNA methylation in particular are highly associated with the development of
diabetes. Protein function is dependent on their proper folding in the endoplasmic reticulum. Defective
protein folding and consequently their functions have also been reported to play a role. Early treatment
of diabetes has proven to be of great benefit, as even transient hyperglycemia may lead to pathological
effects and complications later on. This has been explained by the theory of the development of a
metabolic memory in diabetes. The basis for this metabolic memory was attributed to oxidative stress,
chronic inflammation, non-enzymatic glycation of proteins and importantly, epigenetic changes. This
highlights the importance of linking new therapeutics targeting epigenetic mechanisms with traditional
antidiabetic drugs.
Conclusion:
Although new data is evolving on the relation between DNA methylation, protein misfolding,
and the etiology of diabetes, more studies are required for developing new relevant diagnostics
and therapeutics.
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Affiliation(s)
- Sara M. Ahmed
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
| | - Dina Johar
- Biomedical Sciences Program, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed Medhat Ali
- Biomedical Sciences Program, Zewail City of Science and Technology, Giza, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
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11
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Ghosh A, Smith PES, Qin S, Yi M, Zhou HX. Both Ligands and Macromolecular Crowders Preferentially Bind to Closed Conformations of Maltose Binding Protein. Biochemistry 2019; 58:2208-2217. [PMID: 30950267 DOI: 10.1021/acs.biochem.9b00154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In cellular environments, proteins not only interact with their specific partners but also encounter a high concentration of bystander macromolecules, or crowders. Nonspecific interactions with macromolecular crowders modulate the activities of proteins, but our knowledge about the rules of nonspecific interactions is still very limited. In previous work, we presented experimental evidence that macromolecular crowders acted competitively in inhibiting the binding of maltose binding protein (MBP) with its ligand maltose. Competition between a ligand and an inhibitor may result from binding to either the same site or different conformations of the protein. Maltose binds to the cleft between two lobes of MBP, and in a series of mutants, the affinities increased with an increase in the extent of lobe closure. Here we investigated whether macromolecular crowders also have a conformational or site preference when binding to MBP. The affinities of a polymer crowder, Ficoll70, measured by monitoring tryptophan fluorescence were 3-6-fold higher for closure mutants than for wild-type MBP. Competition between the ligand and crowder, as indicated by fitting of titration data and directly by nuclear magnetic resonance spectroscopy, and their similar preferences for closed MBP conformations further suggest the scenario in which the crowder, like maltose, preferentially binds to the interlobe cleft of MBP. Similar observations were made for bovine serum albumin as a protein crowder. Conformational and site preferences in MBP-crowder binding allude to the paradigm that nonspecific interactions can possess hallmarks of molecular recognition, which may be essential for intracellular organizations including colocalization of proteins and liquid-liquid phase separation.
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Affiliation(s)
- Archishman Ghosh
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Pieter E S Smith
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States
| | - Sanbo Qin
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Myunggi Yi
- Department of Biomedical Engineering , Pukyong National University , Busan 48513 , South Korea
| | - Huan-Xiang Zhou
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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12
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Nandy A, Chakraborty S, Nandi S, Bhattacharyya K, Mukherjee S. Structure, Activity, and Dynamics of Human Serum Albumin in a Crowded Pluronic F127 Hydrogel. J Phys Chem B 2019; 123:3397-3408. [DOI: 10.1021/acs.jpcb.9b00219] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Somen Nandi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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13
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Köhn B, Kovermann M. Macromolecular Crowding Tunes Protein Stability by Manipulating Solvent Accessibility. Chembiochem 2019; 20:759-763. [PMID: 30508270 PMCID: PMC6582440 DOI: 10.1002/cbic.201800679] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 01/10/2023]
Abstract
In all intracellular processes, protein structure and dynamics are subject to the influence of macromolecular crowding (MC). Here, the impact of MC agents of different types and sizes on the model protein Bacillus subtilis Cold shock protein B (BsCspB) during both thermal and chemical denaturation have been comprehensively investigated. We consistently reveal a distinct stabilization of BsCspB in a manner dependent on the MC concentration but not on viscosity, polarity, or size of the MC agent used. This general stabilization has been decoded by use of NMR spectroscopy, through monitoring of chemical shift (CS) perturbations and the intramolecular hydrogen‐bonding networks, as well as local protection of amide protons against exchange with solvent protons. Whereas CSs and hydrogen‐bonding networks are not systematically affected in the presence of MC, we detected a pronounced reduction in exchange in loop regions of BsCspB. We conclude that this reduced accessibility of solvent protons is a key parameter for the increases in protein stability seen under MC.
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Affiliation(s)
- Birgit Köhn
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Research School Chemical Biology (KoRS-CB), Universität Konstanz, Universitätsstrassee 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Research School Chemical Biology (KoRS-CB), Universität Konstanz, Universitätsstrassee 10, 78457, Konstanz, Germany
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