1
|
You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
Collapse
Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| |
Collapse
|
2
|
Gorensek-Benitez AH, Kirk B, Myers JK. Protein Fibrillation under Crowded Conditions. Biomolecules 2022; 12:biom12070950. [PMID: 35883507 PMCID: PMC9312947 DOI: 10.3390/biom12070950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.
Collapse
Affiliation(s)
- Annelise H. Gorensek-Benitez
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, CO 80903, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| | - Bryan Kirk
- Department of Biology, Davidson College, Davidson, NC 28035, USA;
| | - Jeffrey K. Myers
- Department of Chemistry, Davidson College, Davidson, NC 28035, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| |
Collapse
|
3
|
Welte H, Kovermann M. Insights into Protein Stability in Cell Lysate by 19 F NMR Spectroscopy. Chembiochem 2020; 21:3575-3579. [PMID: 32786103 PMCID: PMC7756264 DOI: 10.1002/cbic.202000413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/27/2020] [Indexed: 02/03/2023]
Abstract
In living organisms, protein folding and function take place in an inhomogeneous, highly crowded environment possessing a concentration of diverse macromolecules of up to 400 g/L. It has been shown that the intracellular environment has a pronounced effect on the stability, dynamics and function of the protein under study, and has for this reason to be considered. However, most protein studies neglect the presence of these macromolecules. Consequently, we probe here the overall thermodynamic stability of cold shock protein B from Bacillus subtilis (BsCspB) in cell lysate. We found that an increase in cell lysate concentration causes a monotonic increase in the thermodynamic stability of BsCspB. This result strongly underlines the importance of considering the biological environment when inherent protein parameters are quantitatively determined. Moreover, we demonstrate that targeted application of 19 F NMR spectroscopy operates as an ideal tool for protein studies performed in complex cellular surroundings.
Collapse
Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity KonstanzResearch School Chemical Biology (KoRS-CB)Universitätsstrasse 1078457KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity KonstanzResearch School Chemical Biology (KoRS-CB)Universitätsstrasse 1078457KonstanzGermany
| |
Collapse
|
4
|
Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
Collapse
Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
| |
Collapse
|
5
|
Okuno Y, Szabo A, Clore GM. Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions. J Am Chem Soc 2020; 142:8281-8290. [PMID: 32286812 DOI: 10.1021/jacs.0c00747] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein-small cosolute molecule interactions are ubiquitous and known to modulate the solubility, stability, and function of many proteins. Characterization of such transient weak interactions at atomic resolution remains challenging. In this work, we develop a simple and practical NMR method for extracting both energetic and dynamic information on protein-cosolute interactions from solvent paramagnetic relaxation enhancement (sPRE) measurements. Our procedure is based on an approximate (non-Lorentzian) spectral density that behaves exactly at both high and low frequencies. This spectral density contains two parameters, one global related to the translational diffusion coefficient of the paramagnetic cosolute, and the other residue specific. These parameters can be readily determined from sPRE data, and then used to calculate analytically a concentration normalized equilibrium average of the interspin distance, ⟨r-6⟩norm, and an effective correlation time, τC, that provide measures of the energetics and dynamics of the interaction at atomic resolution. We compare our approach with existing ones, and demonstrate the utility of our method using experimental 1H longitudinal and transverse sPRE data recorded on the protein ubiquitin in the presence of two different nitroxide radical cosolutes, at multiple static magnetic fields. The approach for analyzing sPRE data outlined here provides a powerful tool for deepening our understanding of extremely weak protein-cosolute interactions.
Collapse
Affiliation(s)
- Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Attila Szabo
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
6
|
Judge PT, Sesti EL, Price LE, Albert BJ, Alaniva N, Saliba EP, Halbritter T, Sigurdsson ST, Kyei GB, Barnes AB. Dynamic Nuclear Polarization with Electron Decoupling in Intact Human Cells and Cell Lysates. J Phys Chem B 2020; 124:2323-2330. [DOI: 10.1021/acs.jpcb.9b10494] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick T. Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biochemistry, Biophysics & Structural Biology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Erika L. Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Lauren E. Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Brice J. Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Edward P. Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Thomas Halbritter
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th. Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - George B. Kyei
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63130, United States
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana,
Legon, Accra 02233, Ghana
| | - Alexander B. Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
7
|
An equation for biomimicking macromolecular crowding using Escherichia coli MG1655 strain. Biophys Chem 2019; 254:106244. [PMID: 31446252 DOI: 10.1016/j.bpc.2019.106244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/13/2019] [Accepted: 08/02/2019] [Indexed: 11/20/2022]
Abstract
Macromolecules present in the intracellular environment of a cell are densely packed, resulting in a highly crowded cytosolic environment. This crowded milieu influences several biochemical equilibria such as diffusibility and association constant of biomolecules which impose a serious impact on cellular functions as well as its processes. A number of in silico and in vitro studies have been reported till date about using synthetic crowding agents for resembling such a crowding environment within the cell. Lately, it has been realized that synthetic crowders are not suitable for mimicking the intrinsic environment of the cell. In this study, proteins were assumed to be the major biological molecule which contributes to the crowding environment. We have semi-theoretically determined the total protein concentration within an individual E. coli MG1655 cell which changes notably as the growth curve proceeds from 0.2 to 1.0 OD600. The average range of total cellular protein concentration throughout the batch culture was found to be in the range of 15.2 to 178 fg/fL of cytoplasmic volume. The fundamental knowledge gained through the study was translated to applied research in the form of an equation. We propose an equation that could help to mimic the OD600 dependent crowding environment present within a single cell of E. coli in the desired volume of reaction solution. In a nutshell, the equation provides quantitative estimation of the volume of culture required to prepare the cell lysate for biomimicking the intracellular crowding environment in vitro. This finding provides a new insight into the cellular cytosolic environment that could be used as a platform to frame more cells like environment in cell-free protein synthesis (CFPS) system for synthetic biology applications.
Collapse
|
8
|
Song X, Lv T, Chen J, Wang J, Yao L. Characterization of Residue Specific Protein Folding and Unfolding Dynamics in Cells. J Am Chem Soc 2019; 141:11363-11366. [DOI: 10.1021/jacs.9b04435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiangfei Song
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhang Lv
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jia Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | |
Collapse
|
9
|
Dalaloyan A, Martorana A, Barak Y, Gataulin D, Reuveny E, Howe A, Elbaum M, Albeck S, Unger T, Frydman V, Abdelkader EH, Otting G, Goldfarb D. Tracking Conformational Changes in Calmodulin in vitro, in Cell Extract, and in Cells by Electron Paramagnetic Resonance Distance Measurements. Chemphyschem 2019; 20:1860-1868. [PMID: 31054266 DOI: 10.1002/cphc.201900341] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Indexed: 12/12/2022]
Abstract
It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca2+ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.
Collapse
Affiliation(s)
| | | | | | | | | | - Andrew Howe
- Department of Chemical and Biological Physics
| | | | - Shira Albeck
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Elwy H Abdelkader
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | |
Collapse
|
10
|
Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
Collapse
|
11
|
Grimaldo M, Lopez H, Beck C, Roosen-Runge F, Moulin M, Devos JM, Laux V, Härtlein M, Da Vela S, Schweins R, Mariani A, Zhang F, Barrat JL, Oettel M, Forsyth VT, Seydel T, Schreiber F. Protein Short-Time Diffusion in a Naturally Crowded Environment. J Phys Chem Lett 2019; 10:1709-1715. [PMID: 30897330 DOI: 10.1021/acs.jpclett.9b00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interior of living cells is a dense and polydisperse suspension of macromolecules. Such a complex system challenges an understanding in terms of colloidal suspensions. As a fundamental test we employ neutron spectroscopy to measure the diffusion of tracer proteins (immunoglobulins) in a cell-like environment (cell lysate) with explicit control over crowding conditions. In combination with Stokesian dynamics simulation, we address protein diffusion on nanosecond time scales where hydrodynamic interactions dominate over negligible protein collisions. We successfully link the experimental results on these complex, flexible molecules with coarse-grained simulations providing a consistent understanding by colloid theories. Both experiments and simulations show that tracers in polydisperse solutions close to the effective particle radius Reff = ⟨ Ri3⟩1/3 diffuse approximately as if the suspension was monodisperse. The simulations further show that macromolecules of sizes R > Reff ( R < Reff) are slowed more (less) effectively even at nanosecond time scales, which is highly relevant for a quantitative understanding of cellular processes.
Collapse
Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
- LiPhy , 38402 Saint Martin d'Hères , France
| | - Christian Beck
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Felix Roosen-Runge
- Division of Physical Chemistry , Lund University , Naturvetarvägen 14 , 22100 Lund , Sweden
| | - Martine Moulin
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Valerie Laux
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Stefano Da Vela
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Ralf Schweins
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Alessandro Mariani
- European Synchrotron Radiation Facility (ESRF) , CS 40220, F-38042 Grenoble Cedex 9, France
| | - Fajun Zhang
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | | | - Martin Oettel
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine , Keele University , Staffordshire ST5 5BG , United Kingdom
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Frank Schreiber
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| |
Collapse
|
12
|
Cotranslocational processing of the protein substrate calmodulin by an AAA+ unfoldase occurs via unfolding and refolding intermediates. Proc Natl Acad Sci U S A 2018; 115:E4786-E4795. [PMID: 29735657 DOI: 10.1073/pnas.1721811115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein remodeling by AAA+ enzymes is central for maintaining proteostasis in a living cell. However, a detailed structural description of how this is accomplished at the level of the substrate molecules that are acted upon is lacking. Here, we combine chemical cross-linking and methyl transverse relaxation-optimized NMR spectroscopy to study, at atomic resolution, the stepwise unfolding and subsequent refolding of the two-domain substrate calmodulin by the VAT AAA+ unfoldase from Thermoplasma acidophilum By engineering intermolecular disulphide bridges between the substrate and VAT we trap the substrate at different stages of translocation, allowing structural studies throughout the translocation process. Our results show that VAT initiates substrate translocation by pulling on intrinsically unstructured N or C termini of substrate molecules without showing specificity for a particular amino acid sequence. Although the B1 domain of protein G is shown to unfold cooperatively, translocation of calmodulin leads to the formation of intermediates, and these differ on an individual domain level in a manner that depends on whether pulling is from the N or C terminus. The approach presented generates an atomic resolution picture of substrate unfolding and subsequent refolding by unfoldases that can be quite different from results obtained via in vitro denaturation experiments.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Abriata LA, Spiga E, Peraro MD. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics. Biophys J 2017; 111:743-755. [PMID: 27558718 DOI: 10.1016/j.bpj.2016.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
Collapse
Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Enrico Spiga
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
15
|
Sugiki T, Kobayashi N, Fujiwara T. Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists. Comput Struct Biotechnol J 2017; 15:328-339. [PMID: 28487762 PMCID: PMC5408130 DOI: 10.1016/j.csbj.2017.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data. Owing to the remarkable progress in the past decade, we can easily access suitable and popular analytical resources for NMR structure determination of proteins with high accuracy. Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins. This review should aid NMR specialists aiming to develop new methods that accelerate the structure determination process, and open avenues for non-specialist and life scientists interested in using NMR spectroscopy to solve protein structures.
Collapse
Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
16
|
Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Guohua Xu
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| |
Collapse
|
17
|
Zhang N, An L, Li J, Liu Z, Yao L. Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment. J Am Chem Soc 2017; 139:647-654. [DOI: 10.1021/jacs.6b11058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ning Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jingwen Li
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Liu
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
| | | |
Collapse
|
18
|
Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2016; 56:530-534. [DOI: 10.1002/anie.201609639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Guohua Xu
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - 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; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| |
Collapse
|
19
|
Pérez Santero S, Favretto F, Zanzoni S, Chignola R, Assfalg M, D'Onofrio M. Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level. Arch Biochem Biophys 2016; 606:99-110. [DOI: 10.1016/j.abb.2016.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/16/2016] [Accepted: 07/21/2016] [Indexed: 11/29/2022]
|
20
|
Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol 2016; 428:2943-64. [PMID: 27255863 PMCID: PMC4976022 DOI: 10.1016/j.jmb.2016.05.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 11/17/2022]
Abstract
Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.
Collapse
Affiliation(s)
- Wonpil Im
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, United States.
| | - Arthur Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States.
| | - Ilya A Vakser
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
| |
Collapse
|
21
|
Meini MR, Tomatis PE, Weinreich DM, Vila AJ. Quantitative Description of a Protein Fitness Landscape Based on Molecular Features. Mol Biol Evol 2015; 32:1774-87. [PMID: 25767204 DOI: 10.1093/molbev/msv059] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Understanding the driving forces behind protein evolution requires the ability to correlate the molecular impact of mutations with organismal fitness. To address this issue, we employ here metallo-β-lactamases as a model system, which are Zn(II) dependent enzymes that mediate antibiotic resistance. We present a study of all the possible evolutionary pathways leading to a metallo-β-lactamase variant optimized by directed evolution. By studying the activity, stability and Zn(II) binding capabilities of all mutants in the preferred evolutionary pathways, we show that this local fitness landscape is strongly conditioned by epistatic interactions arising from the pleiotropic effect of mutations in the different molecular features of the enzyme. Activity and stability assays in purified enzymes do not provide explanatory power. Instead, measurement of these molecular features in an environment resembling the native one provides an accurate description of the observed antibiotic resistance profile. We report that optimization of Zn(II) binding abilities of metallo-β-lactamases during evolution is more critical than stabilization of the protein to enhance fitness. A global analysis of these parameters allows us to connect genotype with fitness based on quantitative biochemical and biophysical parameters.
Collapse
Affiliation(s)
- María-Rocío Meini
- Laboratory of Metalloproteins, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Pablo E Tomatis
- Laboratory of Metalloproteins, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, and Center for Computational Molecular Biology, Brown University
| | - Alejandro J Vila
- Laboratory of Metalloproteins, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
22
|
Smith AE, Zhang Z, Pielak GJ, Li C. NMR studies of protein folding and binding in cells and cell-like environments. Curr Opin Struct Biol 2014; 30:7-16. [PMID: 25479354 DOI: 10.1016/j.sbi.2014.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022]
Abstract
Proteins function in cells where the concentration of macromolecules can exceed 300g/L. The ways in which this crowded environment affects the physical properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded conditions. Many of the observations can be understood in terms of interactions between proteins and the rest of the intracellular environment (i.e. quinary interactions). Nevertheless, NMR studies of folding and binding in cells and cell-like environments remain in their infancy. The frontier involves investigations of larger proteins and further efforts in higher eukaryotic cells.
Collapse
Affiliation(s)
- Austin E Smith
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Zeting Zhang
- 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 Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA.
| | - 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 Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China.
| |
Collapse
|
23
|
Goldenberg DP, Argyle B. Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J 2014; 106:905-14. [PMID: 24559993 DOI: 10.1016/j.bpj.2013.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with (2)H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estimated to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of disordered proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
Collapse
Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
| |
Collapse
|
24
|
Hoang J, Prosser RS. Conformational Selection and Functional Dynamics of Calmodulin: A 19F Nuclear Magnetic Resonance Study. Biochemistry 2014; 53:5727-36. [DOI: 10.1021/bi500679c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua Hoang
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S
1A8, Canada
| |
Collapse
|
25
|
Abstract
Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biological functions. Whereas "looking into cells" is typically said in reference to optical microscopy, high-resolution in-cell and on-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful method that offers exciting new possibilities for structural and functional studies in and on live cells. In contrast to conventional imaging techniques, in- and on-cell NMR methods do not provide spatial information on cellular biomolecules. Instead, they enable atomic-resolution insights into the native cell states of proteins, nucleic acids, glycans, and lipids. Here we review recent advances and developments in both fields and discuss emerging concepts that have been delineated with these methods.
Collapse
Affiliation(s)
- Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, Maryland 20852-1448;
| | | |
Collapse
|
26
|
Latham MP, Kay LE. A similar in vitro and in cell lysate folding intermediate for the FF domain. J Mol Biol 2014; 426:3214-3220. [PMID: 25083919 DOI: 10.1016/j.jmb.2014.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/17/2022]
Abstract
Understanding the mechanisms by which proteins fold into their three-dimensional structures, including a description of the intermediates that are formed during the folding process, remains a goal of protein science. Most studies are performed under carefully controlled conditions in which the folding reaction is monitored in a buffer solution that is far from the natural milieu of the cell. Here, we have used (13)C and (1)H relaxation dispersion NMR spectroscopy to study folding of the FF domain in both Escherichia coli and Saccharomyces cerevisiae cellular lysates. We find that a conformationally excited state is populated in both lysates, which is very similar in structure to a folding intermediate observed in previous studies in buffer, with the kinetics and thermodynamics of the interconversion between native and intermediate conformers somewhat changed. The results point to the importance of extending folding studies beyond the test tube yet emphasize that insights can be obtained through careful experiments recorded in controlled buffer solutions.
Collapse
Affiliation(s)
- Michael P Latham
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| |
Collapse
|
27
|
Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. Intrazelluläre NMR- und EPR-Spektroskopie von biologischen Makromolekülen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311320] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
28
|
Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V. In-cell NMR and EPR spectroscopy of biomacromolecules. Angew Chem Int Ed Engl 2014; 53:10300-14. [PMID: 25070284 DOI: 10.1002/anie.201311320] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 12/21/2022]
Abstract
The dream of cell biologists is to be able to watch biological macromolecules perform their duties in the intracellular environment of live cells. Ideally, the observation of both the location and the conformation of these macromolecules with biophysical techniques is desired. The development of many fluorescence techniques, including superresolution fluorescence microscopy, has significantly enhanced our ability to spot proteins and other molecules in the crowded cellular environment. However, the observation of their structure and conformational changes while they attend their business is still very challenging. In principle, NMR and EPR spectroscopy can be used to investigate the conformation and dynamics of biological macromolecules in living cells. The development of in-cell magnetic resonance techniques has demonstrated the feasibility of this approach. Herein we review the different techniques with a focus on liquid-state in-cell NMR spectroscopy, provide an overview of applications, and discuss the challenges that lie ahead.
Collapse
Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt (Germany)
| | | | | | | | | |
Collapse
|
29
|
Spiga E, Abriata LA, Piazza F, Dal Peraro M. Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics. J Phys Chem B 2014; 118:5310-21. [PMID: 24773474 DOI: 10.1021/jp4126705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomistic level. We observe that the protein acts as a seed that speeds up the natural propensity of glucose to cluster at high concentration; the sugar molecules thus aggregate around the protein trapping it inside a dynamic cage. This process extensively dehydrates the protein surface, restricts the motions of the remaining water molecules, and drags the large-scale, collective motions of protein atoms slowing down the rate of exploration of the conformational space despite only a slight dampening of fast, local dynamics. We discuss how these effects could be relevant to the function of sugars as preservation agents in biological materials, and how crowding by small sticky molecules could modulate proteins across different reaction coordinates inside the cellular cytosol.
Collapse
Affiliation(s)
- Enrico Spiga
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | | | | | | |
Collapse
|
30
|
Xu G, Ye Y, Liu X, Cao S, Wu Q, Cheng K, Liu M, Pielak GJ, Li C. Strategies for Protein NMR in Escherichia coli. Biochemistry 2014; 53:1971-81. [DOI: 10.1021/bi500079u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guohua Xu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yansheng Ye
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Xiaoli Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shufen Cao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Qiong Wu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Gary J. Pielak
- Department
of Chemistry and Department of Biochemistry and Biophysics, University of North Carolina−Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| |
Collapse
|
31
|
Abstract
Protein stability is usually studied in simple buffered solutions, but most proteins function inside cells, where the heterogeneous and crowded environment presents a complex, nonideal system. Proteins are expected to behave differently under cellular crowding owing to two types of contacts: hard-core repulsions and weak, chemical interactions. The effect of hard-core repulsions is purely entropic, resulting in volume exclusion owing to the mere presence of the crowders. The weak interactions can be repulsive or attractive, thus enhancing or diminishing the excluded volume, respectively. We used a reductionist approach to assess the effects of intracellular crowding. Escherichia coli cytoplasm was dialyzed, lyophilized, and resuspended at two concentrations. NMR-detected amide proton exchange was then used to quantify the stability of the globular protein chymotrypsin inhibitor 2 (CI2) in these crowded solutions. The cytosol destabilizes CI2, and the destabilization increases with increasing cytosol concentration. This observation shows that the cytoplasm interacts favorably, but nonspecifically, with CI2, and these interactions overcome the stabilizing hard-core repulsions. The effects of the cytosol are even stronger than those of homogeneous protein crowders, reinforcing the biological significance of weak, nonspecific interactions.
Collapse
|
32
|
Biological Water Dynamics and Entropy: A Biophysical Origin of Cancer and Other Diseases. ENTROPY 2013. [DOI: 10.3390/e15093822] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
33
|
Kitevski-LeBlanc JL, Hoang J, Thach W, Larda ST, Prosser RS. 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate. Biochemistry 2013; 52:5780-9. [DOI: 10.1021/bi4010057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julianne L. Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - Joshua Hoang
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - William Thach
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
| | - Sacha Thierry Larda
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
34
|
Abriata LA, Spiga E, Dal Peraro M. All-atom simulations of crowding effects on ubiquitin dynamics. Phys Biol 2013; 10:045006. [DOI: 10.1088/1478-3975/10/4/045006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Latham MP, Kay LE. Probing non-specific interactions of Ca²⁺-calmodulin in E. coli lysate. JOURNAL OF BIOMOLECULAR NMR 2013; 55:239-247. [PMID: 23324860 DOI: 10.1007/s10858-013-9705-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
The biological environment in which a protein performs its function is a crowded milieu containing millions of molecules that can potentially lead to a great many transient, non-specific interactions. NMR spectroscopy is especially well suited to study these weak molecular contacts. Here, non-specific interactions between the Ca(2+)-bound form of calmodulin (CaM) and non-cognate proteins in Escherichia coli lysate are explored using Ile, Leu, Val and Met methyl probes. Changes in CaM methyl chemical shifts as a function of added E. coli lysate are measured to determine a minimum 'average' dissociation constant for interactions between Ca(2+)-CaM and E. coli lysate proteins. (2)H R 2 and (13)C R 1 spin relaxation rates report on the binding reaction as well. Our results further highlight the power of methyl containing side-chains for characterizing biomolecular interactions, even in complex in-cell like environments.
Collapse
Affiliation(s)
- Michael P Latham
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | |
Collapse
|
36
|
Li C, Liu M. Protein dynamics in living cells studied by in-cell NMR spectroscopy. FEBS Lett 2013; 587:1008-11. [PMID: 23318712 DOI: 10.1016/j.febslet.2012.12.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/18/2012] [Accepted: 12/18/2012] [Indexed: 01/06/2023]
Abstract
Most proteins function in cells where protein concentrations can reach 400 g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions.
Collapse
Affiliation(s)
- Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430072, PR China.
| | | |
Collapse
|