1
|
Banayan NE, Loughlin BJ, Singh S, Forouhar F, Lu G, Wong K, Neky M, Hunt HS, Bateman LB, Tamez A, Handelman SK, Price WN, Hunt JF. Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution. Protein Sci 2024; 33:e4898. [PMID: 38358135 PMCID: PMC10868448 DOI: 10.1002/pro.4898] [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: 06/18/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.
Collapse
Affiliation(s)
- Nooriel E. Banayan
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Blaine J. Loughlin
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Shikha Singh
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Farhad Forouhar
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Guanqi Lu
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Kam‐Ho Wong
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Vaccine Research and DevelopmentPfizer Inc.Pearl RiverNew YorkUSA
| | - Matthew Neky
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Columbia UniversityNew YorkNew YorkUSA
| | - Henry S. Hunt
- Department of PhysicsStanford UniversityStanfordCaliforniaUSA
| | | | | | - Samuel K. Handelman
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Department of Pain & Neuronal HealthEli Lily & Co.893 Delaware StIndianapolisIndianaUSA
| | - W. Nicholson Price
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
University of Michigan Law SchoolAnn ArborMichiganUSA
| | - John F. Hunt
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| |
Collapse
|
2
|
KC S, Nguyen K, Nicholson V, Walgren A, Trent T, Gollub E, Romero S, Holehouse AS, Sukenik S, Boothby TC. Disordered proteins interact with the chemical environment to tune their protective function during drying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582506. [PMID: 38464187 PMCID: PMC10925285 DOI: 10.1101/2024.02.28.582506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results demonstrate that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
Collapse
Affiliation(s)
- Shraddha KC
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Kenny Nguyen
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | | | - Annie Walgren
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Tony Trent
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Edith Gollub
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | - Sofia Romero
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | | |
Collapse
|
3
|
Hervø-Hansen S, Polák J, Tomandlová M, Dzubiella J, Heyda J, Lund M. Salt Effects on Caffeine across Concentration Regimes. J Phys Chem B 2023; 127:10253-10265. [PMID: 38058160 DOI: 10.1021/acs.jpcb.3c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to salting-in or salting-out of aqueous proteins. Early work of Tanford led to the discovery that the solvation of molecular surface motifs is proportional to the solvent accessible surface area (SASA), and later studies have shown that the proportionality constant varies with the salt concentration and type. Using multiscale computer simulations combined with vapor-pressure osmometry on caffeine-salt solutions, we reveal that this SASA description captures a rich set of molecular driving forces in tertiary solutions at changing solute and osmolyte concentrations. Central to the theoretical work is a new potential energy function that depends on the instantaneous surface area, salt type, and concentration. Used in, e.g., Monte Carlo simulations, this allows for a highly efficient exploration of many-body interactions and the resulting thermodynamics at elevated solute and salt concentrations.
Collapse
Affiliation(s)
- Stefan Hervø-Hansen
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Markéta Tomandlová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Joachim Dzubiella
- Physikalisches Institut, Albert-Ludwigs Universität Freiburg, Hermann-Herder-Straße 3, Freiburg Im Breisgau D-79104, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Praha 6, Prague CZ-16628, Czech Republic
| | - Mikael Lund
- Division of Computational Chemistry, Department of Chemistry, Lund University, Lund SE 221 00, Sweden
- Lund Institute of Advance Neutron and X-ray Science (LINXS), Lund SE 223 70, Sweden
| |
Collapse
|
4
|
Arsiccio A, Sarter T, Polidori I, Winter G, Pisano R, Shea JE. Thermodynamic Modeling and Experimental Data Reveal That Sugars Stabilize Proteins According to an Excluded Volume Mechanism. J Am Chem Soc 2023. [PMID: 37466340 DOI: 10.1021/jacs.3c04293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We present a new thermodynamic model to investigate the relative effects of excluded volume and soft interaction contributions in determining whether a cosolute will either destabilize or stabilize a protein in solution. This model is unique in considering an atomistically detailed model of the protein and accounting for the preferential accumulation/exclusion of the osmolyte molecules from the protein surface. Importantly, we use molecular dynamics simulations and experiments to validate the model. The experimental approach presents a unique means of decoupling excluded volume and soft interaction contributions using a linear polymeric series of cosolutes with different numbers of glucose subunits, from 1 (glucose) to 8 (maltooctaose), as well as an 8-mer of glucose units in the closed form (γ-CD). By studying the stabilizing effect of cosolutes along this polymeric series using lysozyme as a model protein, we validate the thermodynamic model and show that sugars stabilize proteins according to an excluded volume mechanism.
Collapse
Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tim Sarter
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Ilaria Polidori
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Roberto Pisano
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
| |
Collapse
|
5
|
Mandalaparthy V, Noid WG. A simple theory for interfacial properties of dilute solutions. J Chem Phys 2022; 157:034703. [DOI: 10.1063/5.0098579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent studies suggest that cosolute mixtures may exert significant non-additive effects upon protein stability. The corresponding liquid–vapor interfaces may provide useful insight into these non-additive effects. Accordingly, in this work, we relate the interfacial properties of dilute multicomponent solutions to the interactions between solutes. We first derive a simple model for the surface excess of solutes in terms of thermodynamic observables. We then develop a lattice-based statistical mechanical perturbation theory to derive these observables from microscopic interactions. Rather than adopting a random mixing approximation, this dilute solution theory (DST) exactly treats solute–solute interactions to lowest order in perturbation theory. Although it cannot treat concentrated solutions, Monte Carlo (MC) simulations demonstrate that DST describes the interactions in dilute solutions with much greater accuracy than regular solution theory. Importantly, DST emphasizes a fundamental distinction between the “intrinsic” and “effective” preferences of solutes for interfaces. DST predicts that three classes of solutes can be distinguished by their intrinsic preference for interfaces. While the surface preference of strong depletants is relatively insensitive to interactions, the surface preference of strong surfactants can be modulated by interactions at the interface. Moreover, DST predicts that the surface preference of weak depletants and weak surfactants can be qualitatively inverted by interactions in the bulk. We also demonstrate that DST can be extended to treat surface polarization effects and to model experimental data. MC simulations validate the accuracy of DST predictions for lattice systems that correspond to molar concentrations.
Collapse
Affiliation(s)
- Varun Mandalaparthy
- Department of Chemistry, Penn State University, University Park, State College, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, Penn State University, University Park, State College, Pennsylvania 16802, USA
| |
Collapse
|
6
|
Nishinami S, Arakawa T, Shiraki K. Classification of protein solubilizing additives by fluorescence assay. Int J Biol Macromol 2022; 203:695-702. [PMID: 35090940 DOI: 10.1016/j.ijbiomac.2022.01.137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022]
Abstract
Aromatic interaction plays a crucial role in controlling protein interaction by additives. Here we investigated the interaction of protein salting-in (solubilizing) additives with tryptophan (Trp), tyrosine (Tyr), indole, and proteins based on their fluorescence spectra. Five salting-in additives, i.e., arginine (Arg), urea, guanidine (Gdn), ethylene glycol (EG), and magnesium chloride (MgCl2), showed different effects on the fluorescence properties of Trp and Tyr. Arg significantly reduced fluorescence intensity of Trp and Tyr, as was the case for glycine to a lesser extent. MgCl2 and calcium chloride (CaCl2) showed little effect on the aromatic fluorescence spectra. Gdn also showed little effect on the aromatic fluorescence spectra of Trp and Tyr even at high concentrations. EG increased the aromatic fluorescence intensity of Trp and Tyr with blue-shifted emission wavelength. Urea enhanced fluorescence of Trp and Tyr without altering emission wavelength. These results indicate that the protein solubilizing additives interact with aromatic groups differently.
Collapse
Affiliation(s)
- Suguru Nishinami
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, CA 92130, United States
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
| |
Collapse
|
7
|
Abstract
It has been a long-standing conviction that a protein's native fold is selected from a vast number of conformers by the optimal constellation of enthalpically favorable interactions. In marked contrast, this Perspective introduces a different mechanism, one that emphasizes conformational entropy as the principal organizer in protein folding while proposing that the conventional view is incomplete. This mechanism stems from the realization that hydrogen bond satisfaction is a thermodynamic necessity. In particular, a backbone hydrogen bond may add little to the stability of the native state, but a completely unsatisfied backbone hydrogen bond would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization, typically between -5 and -15 kcal/mol under physiological conditions. Consequently, upon folding, buried backbone polar groups must form hydrogen bonds, and they do so by assembling scaffolds of α-helices and/or strands of β-sheet, the only conformers in which, with rare exception, hydrogen bond donors and acceptors are exactly balanced. In addition, only a few thousand viable scaffold topologies are possible for a typical protein domain. This thermodynamic imperative winnows the folding population by culling conformers with unsatisfied hydrogen bonds, thereby reducing the entropy cost of folding. Importantly, conformational restrictions imposed by backbone···backbone hydrogen bonding in the scaffold are sequence-independent, enabling mutation─and thus evolution─without sacrificing the structure.
Collapse
Affiliation(s)
- George D Rose
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2683, United States
| |
Collapse
|
8
|
Kar M, Posey AE, Dar F, Hyman AA, Pappu RV. Glycine-Rich Peptides from FUS Have an Intrinsic Ability to Self-Assemble into Fibers and Networked Fibrils. Biochemistry 2021; 60:3213-3222. [PMID: 34648275 PMCID: PMC10715152 DOI: 10.1021/acs.biochem.1c00501] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycine-rich regions feature prominently in intrinsically disordered regions (IDRs) of proteins that drive phase separation and the regulated formation of membraneless biomolecular condensates. Interestingly, the Gly-rich IDRs seldom feature poly-Gly tracts. The protein fused in sarcoma (FUS) is an exception. This protein includes two 10-residue poly-Gly tracts within the prion-like domain (PLD) and at the interface between the PLD and the RNA binding domain. Poly-Gly tracts are known to be highly insoluble, being potent drivers of self-assembly into solid-like fibrils. Given that the internal concentrations of FUS and FUS-like molecules cross the high micromolar and even millimolar range within condensates, we reasoned that the intrinsic insolubility of poly-Gly tracts might be germane to emergent fluid-to-solid transitions within condensates. To assess this possibility, we characterized the concentration-dependent self-assembly for three non-overlapping 25-residue Gly-rich peptides derived from FUS. Two of the three peptides feature 10-residue poly-Gly tracts. These peptides form either long fibrils based on twisted ribbon-like structures or self-supporting gels based on physical cross-links of fibrils. Conversely, the peptide with similar Gly contents but lacking a poly-Gly tract does not form fibrils or gels. Instead, it remains soluble across a wide range of concentrations. Our findings highlight the ability of poly-Gly tracts within IDRs that drive phase separation to undergo self-assembly. We propose that these tracts are likely to contribute to nucleation of fibrillar solids within dense condensates formed by FUS.
Collapse
Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Ammon E. Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Anthony A. Hyman
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| |
Collapse
|
9
|
Joseph JA, Reinhardt A, Aguirre A, Chew PY, Russell KO, Espinosa JR, Garaizar A, Collepardo-Guevara R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. NATURE COMPUTATIONAL SCIENCE 2021; 1:732-743. [PMID: 35795820 PMCID: PMC7612994 DOI: 10.1038/s43588-021-00155-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Various physics- and data-driven sequence-dependent protein coarse-grained models have been developed to study biomolecular phase separation and elucidate the dominant physicochemical driving forces. Here, we present Mpipi, a multiscale coarse-grained model that describes almost quantitatively the change in protein critical temperatures as a function of amino-acid sequence. The model is parameterised from both atomistic simulations and bioinformatics data and accounts for the dominant role of π-π and hybrid cation-π/π-π interactions and the much stronger attractive contacts established by arginines than lysines. We provide a comprehensive set of benchmarks for Mpipi and seven other residue-level coarse-grained models against experimental radii of gyration and quantitative in-vitro phase diagrams; Mpipi predictions agree well with experiment on both fronts. Moreover, it can account for protein-RNA interactions, correctly predicts the multiphase behaviour of a charge-matched poly-arginine/poly-lysine/RNA system, and recapitulates experimental LLPS trends for sequence mutations on FUS, DDX4 and LAF-1 proteins.
Collapse
Affiliation(s)
- Jerelle A. Joseph
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Anne Aguirre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kieran O. Russell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Jorge R. Espinosa
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Adiran Garaizar
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| |
Collapse
|
10
|
Insight into the protein salting-in mechanism of arginine, magnesium chloride and ethylene glycol: Solvent interaction with aromatic solutes. Int J Biol Macromol 2021; 188:670-677. [PMID: 34400229 DOI: 10.1016/j.ijbiomac.2021.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022]
Abstract
Key factors in the salting-in effects on proteins of additives are their interactions with aromatic groups. We studied the interaction of four aromatic solutes, benzyl alcohol (BA), phenol, 4-hydroxybenzyl alcohol (4-HBA) and methyl gallate (MG), with different salting-in additives, arginine hydrochloride (ArgHCl), magnesium chloride (MgCl2), ethylene glycol (EG), and guanidine hydrochloride (GdnHCl) using solubility measurements. We used sodium chloride (NaCl) as a control. MgCl2 decreased the solubility of the four aromatic solutes with weak solute dependence. In contrast, ArgHCl, GdnHCl, and EG increased the solubility of four aromatic solutes with a similar solute dependence. Their salting-in effects were weaker on BA and 4-HBA and stronger on phenol and MG. These results indicate that attached groups alter the aromatic properties, affecting the interactions between the benzene ring and these three additives. More importantly, the observed results demonstrate that the salting-in mechanism is different between MgCl2, EG and ArgHCl, which should play a role in their effects on protein solubility.
Collapse
|
11
|
Katyal N, Sharma S, Deep S. Delving into controversial dichotomy of direct and indirect mechanisms of Trehalose: In search of unanimous consensus. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Adams E, Pezzotti S, Ahlers J, Rüttermann M, Levin M, Goldenzweig A, Peleg Y, Fleishman SJ, Sagi I, Havenith M. Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction. JACS AU 2021; 1:1076-1085. [PMID: 34337607 PMCID: PMC8317155 DOI: 10.1021/jacsau.1c00155] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 05/15/2023]
Abstract
Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.
Collapse
Affiliation(s)
- Ellen
M. Adams
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Simone Pezzotti
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Jonas Ahlers
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Maximilian Rüttermann
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Maxim Levin
- Department
of Biological Regulation, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Adi Goldenzweig
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Yoav Peleg
- Structural
Proteomics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J. Fleishman
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Irit Sagi
- Department
of Biological Regulation, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Martina Havenith
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| |
Collapse
|
13
|
Markin CJ, Mokhtari DA, Sunden F, Appel MJ, Akiva E, Longwell SA, Sabatti C, Herschlag D, Fordyce PM. Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. Science 2021; 373:373/6553/eabf8761. [PMID: 34437092 DOI: 10.1126/science.abf8761] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a microfluidic platform for high-throughput expression, purification, and characterization of more than 1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA (phosphate-irrepressible alkaline phosphatase of Flavobacterium), we performed more than 670,000 reactions and determined more than 5000 kinetic and physical constants for multiple substrates and inhibitors. We uncovered extensive kinetic partitioning to a misfolded state and isolated catalytic effects, revealing spatially contiguous regions of residues linked to particular aspects of function. Regions included active-site proximal residues but extended to the enzyme surface, providing a map of underlying architecture not possible to derive from existing approaches. HT-MEK has applications that range from understanding molecular mechanisms to medicine, engineering, and design.
Collapse
Affiliation(s)
- C J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - F Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - E Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - S A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - C Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub; San Francisco, CA 94110, USA
| |
Collapse
|
14
|
Schmit JD, Feric M, Dundr M. How Hierarchical Interactions Make Membraneless Organelles Tick Like Clockwork. Trends Biochem Sci 2021; 46:525-534. [PMID: 33483232 PMCID: PMC8195823 DOI: 10.1016/j.tibs.2020.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates appear throughout the cell, serving many different biochemical functions. We argue that condensate functionality is optimized when the interactions driving condensation vary widely in affinity. Strong interactions provide structural specificity needed to encode functional properties but carry the risk of kinetic arrest, while weak interactions allow the system to remain dynamic but do not restrict the conformational ensemble enough to sustain specific functional features. To support our opinion, we describe illustrative examples of the interplay of strong and weak interactions that are found in the nucleolus, SPOP/DAXX condensates, polySUMO/polySIM condensates, chromatin, and stress granules. The common feature of these systems is a hierarchical assembly motif in which weak, transient interactions condense structurally defined functional units.
Collapse
Affiliation(s)
- Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
| | - Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Miroslav Dundr
- Center for Cancer Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA.
| |
Collapse
|
15
|
Kaplan AR, Olson R, Alexandrescu AT. Protein yoga: Conformational versatility of the Hemolysin II C-terminal domain detailed by NMR structures for multiple states. Protein Sci 2021; 30:990-1005. [PMID: 33733504 DOI: 10.1002/pro.4066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 11/05/2022]
Abstract
The C-terminal domain of Bacillus cereus hemolysin II (HlyIIC), stabilizes the trans-membrane-pore formed by the HlyII toxin and may aid in target cell recognition. Initial efforts to determine the NMR structure of HlyIIC were hampered by cis/trans isomerization about the single proline at position 405 that leads to doubling of NMR resonances. We used the mutant P405M-HlyIIC that eliminates the cis proline to determine the NMR structure of the domain, which revealed a novel fold. Here, we extend earlier studies to the NMR structure determination of the cis and trans states of WT-HlyIIC that exist simultaneously in solution. The primary structural differences between the cis and trans states are in the loop that contains P405, and structurally adjacent loops. Thermodynamic linkage analysis shows that at 25 C the cis proline, which already has a large fraction of 20% in the unfolded protein, increases to 50% in the folded state due to coupling with the global stability of the domain. The P405M or P405A substitutions eliminate heterogeneity due to proline isomerization but lead to the formation of a new dimeric species. The NMR structure of the dimer shows that it is formed through domain-swapping of strand β5, the last segment of secondary structure following P405. The presence of P405 in WT-HlyIIC strongly disfavors the dimer compared to the P405M-HlyIIC or P405A-HlyIIC mutants. The WT proline may thus act as a "gatekeeper," warding off aggregative misfolding.
Collapse
Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
16
|
Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein. QRB DISCOVERY 2021. [PMID: 37529678 PMCID: PMC10392690 DOI: 10.1017/qrd.2020.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Although the consequences of the crowded cell environments may affect protein folding, function and misfolding reactions, these processes are often studied in dilute solutions in vitro. We here used biophysical experiments to investigate the amyloid fibril formation process of the fish protein apo-β-parvalbumin in solvent conditions that mimic steric and solvation aspects of the in vivo milieu. Apo-β-parvalbumin is a folded protein that readily adopts an amyloid state via a nucleation–elongation mechanism. Aggregation experiments in the presence of macromolecular crowding agents (probing excluded volume, entropic effects) as well as small molecule osmolytes (probing solvation, enthalpic effects) revealed that both types of agents accelerate overall amyloid formation, but the elongation step was faster with macromolecular crowding agents but slower in the presence of osmolytes. The observations can be explained by the steric effects of excluded volume favoring assembled states and that amyloid nucleation does not involve monomer unfolding. In contrast, the solvation effects due to osmolyte presence promote nucleation but not elongation. Therefore, the amyloid-competent nuclei must be compact with less osmolytes excluded from the surface than either the folded monomers or amyloid fibers. We conclude that, in contrast to other amyloidogenic folded proteins, amyloid formation of apo-β-parvalbumin is accelerated by crowded cell-like conditions due to a nucleation process that does not involve large-scale protein unfolding.
Collapse
|
17
|
Stressing crystals with solutes: Effects of added solutes on crystalline caffeine and their relevance to determining transfer free energies. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
18
|
Holehouse AS, Sukenik S. Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning. J Chem Theory Comput 2020; 16:1794-1805. [DOI: 10.1021/acs.jctc.9b00604] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, UC Merced, Merced, California 95340, United States
| |
Collapse
|
19
|
Abstract
Intrinsically disordered proteins (IDPs) can adopt a range of conformations from globules to swollen coils. This large range of conformational preferences for different IDPs raises the question of how conformational preferences are encoded by sequence. Global compositional features of a sequence such as the fraction of charged residues and the net charge per residue engender certain conformational biases. However, more specific sequence features such as the patterning of oppositely charged residues, expansion driving residues, or residues that can undergo posttranslational modifications can also influence the conformational ensembles of an IDP. Here, we outline how to calculate important global compositional features and patterning metrics that can be used to classify IDPs into different conformational classes and predict relative changes in conformation for sequences with the same amino acid composition. Although increased effort has been devoted to determining conformational properties of IDPs in recent years, quantitative predictions of conformation directly from sequence remain difficult and often inaccurate. Thus, if quantitative predictions of conformational properties are desired, then sequence-specific simulations must be performed.
Collapse
Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
20
|
Katyal N, Deep S. A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways. Phys Chem Chem Phys 2019; 21:24269-24285. [PMID: 31670327 DOI: 10.1039/c9cp03763b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.
Collapse
Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, Delhi, India.
| | | |
Collapse
|
21
|
Banks DD, Cordia JF, Spasojevic V, Sun J, Franc S, Cho Y. Isotonic concentrations of excipients control the dimerization rate of a therapeutic immunoglobulin G1 antibody during refrigerated storage based on their rank order of native-state interaction. Protein Sci 2019; 27:2073-2083. [PMID: 30267438 DOI: 10.1002/pro.3518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/06/2018] [Accepted: 09/25/2018] [Indexed: 01/12/2023]
Abstract
Inert co-solutes, or excipients, are often included in protein biologic formulations to adjust the tonicity of liquid dosage forms intended for subcutaneous delivery. Despite the low concentration of their use, many of these excipients alter protein-protein interactions such as dimerization and aggregation rates of high concentration monoclonal antibody (mAb) therapeutics to varying extents during long-term refrigerated clinical storage, challenging the formulation scientist to make informed excipient selections at the earliest stages of development when protein supply and time are often limited. The objectives of this study were to better understand how isotonic concentrations of excipients influence the dimerization rates of a model mAb stored at refrigerated and room temperatures and explore protein sparing biophysical methods capable of predicting this dependence. Despite their prevalence of use in the biopharmaceutical industry, methods for assessing conformational stability such differential scanning calorimetry and isothermal equilibrium unfolding showed little predictive power and we highlight some of the assumptions and technical challenges of their use with mAbs. Conversely, measures of colloidal stability of the native-state such as preferential interaction coefficients measured by vapor pressure osmometry and solubility assessed by polyethylene-glycol induced precipitation correlated reasonably well with the mAb dimerization data and are most consistent with the excipients tested minimizing dimerization by interacting favorably with the residues comprising the protein-protein association interface.
Collapse
Affiliation(s)
- Douglas D Banks
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jon F Cordia
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Vladimir Spasojevic
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jeonghoon Sun
- Department of Biotherapeutics, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Sarah Franc
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Younhee Cho
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| |
Collapse
|
22
|
Choi JM, Pappu RV. Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics. J Chem Theory Comput 2019; 15:1367-1382. [PMID: 30633502 PMCID: PMC10749164 DOI: 10.1021/acs.jctc.8b00573] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of examples to highlight the preservation of accuracies as well as examples that demonstrate the improvements. Our efforts show how the recent experimentally derived and computationally optimized coil-library landscapes can be used as a touchstone for quantifying errors and making improvements to molecular mechanics force fields.
Collapse
Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
| |
Collapse
|
23
|
Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers. J Mol Biol 2018; 430:4619-4635. [DOI: 10.1016/j.jmb.2018.06.031] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022]
|
24
|
Li J, Hilser VJ. Assessing Allostery in Intrinsically Disordered Proteins With Ensemble Allosteric Model. Methods Enzymol 2018; 611:531-557. [PMID: 30471699 DOI: 10.1016/bs.mie.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intrinsically disordered (ID) proteins have been shown to play a major role in signaling in a broad range of proteins, using a process known as allostery, wherein the protein can integrate one or a number of inputs to regulate its function. The disorder-mediated allostery can be understood energetically with ensemble allosteric model (EAM). In this model, the molecule without effectors is considered as an ensemble of preexisting conformations, and effector binding is treated as an energetic perturbation of the ensemble to redistribute the microstates that are favorable or unfavorable to the second binding partner. As it only considers the intrinsic energetics of the system and does not depend on a crystallographic structure, it can be applied to both structured proteins, ID proteins, and mixed proteins with both structured and ID domains. Simulation with EAM on the basis of experimental data can help quantitatively explain experimental observations, as well as to make predictions to direct future research. This has recently been illustrated with the case of human glucocorticoid receptor, a multidomain transcription factor that contains both structured and disordered regions. In this chapter, we describe the assays for measuring the transcriptional activity, binding affinity to cognate DNA, conformational stability, either on single domain or tandem coupled domains in the GR two-domain isoforms. We then explain how these data are utilized as input parameters or constraints in the EAM for quantitative estimates of stabilities and coupling energies for each domain through global minimization method.
Collapse
Affiliation(s)
- Jing Li
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Vincent J Hilser
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Department of Biology, Johns Hopkins University, Baltimore, MD, United States.
| |
Collapse
|
25
|
Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
|
26
|
Ohmae E, Hamajima Y, Nagae T, Watanabe N, Kato C. Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:680-691. [PMID: 29630970 DOI: 10.1016/j.bbapap.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Abstract
We previously found that the enzymatic activity of 3-isopropylmalate dehydrogenase from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 (SbIPMDH) was pressure-tolerant up to 100 MPa, but that from its atmospheric congener S. oneidensis strain MR-1 (SoIPMDH) was pressure-sensitive. Such characteristics were determined by only one amino acid residue at position 266, serine (SoIPMDH) or alanine (SbIPMDH) [Y. Hamajima et al. Extremophiles 20: 177, 2016]. In this study, we investigated the structural stability of these enzymes. At pH 7.6, SoIPMDH was slightly more stable against hydrostatic pressure than SbIPMDH, contrary to the physiological pressures of their normal environments. Pressure unfolding of these IPMDHs followed a two-state unfolding model between a native dimer and two unfolded monomers, and the dimer structure was pressure-tolerant up to 200 MPa, employing a midpoint pressure of 245.3 ± 0.1 MPa and a volume change of -225 ± 24 mL mol-1 for the most unstable mutant, SbIPMDH A266S. Thus, their pressure-dependent activity did not originate from structural perturbations such as unfolding or dimer dissociation. Conversely, urea-induced unfolding of these IPMDHs followed a three-state unfolding model, including a dimer intermediate. Interestingly, the first transition was strongly pH-dependent but pressure-independent; however, the second transition showed the opposite pattern. Obtained volume changes due to urea-induced unfolding were almost equal for both IPMDHs, approximately +10 and -30 mL mol-1 for intermediate formation and dimer dissociation, respectively. These results indicated that both IPMDHs have similar structural stability, and a pressure-adaptation mechanism was provided for only the enzymatic activity of SbIPMDH.
Collapse
Affiliation(s)
- Eiji Ohmae
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Yuki Hamajima
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan; Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi 464-8603, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| |
Collapse
|
27
|
Su Z, Ravindhran G, Dias CL. Effects of Trimethylamine-N-oxide (TMAO) on Hydrophobic and Charged Interactions. J Phys Chem B 2018; 122:5557-5566. [DOI: 10.1021/acs.jpcb.7b11847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Gopal Ravindhran
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| |
Collapse
|
28
|
Tischer A, Machha VR, Rösgen J, Auton M. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams. Biopolymers 2018; 109:e23106. [PMID: 29457634 DOI: 10.1002/bip.23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 11/09/2022]
Abstract
Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how Δ H and the urea m-value interconvert through the slope of cm versus T, ( ∂ c m / ∂ T ) = Δ H / ( m T ) . This relationship permits the calculation of Δ H at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from Δ H obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of Δ H and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall free energy.
Collapse
Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Venkata R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jörg Rösgen
- Department Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, 17033
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
29
|
Lin Y, Currie SL, Rosen MK. Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs. J Biol Chem 2017; 292:19110-19120. [PMID: 28924037 PMCID: PMC5704491 DOI: 10.1074/jbc.m117.800466] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/12/2017] [Indexed: 01/04/2023] Open
Abstract
Liquid–liquid phase separation (LLPS) is thought to contribute to the establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules. To understand how folded domains and IDRs can cooperate to modulate LLPS, we generated a series of engineered proteins. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. We found that the wild-type IDR promotes LLPS of the polySH3–polyPRM system, decreasing the phase separation threshold concentration by 8-fold. Systematic mutation of tyrosine residues in Gly/Ser-Tyr-Gly/Ser motifs of the IDR reduced this effect, depending on the number but not on the position of these substitutions. Mutating all tyrosines to non-aromatic residues or phosphorylating the IDR raised the phase separation threshold above that of the unmodified polySH3–polyPRM pair. These results show that low-complexity IDRs can modulate LLPS both positively and negatively, depending on the degree of aromaticity and phosphorylation status. Our findings provide plausible mechanisms by which these sequences could alter RNA granule properties on evolutionary and cellular timescales.
Collapse
Affiliation(s)
- Yuan Lin
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Simon L Currie
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Michael K Rosen
- From the Department of Biophysics, University of Texas Southwestern Medical Center and .,the Howard Hughes Medical Institute, Dallas, Texas 75390
| |
Collapse
|
30
|
Su Z, Mahmoudinobar F, Dias CL. Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins. PHYSICAL REVIEW LETTERS 2017; 119:108102. [PMID: 28949191 DOI: 10.1103/physrevlett.119.108102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 05/16/2023]
Abstract
To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.
Collapse
Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Farbod Mahmoudinobar
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| |
Collapse
|
31
|
Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates. Biophys J 2016; 110:1280-90. [PMID: 27028638 DOI: 10.1016/j.bpj.2015.12.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/08/2015] [Accepted: 12/31/2015] [Indexed: 12/19/2022] Open
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments.
Collapse
|
32
|
Zimmermann MT, Tischer A, Whitten ST, Auton M. Structural origins of misfolding propensity in the platelet adhesive von Willebrand factor A1 domain. Biophys J 2016. [PMID: 26200876 DOI: 10.1016/j.bpj.2015.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The von Willebrand factor (VWF) A1 and A3 domains are structurally isomorphic yet exhibit distinct mechanisms of unfolding. The A1 domain, responsible for platelet adhesion to VWF in hemostasis, unfolds through a molten globule intermediate in an apparent three-state mechanism, while A3 unfolds by a classical two-state mechanism. Inspection of the sequences or structures alone does not elucidate the source of this thermodynamic conundrum; however, the three-state character of the A1 domain suggests that it has more than one cooperative substructure yielding two separate unfolding transitions not present in A3. We investigate the extent to which structural elements contributing to intermediate conformations can be identified using a residue-specific implementation of the structure-energy-equivalence-of-domains algorithm (SEED), which parses proteins of known structure into their constituent thermodynamically cooperative components using protein-group-specific, transfer free energies. The structural elements computed to contribute to the non-two-state character coincide with regions where Von Willebrand disease mutations induce misfolded molten globule conformations of the A1 domain. This suggests a mechanism for the regulation of rheological platelet adhesion to A1 based on cooperative flexibility of the α2 and α3 helices flanking the platelet GPIbα receptor binding interface.
Collapse
Affiliation(s)
- Michael T Zimmermann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Alexander Tischer
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Matthew Auton
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
33
|
Auton M. Untangling a Structurally Resolved Protein Folding Intermediate. Biophys J 2016; 110:1205-6. [PMID: 27028629 PMCID: PMC4816685 DOI: 10.1016/j.bpj.2016.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
34
|
Ruff KM, Harmon TS, Pappu RV. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences. J Chem Phys 2015; 143:243123. [PMID: 26723608 PMCID: PMC4644154 DOI: 10.1063/1.4935066] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/21/2015] [Indexed: 01/28/2023] Open
Abstract
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
Collapse
Affiliation(s)
- Kiersten M Ruff
- Computational and Systems Biology Program and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA
| | - Tyler S Harmon
- Department of Physics and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, CB 1097, St. Louis, Missouri 63130-4899, USA
| |
Collapse
|
35
|
Kashid SM, Jin GY, Bagchi S, Kim YS. Cosolvent Effects on Solute–Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations. J Phys Chem B 2015; 119:15334-43. [DOI: 10.1021/acs.jpcb.5b08643] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Somnath M. Kashid
- Physical
and Materials Chemistry Division—CSIR, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Geun Young Jin
- Department
of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
| | - Sayan Bagchi
- Physical
and Materials Chemistry Division—CSIR, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Yung Sam Kim
- Department
of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
| |
Collapse
|
36
|
Chalikian TV. Effect of cosolvent on protein stability: a theoretical investigation. J Chem Phys 2015; 141:22D504. [PMID: 25494775 DOI: 10.1063/1.4895530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a statistical thermodynamic algorithm for analyzing solvent-induced folding/unfolding transitions of proteins. The energetics of protein transitions is governed by the interplay between the cavity formation contribution and the term reflecting direct solute-cosolvent interactions. The latter is viewed as an exchange reaction in which the binding of a cosolvent to a solute is accompanied by release of waters of hydration to the bulk. Our model clearly differentiates between the stoichiometric and non-stoichiometric interactions of solvent or co-solvent molecules with a solute. We analyzed the urea- and glycine betaine (GB)-induced conformational transitions of model proteins of varying size which are geometrically approximated by a sphere in their native state and a spherocylinder in their unfolded state. The free energy of cavity formation and its changes accompanying protein transitions were computed based on the concepts of scaled particle theory. The free energy of direct solute-cosolvent interactions were analyzed using empirical parameters previously determined for urea and GB interactions with low molecular weight model compounds. Our computations correctly capture the mode of action of urea and GB and yield realistic numbers for (∂ΔG°/∂a3)T,P which are related to the m-values of protein denaturation. Urea is characterized by negative values of (∂ΔG°/∂a3)T,P within the entire range of urea concentrations analyzed. At concentrations below ∼1 M, GB exhibits positive values of (∂ΔG°/∂a3)T,P which turn positive at higher GB concentrations. The balance between the thermodynamic contributions of cavity formation and direct solute-cosolvent interactions that, ultimately, defines the mode of cosolvent action is extremely subtle. A 20% increase or decrease in the equilibrium constant for solute-cosolvent binding may change the sign of (∂ΔG°/∂a3)T,P thereby altering the mode of cosolvent action (stabilizing to destabilizing or vice versa).
Collapse
Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| |
Collapse
|
37
|
Hong J, Gierasch LM, Liu Z. Its preferential interactions with biopolymers account for diverse observed effects of trehalose. Biophys J 2015; 109:144-53. [PMID: 26153711 PMCID: PMC4572414 DOI: 10.1016/j.bpj.2015.05.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 10/23/2022] Open
Abstract
Biopolymer homeostasis underlies the health of organisms, and protective osmolytes have emerged as one strategy used by Nature to preserve biopolymer homeostasis. However, a great deal remains unknown about the mechanism of action of osmolytes. Trehalose, as a prominent example, stabilizes proteins against denaturation by extreme temperature and denaturants, preserves membrane integrity upon freezing or in dry conditions, inhibits polyQ-mediated protein aggregation, and suppresses the aggregation of denatured proteins. The underlying thermodynamic mechanisms of such diverse effects of trehalose remain unclear or controversial. In this study, we applied the surface-additive method developed in the Record laboratory to attack this issue. We characterized the key features of trehalose-biopolymer preferential interactions and found that trehalose has strong unfavorable interactions with aliphatic carbon and significant favorable interactions with amide/anionic oxygen. This dissection has allowed us to elucidate the diverse effects of trehalose and to identify the crucial functional group(s) responsible for its effects. With (semi)quantitative thermodynamic analysis, we discovered that 1) the unfavorable interaction of trehalose with hydrophobic surfaces is the dominant factor in its effect on protein stability, 2) the favorable interaction of trehalose with polar amides enables it to inhibit polyQ-mediated protein aggregation and the aggregation of denatured protein in general, and 3) the favorable interaction of trehalose with phosphate oxygens, together with its unfavorable interaction with aliphatic carbons, enables trehalose to preserve membrane integrity in aqueous solution. These results provide a basis for a full understanding of the role of trehalose in biopolymer homeostasis and the reason behind its evolutionary selection as an osmolyte, as well as for a better application of trehalose as a chemical chaperone.
Collapse
Affiliation(s)
- Jiang Hong
- School of Life Science, Shanghai University, Shanghai, China.
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Zhicheng Liu
- School of Life Science, Shanghai University, Shanghai, China
| |
Collapse
|
38
|
Abstract
Virtually all taxa use osmolytes to protect cells against biochemical stress. Osmolytes often occur in mixtures, such as the classical combination of urea with TMAO (trimethylamine N-oxide) in cartilaginous fish or the cocktail of at least six different osmolytes in the kidney. The concentration patterns of osmolyte mixtures found in vivo make it likely that synergy between them plays an important role. Using statistical mechanical n-component Kirkwood-Buff theory, we show from first principles that synergy in protein-osmolyte systems can arise from two separable sources: (1) mutual alteration of protein surface solvation and (2) effects mediated through bulk osmolyte chemical activities. We illustrate both effects in a four-component system with the experimental example of the unfolding of a notch ankyrin domain in urea-TMAO mixtures, which make urea a less effective denaturant and TMAO a more effective stabilizer. Protein surface effects are primarily responsible for this synergy. The specific patterns of surface solvation point to denatured state expansion as the main factor, as opposed to direct competition.
Collapse
Affiliation(s)
- Jörg Rösgen
- Department of Biochemistry
and Molecular Biology, Penn State University
College of Medicine, Hershey, Pennsylvania 17033, United States
| |
Collapse
|
39
|
The role of the concentration scale in the definition of transfer free energies. Biophys Chem 2015; 196:68-76. [DOI: 10.1016/j.bpc.2014.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 11/18/2022]
|
40
|
Cafiso DS. Identifying and quantitating conformational exchange in membrane proteins using site-directed spin labeling. Acc Chem Res 2014; 47:3102-9. [PMID: 25152957 PMCID: PMC4204925 DOI: 10.1021/ar500228s] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein structures are not static but sample different conformations
over a range of amplitudes and time scales. These fluctuations may
involve relatively small changes in bond angles or quite large rearrangements
in secondary structure and tertiary fold. The equilibrium between
discrete structural substates on the microsecond to millisecond time
scale is sometimes termed conformational exchange. Protein dynamics
and conformational exchange are believed to provide the basis for
many important activities, such as protein–protein and protein–ligand
interactions, enzymatic activity and protein allostery; however, for
many proteins, the dynamics and conformational exchange that lead
to function are poorly defined. Spectroscopic methods, such
as NMR, are among the most important
methods to explore protein dynamics and conformational exchange; however,
they are difficult to implement in some systems and with some types
of exchange events. Site-directed spin labeling (SDSL) is an EPR based
approach that is particularly well-suited to high molecular-weight
systems such as membrane proteins. Because of the relatively fast
time scale for EPR spectroscopy, it is an excellent method to examine
exchange. Conformations that are in exchange are captured as distinct
populations in the EPR spectrum, and this feature when combined with
the use of methods that can shift the free energy of conformational
substates allows one to identify regions of proteins that are in dynamic
exchange. In addition, modern pulse EPR methods have the ability to
examine conformational heterogeneity, resolve discrete protein states,
and identify the substates in exchange. Protein crystallography
has provided high-resolution models for
a number of membrane proteins; but because of conformational exchange,
these models do not always reflect the structures that are present
when the protein is in a native bilayer environment. In the case of
the Escherichia coli vitamin B12 transporter,
BtuB, the energy coupling segment of this protein undergoes a substrate-dependent
unfolding, which acts to couple this outer-membrane protein to the
inner-membrane protein TonB. EPR spectroscopy demonstrates that the
energy coupling segment is in equilibrium between ordered and disordered
states, and that substrate binding shifts this equilibrium to favor
an unfolded state. However, in crystal structures of BtuB, this segment
is resolved and folded within the protein, and neither the presence
of this equilibrium nor the substrate-induced change is revealed.
This is a result of the solute environment and the crystal lattice,
both of which act to stabilize one conformational substate of the
transporter. Using SDSL, it can be shown that conformational
exchange is present
in other regions of BtuB and in other members of this transporter
family. Conformational exchange has also been examined in systems
such as the plasma membrane SNARE protein, syntaxin 1A, where dynamics
are controlled by regulatory proteins such as munc18. Regulating the
microsecond to millisecond time scale dynamics in the neuronal SNAREs
is likely to be a key feature that regulates assembly of the SNAREs
and neurotransmitter release.
Collapse
Affiliation(s)
- David S. Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904-4319, United States
| |
Collapse
|
41
|
Cohen P, Dill KA, Jaswal SS. Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions. J Phys Chem B 2014; 118:10618-23. [PMID: 25141127 DOI: 10.1021/jp506379r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is common to denature proteins by using high temperatures or by adding guanidinium chloride (GdmCl). However, the physical mechanism of denaturation is not well understood. Based on extensive experimental data, we developed a thermodynamic binding-polynomial model for the process of transferring nonpolar amino acids from water into GdmCl solutions, as a function of temperature and GdmCl concentration. To mimic nonpolar amino acids, we utilized the model compound, N-acetyl-tryptophanamide (NATA). We find that all nonpolar amino acids behave like NATA, with a scale factor linearly dependent on the surface area. Our model with three thermodynamic parameters fully captures the nonlinear dependencies on both the temperature and GdmCl concentration: binding the first guanidinium ion (Gdm(+)) to NATA has favorable entropy and unfavorable enthalpy of desolvation (ΔS = +11.7 cal/mol, ΔH = +3.9 kcal/mol), while cooperativity of binding a second Gdm(+) has a small contribution (K = 0.032 ± 0.003). This model may be useful for a better understanding of protein denaturation by temperature and GdmCl.
Collapse
Affiliation(s)
- Paul Cohen
- Department of Chemistry, Amherst College , P.O. Box 5000, Amherst, Massachusetts 01002, United States
| | | | | |
Collapse
|
42
|
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1401] [Impact Index Per Article: 140.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Robin van der Lee
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Centre
for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The
Netherlands
| | - Marija Buljan
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Benjamin Lang
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gary W. Daughdrill
- Department
of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Boulevard, Suite 321, Tampa, Florida 33612, United States
| | - A. Keith Dunker
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, H-4032 Debrecen, Nagyerdei krt 98, Hungary
| | - Julian Gough
- Department
of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, United Kingdom
| | - Joerg Gsponer
- Department
of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David
T. Jones
- Bioinformatics
Group, Department of Computer Science, University
College London, London, WC1E 6BT, United Kingdom
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular
Genetics, and Department of Computer Science, University
of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Richard
W. Kriwacki
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Christopher J. Oldfield
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Peter Tompa
- VIB Department
of Structural Biology, Vrije Universiteit
Brussel, Brussels, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vladimir N. Uversky
- Department
of Molecular Medicine and USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation,
Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Peter
E. Wright
- Department
of Integrative Structural and Computational Biology and Skaggs Institute
of Chemical Biology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
43
|
Tischer A, Pultke H, Topf A, Auton M, Lange C, Lilie H. The effects ofN-ethyl-N′-methyl imidazolium chloride on the solubility, stability and aggregation of tc-rPA. FEBS J 2014; 281:1738-49. [DOI: 10.1111/febs.12736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/18/2014] [Accepted: 01/29/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Tischer
- Division of Hematology; Departments of Internal Medicine, Biochemistry and Molecular Biology; Mayo Clinic; Rochester MN USA
| | | | - Andrea Topf
- Institut für Biophysikalische Chemie; Medizinische Hochschule Hannover; Germany
| | - Matthew Auton
- Division of Hematology; Departments of Internal Medicine, Biochemistry and Molecular Biology; Mayo Clinic; Rochester MN USA
| | | | - Hauke Lilie
- Institut für Biochemie und Biotechnologie; Martin-Luther-Universität Halle-Wittenberg; Halle (Saale) Germany
| |
Collapse
|
44
|
Levy-Sakin M, Berger O, Feibish N, Sharon N, Schnaider L, Shmul G, Amir Y, Buzhansky L, Gazit E. The influence of chemical chaperones on enzymatic activity under thermal and chemical stresses: common features and variation among diverse chemical families. PLoS One 2014; 9:e88541. [PMID: 24520396 PMCID: PMC3919781 DOI: 10.1371/journal.pone.0088541] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups.
Collapse
Affiliation(s)
- Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Or Berger
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Nir Feibish
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Noa Sharon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shmul
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaniv Amir
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ludmila Buzhansky
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| |
Collapse
|
45
|
Moeser B, Horinek D. Unified Description of Urea Denaturation: Backbone and Side Chains Contribute Equally in the Transfer Model. J Phys Chem B 2013; 118:107-14. [DOI: 10.1021/jp409934q] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Beate Moeser
- Institut
für Physikalische
und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Dominik Horinek
- Institut
für Physikalische
und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| |
Collapse
|
46
|
Macdonald RD, Khajehpour M. Effects of the osmolyte TMAO (Trimethylamine-N-oxide) on aqueous hydrophobic contact-pair interactions. Biophys Chem 2013; 184:101-7. [DOI: 10.1016/j.bpc.2013.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 10/26/2022]
|
47
|
Silvers TR, Myers JK. Osmolyte Effects on the Self-Association of Concanavalin A: Testing Theoretical Models. Biochemistry 2013; 52:9367-74. [DOI: 10.1021/bi401049s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas R. Silvers
- Department
of Chemistry, Davidson College, Box
7120, Davidson, North Carolina 28035, United States
| | - Jeffrey K. Myers
- Department
of Chemistry, Davidson College, Box
7120, Davidson, North Carolina 28035, United States
| |
Collapse
|
48
|
Diehl RC, Guinn EJ, Capp MW, Tsodikov OV, Record MT. Quantifying additive interactions of the osmolyte proline with individual functional groups of proteins: comparisons with urea and glycine betaine, interpretation of m-values. Biochemistry 2013; 52:5997-6010. [PMID: 23909383 DOI: 10.1021/bi400683y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To quantify interactions of the osmolyte l-proline with protein functional groups and predict their effects on protein processes, we use vapor pressure osmometry to determine chemical potential derivatives dμ2/dm3 = μ23, quantifying the preferential interactions of proline (component 3) with 21 solutes (component 2) selected to display different combinations of aliphatic or aromatic C, amide, carboxylate, phosphate or hydroxyl O, and amide or cationic N surface. Solubility data yield μ23 values for four less-soluble solutes. Values of μ23 are dissected using an ASA-based analysis to test the hypothesis of additivity and obtain α-values (proline interaction potentials) for these eight surface types and three inorganic ions. Values of μ23 predicted from these α-values agree with the experiment, demonstrating additivity. Molecular interpretation of α-values using the solute partitioning model yields partition coefficients (Kp) quantifying the local accumulation or exclusion of proline in the hydration water of each functional group. Interactions of proline with native protein surfaces and effects of proline on protein unfolding are predicted from α-values and ASA information and compared with experimental data, with results for glycine betaine and urea, and with predictions from transfer free energy analysis. We conclude that proline stabilizes proteins because of its unfavorable interactions with (exclusion from) amide oxygens and aliphatic hydrocarbon surfaces exposed in unfolding and that proline is an effective in vivo osmolyte because of the osmolality increase resulting from its unfavorable interactions with anionic (carboxylate and phosphate) and amide oxygens and aliphatic hydrocarbon groups on the surface of cytoplasmic proteins and nucleic acids.
Collapse
Affiliation(s)
- Roger C Diehl
- Department of Biochemistry and ‡Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | | | | | | | | |
Collapse
|
49
|
Direct observation of protein unfolded state compaction in the presence of macromolecular crowding. Biophys J 2013; 104:694-704. [PMID: 23442920 DOI: 10.1016/j.bpj.2012.12.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/20/2012] [Accepted: 12/06/2012] [Indexed: 11/22/2022] Open
Abstract
Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms of protein stability, structural dimensions and folding dynamics using a sugar-based crowding agent, dextran 20, and the small ribosomal protein S16 as a model system. To specifically address dimensions, we labeled the protein with BODIPY at two positions and measured Trp-BODIPY distances under different conditions. As expected, we found that dextran 20 (200 mg/ml) stabilized the variants against urea-induced unfolding. At conditions where the protein is unfolded, Förster resonance energy transfer measurements reveal that in the presence of dextran, the unfolded ensemble is more compact and there is residual structure left as probed by far-ultraviolet circular dichroism. In the presence of a crowding agent, folding rates are faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is favored. Our study provides direct evidence for protein unfolded-state compaction in the presence of macromolecular crowding along with its energetic and kinetic consequences.
Collapse
|
50
|
Affiliation(s)
- B Montgomery Pettitt
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555-0304 , USA.
| |
Collapse
|