1
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Liu Z, Grigas AT, Sumner J, Knab E, Davis CM, O'Hern CS. Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling. ARXIV 2024:arXiv:2405.07983v1. [PMID: 38800659 PMCID: PMC11118665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs N r that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, N r / N ≲ 0.08 , where N is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo. Significance Determining protein structure in vivo is essential for understanding protein function. Most protein structures have been studied in non-physiological conditions using x-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. Thus, we do not know whether the cellular environment significantly affects protein structure. We emphasize the benefits of FRET-assisted molecular dynamics simulations in characterizing protein structure in vivo at the atomic scale. We identify the minimum number of FRET pairs that can induce conformational changes in several proteins, including one that has been characterized using in-cell NMR.
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Affiliation(s)
- Zhuoyi Liu
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
| | - Alex T Grigas
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520, USA
| | - Jacob Sumner
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520, USA
| | - Edward Knab
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA
| | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA
| | - Corey S O'Hern
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut, 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520, USA
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2
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Choi AA, Xu K. Single-Molecule Diffusivity Quantification Unveils Ubiquitous Net Charge-Driven Protein-Protein Interaction. J Am Chem Soc 2024; 146:10973-10978. [PMID: 38576203 PMCID: PMC11023747 DOI: 10.1021/jacs.4c02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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3
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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4
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Katti SS, Igumenova TI. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565546. [PMID: 38405767 PMCID: PMC10888879 DOI: 10.1101/2023.11.03.565546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca 2+ and Zn 2+ . The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd 2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn 2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd 2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α 3 DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
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5
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Wang Y, Unnikrishnan M, Ramsey B, El Andlosy D, Keeley AT, Murphy CJ, Gruebele M. In-Cell Association of a Bioorthogonal Tubulin. Biomacromolecules 2024; 25:1282-1290. [PMID: 38251876 DOI: 10.1021/acs.biomac.3c01253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.
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Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brooke Ramsey
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Driss El Andlosy
- Computer Science and Technologies Department, Parkland Community College, Champaign, Illinois 61821, United States
| | - Alex T Keeley
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Caviglia B, Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Petrillo C, Peters J, Sterpone F, Paciaroni A. Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability. J Phys Chem Lett 2024; 15:1435-1441. [PMID: 38291814 DOI: 10.1021/acs.jpclett.3c03351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.
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Affiliation(s)
- Beatrice Caviglia
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Daniele Di Bari
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague, Czech Republic
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Judith Peters
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique (CNRS), Univ. Grenoble Alpes, 140 Rue de la Physique, 38402 Saint-Martin-d'Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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7
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Li H, Zheng YH, Gates WP, Villacorta FJ, Ohira-Kawamura S, Kawakita Y, Ikeda K, Bordallo HN. Role of Exchange Cations and Layer Charge on the Dynamics of Confined Water. J Phys Chem A 2024; 128:261-270. [PMID: 38135662 DOI: 10.1021/acs.jpca.3c05649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Describing the dynamic behavior of water confined in clay minerals is a fascinating challenge and crucial in many research areas, ranging from materials science and geotechnical engineering to environmental sustainability. Water is the most abundant resource on Earth, and the high reactivity of naturally occurring hydrous clay minerals used since prehistoric times for a variety of applications means that water-clay interaction is a ubiquitous phenomenon in nature. We have attempted to experimentally distinguish the rotational dynamics and translational diffusion of two distinct populations of interlayer water, confined and ultraconfined, in the sodium (Na) forms of two smectite clay minerals, montmorillonite (Mt) and hectorite (Ht). Samples hydrated at a pseudo one-layer hydration (1LH) state under ambient conditions were studied with quasi-elastic neutron scattering (QENS) between 150 and 300 K. Using a simplified revised jump-diffusion and rotation-diffusion model (srJRM), we observed that while interlayer water near the ditrigonal cavity in Ht forms strong H-bonds to both adjacent surface O and structural OH, H-bonding of other more prevalent interlayer water with the surface O is weaker compared to Mt, inducing a higher temperature for dynamical changes of confined water. Given the lower layer charge and faster dynamics observed for Ht compared to Mt, we consider this strong evidence confirming the influence of the interlayer cation and surfaces on confined water dynamics.
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Affiliation(s)
- Hua Li
- Department of Physics, Jinan University, Guangzhou 510632, China
| | - Yin-Hao Zheng
- Department of Physics, Jinan University, Guangzhou 510632, China
| | - Will P Gates
- Institute for Frontier Materials, Deakin University, Melbourne-Burwood, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - F J Villacorta
- ESS-Bilbao, Parque Científico y Tecnológico Bizkaia Nave 201, 48170 Zamudio, Spain
| | | | - Yukinobu Kawakita
- Neutron Science Section, MLF Division, J-PARC Center, Tokai 319-1106, Japan
| | - Kazutaka Ikeda
- Neutron Science Section, MLF Division, J-PARC Center, Tokai 319-1106, Japan
- Neutron Industrial Application Promotion Center, CROSS, 203-1 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan
| | - Heloisa N Bordallo
- The Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen, Denmark
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8
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Samuel Russell PP, Alaeen S, Pogorelov TV. In-Cell Dynamics: The Next Focus of All-Atom Simulations. J Phys Chem B 2023; 127:9863-9872. [PMID: 37793083 PMCID: PMC10874638 DOI: 10.1021/acs.jpcb.3c05166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The cell is a crowded space where large biomolecules and metabolites are in continuous motion. Great strides have been made in in vitro studies of protein dynamics, folding, and protein-protein interactions, and much new data are emerging of how they differ in the cell. In this Perspective, we highlight the current progress in atomistic modeling of in-cell environments, both bacteria and mammals, with emphasis on classical all-atom molecular dynamics simulations. These simulations have been recently used to capture and characterize functional and non-functional protein-protein interactions, protein folding dynamics of small proteins with varied topologies, and dynamics of metabolites. We further discuss the challenges and efforts for updating modern force fields critical to the progress of cellular environment simulations. We also briefly summarize developments in relevant state-of-the-art experimental techniques. As computational and experimental methodologies continue to progress and produce more directly comparable data, we are poised to capture the complex atomistic picture of the cell.
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Affiliation(s)
- Premila P Samuel Russell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sepehr Alaeen
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Taras V Pogorelov
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Wang XW, Zhang X, Cui CY, Li B, Goldfarb D, Yang Y, Su XC. Stabilizing Nitroxide Spin Labels for Structural and Conformational Studies of Biomolecules by Maleimide Treatment. Chemistry 2023; 29:e202301350. [PMID: 37354082 DOI: 10.1002/chem.202301350] [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: 04/28/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023]
Abstract
Nitroxide (NO) spin radicals are effective in characterizing structures, interactions and dynamics of biomolecules. The EPR applications in cell lysates or intracellular milieu require stable spin labels, but NO radicals are unstable in such conditions. We showed that the destabilization of NO radicals in cell lysates or even in cells is caused by NADPH/NADH related enzymes, but not by the commonly believed reducing reagents such as GSH. Maleimide stabilizes the NO radicals in the cell lysates by consumption of the NADPH/NADH that are essential for the enzymes involved in destabilizing NO radicals, instead of serving as the solo thiol scavenger. The maleimide treatment retains the crowding properties of the intracellular components and allows to perform long-time EPR measurements of NO labeled biomolecules close to the intracellular conditions. The strategy of maleimide treatment on cell lysates for the EPR applications has been demonstrated on double electron-electron resonance (DEER) measurements on a number of NO labeled protein samples. The method opens a broad application range for the NO labeled biomolecules by EPR in conditions that resemble the intracellular milieu.
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Affiliation(s)
- Xi-Wei Wang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xing Zhang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
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10
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Vallina Estrada E, Zhang N, Wennerström H, Danielsson J, Oliveberg M. Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Curr Opin Struct Biol 2023; 81:102625. [PMID: 37331204 DOI: 10.1016/j.sbi.2023.102625] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably 'fluid' for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the 'random' protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.
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Affiliation(s)
- Eloy Vallina Estrada
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Nannan Zhang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Håkan Wennerström
- Division of Physical Chemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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11
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-Molecule Displacement Mapping Unveils Sign-Asymmetric Protein Charge Effects on Intraorganellar Diffusion. NANO LETTERS 2023; 23:1711-1716. [PMID: 36802676 PMCID: PMC10044514 DOI: 10.1021/acs.nanolett.2c04379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ∼40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, hence a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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Affiliation(s)
- Limin Xiang
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
- College of Chemistry and Molecular Sciences & TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Rui Yan
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Wan Li
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
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12
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525611. [PMID: 36747807 PMCID: PMC9900983 DOI: 10.1101/2023.01.26.525611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SM d M), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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13
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Rickard MM, Luo H, De Lio A, Gruebele M, Pogorelov TV. Impact of the Cellular Environment on Adenosine Triphosphate Conformations. J Phys Chem Lett 2022; 13:9809-9814. [PMID: 36228115 PMCID: PMC10077521 DOI: 10.1021/acs.jpclett.2c02375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The cytoplasm is an environment crowded by macromolecules and filled with metabolites and ions. Recent experimental and computational studies have addressed how this environment affects protein stability, folding kinetics, and protein-protein and protein-nucleic acid interactions, though its impact on metabolites remains largely unknown. Here we show how a simulated cytoplasm affects the conformation of adenosine triphosphate (ATP), a key energy source and regulatory metabolite present at high concentrations in cells. Analysis of our all-atom model of a small volume of the Escherichia coli cytoplasm when contrasted with ATP modeled in vitro or resolved with protein structures deposited in the Protein Data Bank reveals that ATP molecules bound to proteins in cell form specific pitched conformations that are not observed at significant concentrations in the other environments. We hypothesize that these interactions evolved to fulfill functional roles when ATP interacts with protein surfaces.
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Affiliation(s)
- Meredith M. Rickard
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Haolin Luo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Ashley De Lio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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14
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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15
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On the osmotic pressure of cells. QRB DISCOVERY 2022. [PMID: 37529285 PMCID: PMC10392628 DOI: 10.1017/qrd.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
The chemical potential of water (
$ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $
) provides an essential thermodynamic characterization of the environment of living organisms, and it is of equal significance as the temperature. For cells,
$ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $
is conventionally expressed in terms of the osmotic pressure (πosm). We have previously suggested that the main contribution to the intracellular πosm of the bacterium E. coli is from soluble negatively-charged proteins and their counter-ions. Here, we expand on this analysis by examining how evolutionary divergent cell types cope with the challenge of maintaining πosm within viable values. Complex organisms, like mammals, maintain constant internal πosm ≈ 0.285 osmol, matching that of 0.154 M NaCl. For bacteria it appears that optimal growth conditions are found for similar or slightly higher πosm (0.25-0.4 osmol), despite that they represent a much earlier stage in evolution. We argue that this value reflects a general adaptation for optimising metabolic function under crowded intracellular conditions. Environmental πosm that differ from this optimum require therefore special measures, as exemplified with gram-positive and gram-negative bacteria. To handle such situations, their membrane encapsulations allow for a compensating turgor pressure that can take both positive and negative values, where positive pressures allow increased frequency of metabolic events through increased intracellular protein concentrations. A remarkable exception to the rule of 0.25-0.4 osmol, is found for halophilic archaea with internal πosm ≈ 15 osmol. The internal organization of these archaea differs in that they utilize a repulsive electrostatic mechanism operating only in the ionic-liquid regime to avoid aggregation, and that they stand out from other organisms by having no turgor pressure.
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16
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Sörensen T, Leeb S, Danielsson J, Oliveberg M. Polyanions Cause Protein Destabilization Similar to That in Live Cells. Biochemistry 2021; 60:735-746. [PMID: 33635054 PMCID: PMC8028048 DOI: 10.1021/acs.biochem.0c00889] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/11/2021] [Indexed: 12/25/2022]
Abstract
The structural stability of proteins is found to markedly change upon their transfer to the crowded interior of live cells. For some proteins, the stability increases, while for others, it decreases, depending on both the sequence composition and the type of host cell. The mechanism seems to be linked to the strength and conformational bias of the diffusive in-cell interactions, where protein charge is found to play a decisive role. Because most proteins, nucleotides, and membranes carry a net-negative charge, the intracellular environment behaves like a polyanionic (Z:1) system with electrostatic interactions different from those of standard 1:1 ion solutes. To determine how such polyanion conditions influence protein stability, we use negatively charged polyacetate ions to mimic the net-negatively charged cellular environment. The results show that, per Na+ equivalent, polyacetate destabilizes the model protein SOD1barrel significantly more than monoacetate or NaCl. At an equivalent of 100 mM Na+, the polyacetate destabilization of SOD1barrel is similar to that observed in live cells. By the combined use of equilibrium thermal denaturation, folding kinetics, and high-resolution nuclear magnetic resonance, this destabilization is primarily assigned to preferential interaction between polyacetate and the globally unfolded protein. This interaction is relatively weak and involves mainly the outermost N-terminal region of unfolded SOD1barrel. Our findings point thus to a generic influence of polyanions on protein stability, which adds to the sequence-specific contributions and needs to be considered in the evaluation of in vivo data.
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Affiliation(s)
- Therese Sörensen
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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17
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Speer SL, Zheng W, Jiang X, Chu IT, Guseman AJ, Liu M, Pielak GJ, Li C. The intracellular environment affects protein-protein interactions. Proc Natl Acad Sci U S A 2021; 118:e2019918118. [PMID: 33836588 PMCID: PMC7980425 DOI: 10.1073/pnas.2019918118] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions are essential for life but rarely thermodynamically quantified in living cells. In vitro efforts show that protein complex stability is modulated by high concentrations of cosolutes, including synthetic polymers, proteins, and cell lysates via a combination of hard-core repulsions and chemical interactions. We quantified the stability of a model protein complex, the A34F GB1 homodimer, in buffer, Escherichia coli cells and Xenopus laevis oocytes. The complex is more stable in cells than in buffer and more stable in oocytes than E. coli Studies of several variants show that increasing the negative charge on the homodimer surface increases stability in cells. These data, taken together with the fact that oocytes are less crowded than E. coli cells, lead to the conclusion that chemical interactions are more important than hard-core repulsions under physiological conditions, a conclusion also gleaned from studies of protein stability in cells. Our studies have implications for understanding how promiscuous-and specific-interactions coherently evolve for a protein to properly function in the crowded cellular environment.
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Affiliation(s)
- Shannon L Speer
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Wenwen Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071 Wuhan, China
- Graduate University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071 Wuhan, China
- Graduate University of Chinese Academy of Sciences, 100049 Beijing, China
| | - I-Te Chu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Alex J Guseman
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599;
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071 Wuhan, China;
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18
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Gopan G, Gruebele M, Rickard M. In-cell protein landscapes: making the match between theory, simulation and experiment. Curr Opin Struct Biol 2020; 66:163-169. [PMID: 33254078 DOI: 10.1016/j.sbi.2020.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/10/2020] [Indexed: 11/26/2022]
Abstract
Theory, computation and experiment have matched up for the folding of small proteins in vitro, a difficult feat because folding energy landscapes are fairly smooth and free energy differences between states are small. Smoothness means that protein structure and folding are susceptible to the local environment inside living cells. Theory, computation and experiment are now exploring cellular modulation of energy landscapes. Interesting concepts have emerged, such as co-evolution of protein surfaces with their cellular environment to reduce detrimental interactions. Here we look at very recent work beginning to bring together theory, simulations and experiments in the area of protein landscape modulation, to see what problems might be solved in the near future by combining these approaches.
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Affiliation(s)
- Gopika Gopan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Meredith Rickard
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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19
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Leeb S, Yang F, Oliveberg M, Danielsson J. Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. J Phys Chem B 2020; 124:10698-10707. [PMID: 33179918 PMCID: PMC7735724 DOI: 10.1021/acs.jpcb.0c08274] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/22/2020] [Indexed: 12/26/2022]
Abstract
In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T1) and transverse (T2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T2 implies significantly higher apparent viscosity than T1. At first sight, the effect on T1 and T2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T1 and T2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T1 and T2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.
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Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
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