1
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Adibi L, Yaghmaei P, Maghami P, Ebrahim-Habibi A. Phenylalanine as an effective stabilizer and aggregation inhibitor of Bacillus amyloliquefaciens alpha-amylase. AMB Express 2024; 14:69. [PMID: 38850460 PMCID: PMC11162409 DOI: 10.1186/s13568-024-01712-5] [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: 12/06/2023] [Accepted: 04/28/2024] [Indexed: 06/10/2024] Open
Abstract
Aromatic compounds are known anti-amyloid aggregates. Their effect on amorphous aggregates of proteins is, however, less studied. We chose aromatic amino acids Trp, Tyr, and Phe, as well as another known stabilizer (i.e. Arg), as potential compatible solvents to be tested on Bacillus amyloliquefaciens alpha-amylase (BAA). Among these additives, Phe was the only one to be effective on the thermal inactivation and amorphous aggregation of BAA, while preserving its intrinsic activity. A concentration of 50 mM Phe was used to test its potential in counteracting the deleterious effect of BAA amorphous aggregates in vivo. After 21 days of daily subcutaneous injections of the native enzyme to mice, amorphous aggregates of BAA, as well as aggregates produced in presence of 50 mM Phe, the tissues located at the site of injection were studied histologically. Amorphous aggregates caused an increase in macrophages and lipid droplets. Serum levels of IL6 and TNF-α were also accordingly elevated and indicative of an inflammation state. Aggregates also resulted into increased levels of glucose, triglycerides and cholesterol, as well as liver enzymes SGOT and SGPT. On the other hand, the presence of Phe prevented this exacerbated inflammatory state and the subsequent impairment of biochemical parameters. In conclusion, Phe is an interesting compound for both stabilizing proteins and counteracting the pathological effect of amorphous aggregates.
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Affiliation(s)
- Leila Adibi
- Department of Biology, Science and Research Branch, Islamic Azad University, North Sattaree Avenue, 1477893855, Tehran, Iran
| | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, North Sattaree Avenue, 1477893855, Tehran, Iran.
| | - Parvaneh Maghami
- Department of Biology, Science and Research Branch, Islamic Azad University, North Sattaree Avenue, 1477893855, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Jalal-al-Ahmad Street, Chamran Highway, 1411713137, Tehran, Iran.
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, 1411713137, Tehran, Iran.
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2
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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.
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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
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3
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Ma Y, Qiu Y, Yu C, Li S, Xu H. Design and construction of a Bacillus amyloliquefaciens cell factory for hyaluronic acid synthesis from Jerusalem artichoke inulin. Int J Biol Macromol 2022; 205:410-418. [PMID: 35202630 DOI: 10.1016/j.ijbiomac.2022.02.100] [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: 09/26/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/05/2022]
Abstract
Hyaluronic acid (HA), a high-value biomacromolecule, has wide applications in medical, cosmetic and food fields. Currently, employing the safe-grade microorganisms for de novo biosynthesis of HA from renewable substrates has become a promising alternative. In this study, we established a Bacillus amyloliquefaciens strain as platform for HA production from Jerusalem artichoke inulin. Firstly, the different HA and UDP-GlcUA synthase genes were introduced into B. amyloliquefaciens to construct the HA synthesis pathway. Secondly, the byproduct polysaccharides were removed by knocking sacB and epsA-O using CRISPR/Cas9n system, resulting in a 13% increase in HA production. Finally, 2.89 g/L HA with a high molecular weight of 1.5 MDa was obtained after optimizing fermentation conditions and adding osmotic agents. This study demonstrates the engineered B. amyloliquefaciens can effectively synthesize HA with Jerusalem artichoke inulin and provides a green route for HA production.
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Affiliation(s)
- Yanqin Ma
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, PR China
| | - Caiyuan Yu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
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4
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Kaczkowska E, Panuszko A, Bruździak P. Interactions in Ternary Aqueous Solutions of NMA and Osmolytes-PARAFAC Decomposition of FTIR Spectra Series. Int J Mol Sci 2021; 22:ijms222111684. [PMID: 34769114 PMCID: PMC8584171 DOI: 10.3390/ijms222111684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Intermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel Factor Analysis (PARAFAC) decomposition of ternary solution spectra into parts that are easier to analyze. Systems of the NMA–water–osmolyte-type were used to test the method and to elucidate information on the interactions between N-Methylacetamide (NMA, a simple peptide model) with stabilizing (trimethylamine N-oxide, glycine, glycine betaine) and destabilizing osmolytes (n-butylurea and tetramethylurea). Systems that contain stabilizers change their vibrational structure to a lesser extent than those with denaturants. Changes in the latter are strong and can be related to the formation of direct NMA–destabilizer interactions.
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5
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Dawn A, Deep S. An improved strategy of TGFβ3 expression in Escherichia coli: Exploiting folding modulators for a switch from misfolded to folded form. Int J Biol Macromol 2020; 167:787-795. [PMID: 33278443 DOI: 10.1016/j.ijbiomac.2020.11.212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/11/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Transforming growth factor beta 3 (TGFβ3) exhibits a complex native structure featuring the presence of multiple disulfide bonds forming the active dimer. Consequently, its heterologous expression in microbial system invariably leads to inclusion body (IB) formation. In this study, we observed an interesting phenomenon of switching a significant fraction of misfolded TGFβ3 to folded form by modulating the cellular protein folding machinery. We carried out co-expression experiments with chaperones and demonstrated the requirement of a coordinated action of DnaK-DnaJ-GrpE and GroESL, to achieve the native soluble conformation of TGFβ3, during over-expression in E. coli. The novelty of this study lies in the fact that orchestration of a group of chaperones to work in concert for efficient folding and assembly of TGFβ3-like cytokines has not been widely explored. Additionally, we have also demonstrated that presence of osmolytes (sorbitol or trehalose) in the growth media have an appreciable impact on the solubility of TGFβ3. We have further shown a synergism between the effects of molecular chaperone and osmolytes on the solubility of TGFβ3. We have confirmed the functionality of soluble TGFβ3 by performing binding interactions with its cognate receptor TβRII. Our study delineates the fact that an effective combination of chaperones or optimum concentration of compatible osmolyte, can efficiently abrogate competing aggregation pathways and help attain the native conformation of a cysteine rich cytokine in a facile manner.
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Affiliation(s)
- Amrita Dawn
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, India.
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6
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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]
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7
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Ramanujam V, Alderson TR, Pritišanac I, Ying J, Bax A. Protein structural changes characterized by high-pressure, pulsed field gradient diffusion NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 312:106701. [PMID: 32113145 PMCID: PMC7153785 DOI: 10.1016/j.jmr.2020.106701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Pulsed-field gradient NMR spectroscopy is widely used to measure the translational diffusion and hydrodynamic radius (Rh) of biomolecules in solution. For unfolded proteins, the Rh provides a sensitive reporter on the ensemble-averaged conformation and the extent of polypeptide chain expansion as a function of added denaturant. Hydrostatic pressure is a convenient and reversible alternative to chemical denaturants for the study of protein folding, and enables NMR measurements to be performed on a single sample. While the impact of pressure on the viscosity of water is well known, and our water diffusivity measurements agree closely with theoretical expectations, we find that elevated pressures increase the Rh of dioxane and other small molecules by amounts that correlate with their hydrophobicity, with parallel increases in rotational friction indicated by 13C longitudinal relaxation times. These data point to a tighter coupling with water for hydrophobic surfaces at elevated pressures. Translational diffusion measurement of the unfolded state of a pressure-sensitized ubiquitin mutant (VA2-ubiquitin) as a function of hydrostatic pressure or urea concentration shows that Rh values of both the folded and the unfolded states remain nearly invariant. At ca 23 Å, the Rh of the fully pressure-denatured state is essentially indistinguishable from the urea-denatured state, and close to the value expected for an idealized random coil of 76 residues. The intrinsically disordered protein (IDP) α-synuclein shows slight compaction at pressures above 2 kbar. Diffusion of unfolded ubiquitin and α-synuclein is significantly impacted by sample concentration, indicating that quantitative measurements need to be carried out under dilute conditions.
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Affiliation(s)
- Venkatraman Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Iva Pritišanac
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.
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8
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Tischer A, Machha VR, Moon-Tasson L, Benson LM, Auton M. Glycosylation sterically inhibits platelet adhesion to von Willebrand factor without altering intrinsic conformational dynamics. J Thromb Haemost 2020; 18:79-90. [PMID: 31479573 PMCID: PMC6940534 DOI: 10.1111/jth.14628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/26/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND A molecular basis for von Willebrand factor (VWF) self-inhibition has been proposed by which the N-terminal and C-terminal flanking sequences of the globular A1 domain disulfide loop bind to and suppress the conformational dynamics of A1. These flanking sequences are rich in O-linked glycosylation (OLG), which is known to suppress platelet adhesion to VWF, presumably by steric hindrance. The inhibitory mechanism remains unresolved as to whether inhibition is due to steric exclusion by OLGs or a direct self-association interaction that stabilizes the domain. OBJECTIVES The platelet adhesive function, thermodynamic stability, and conformational dynamics of the wild-type and type 2M G1324S A1 domain lacking glycosylation (Escherichia coli) are compared with the wild-type glycosylated A1 domain (HEK293 cell culture) to decipher the self-inhibitory mechanism. METHODS Surface plasmon resonance and analytical rheology are utilized to assess Glycoprotein Ibα (GPIbα) binding at equilibrium and platelet adhesion under shear flow. The conformational stability is assessed through a combination of protein unfolding thermodynamics and hydrogen-deuterium exchange mass spectrometry (HXMS). RESULTS A1 glycosylation inhibits both GPIbα binding and platelet adhesion. Glycosylation increases the hydrodynamic size of A1 and stabilizes the thermal unfolding of A1 without changing its equilibrium stability. Glycosylation does not alter the intrinsic conformational dynamics of the A1 domain. CONCLUSIONS These studies invalidate the proposed inhibition through conformational suppression since glycosylation within these flanking sequences does not alter the native state stability or the conformational dynamics of A1. Rather, they confirm a mechanism by which glycosylation sterically hinders platelet adhesion to the A1 domain at equilibrium and under rheological shear stress.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Venkata R. Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Laurie Moon-Tasson
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Linda M. Benson
- Proteomics Core, Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
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9
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Majumder S, Hansmann UHE, Janke W. Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse. Macromolecules 2019; 52:5491-5498. [PMID: 31631912 PMCID: PMC6795215 DOI: 10.1021/acs.macromol.9b00562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/31/2019] [Indexed: 11/30/2022]
Abstract
![]()
The
collapse of the polypeptide backbone is an integral part of
protein folding. Using polyglycine as a probe, we explore the nonequilibrium
pathways of protein collapse in water. We find that the collapse depends
on the competition between hydration effects and intrapeptide interactions.
Once intrapeptide van der Waal interactions dominate, the chain collapses
along a nonequilibrium pathway characterized by formation of pearl-necklace-like
local clusters as intermediates that eventually coagulate into a single
globule. By describing this coarsening through the contact probability
as a function of distance along the chain, we extract a time-dependent
length scale that grows in a linear fashion. The collapse dynamics
is characterized by a dynamical critical exponent z ≈ 0.5 that is much smaller than the values of z = 1–2 reported for nonbiological polymers. This difference
in the exponents is explained by the instantaneous formation of intrachain
hydrogen bonds and local ordering that may be correlated with the
observed fast folding times of proteins.
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Affiliation(s)
- Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany
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10
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Ferrie JJ, Haney CM, Yoon J, Pan B, Lin YC, Fakhraai Z, Rhoades E, Nath A, Petersson EJ. Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein. Biophys J 2019; 114:53-64. [PMID: 29320696 DOI: 10.1016/j.bpj.2017.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/21/2017] [Accepted: 11/06/2017] [Indexed: 01/24/2023] Open
Abstract
We describe a strategy for experimentally-constraining computational simulations of intrinsically disordered proteins (IDPs), using α-synuclein, an IDP with a central role in Parkinson's disease pathology, as an example. Previously, data from single-molecule Förster Resonance Energy Transfer (FRET) experiments have been effectively utilized to generate experimentally constrained computational models of IDPs. However, the fluorophores required for single-molecule FRET experiments are not amenable to the study of short-range (<30 Å) interactions. Using ensemble FRET measurements allows one to acquire data from probes with multiple distance ranges, which can be used to constrain Monte Carlo simulations in PyRosetta. To appropriately employ ensemble FRET data as constraints, we optimized the shape and weight of constraining potentials to afford ensembles of structures that are consistent with experimental data. We also used this approach to examine the structure of α-synuclein in the presence of the compacting osmolyte trimethylamine-N-oxide. Despite significant compaction imparted by 2 M trimethylamine-N-oxide, the underlying ensemble of α-synuclein remains largely disordered and capable of aggregation, also in agreement with experimental data. These proof-of-concept experiments demonstrate that our modeling protocol enables one to efficiently generate experimentally constrained models of IDPs that incorporate atomic-scale detail, allowing one to study an IDP under a variety of conditions.
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Affiliation(s)
- John J Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Conor M Haney
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jimin Yoon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yi-Chih Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zahra Fakhraai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Abhinav Nath
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.
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11
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Adamczak B, Kogut M, Czub J. Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions. Phys Chem Chem Phys 2018; 20:11174-11182. [PMID: 29629459 DOI: 10.1039/c7cp07436k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage by enthalpically-driven association with the protein, acting synergistically with temperature to induce unfolding. In contrast, betaine is sterically excluded from the protein surface thereby exerting entropic depletion forces that contribute to the stabilization of the native state. In fact, we find that while at low temperatures betaine slightly increases the folding free energy of Trp-cage by promoting another near-native conformation, it protects the protein against temperature-induced denaturation. This, in turn, can be attributed to enhanced exclusion of betaine at higher temperatures that arises from less attractive interactions with the protein surface.
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Affiliation(s)
- Beata Adamczak
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland.
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12
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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.
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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
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13
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Bychkova VE, Semisotnov GV, Balobanov VA, Finkelstein AV. The Molten Globule Concept: 45 Years Later. BIOCHEMISTRY (MOSCOW) 2018; 83:S33-S47. [DOI: 10.1134/s0006297918140043] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Lyashchenko AK, Dunyashev VS, Zasetsky AY. Effects of concentration on the microwave dielectric spectra of aqueous urea solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417050168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Gao M, Arns L, Winter R. Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mimi Gao
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Loana Arns
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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16
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Gao M, Arns L, Winter R. Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts. Angew Chem Int Ed Engl 2017; 56:2302-2306. [PMID: 28102930 DOI: 10.1002/anie.201611843] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Indexed: 12/31/2022]
Abstract
Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state. Further, we find a strong interplay between water, salt, and osmolyte in driving the thermodynamics and defining the temperature and pressure stability limit of the RNA. Our results support a universal working mechanism of TMAO and urea to (de)stabilize proteins and the RNA.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Loana Arns
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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17
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme. Biochem J 2016; 473:3705-3724. [DOI: 10.1042/bcj20160604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
Osmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical denaturation of lysozyme in different solvent conditions to study the molecular mechanism by which two biologically relevant osmolytes, denaturing (urea) and stabilizing (betaine), affect the folding equilibrium. We found that urea interacts favorably with all types of residues via both hydrogen bonds and dispersion forces, and therefore accumulates in a diffuse solvation shell around the protein. This not only provides an enthalpic stabilization of the unfolded state, but also weakens the hydrophobic effect, as hydrophobic forces promote the association of urea with nonpolar residues, facilitating the unfolding. In contrast, we observed that betaine is excluded from the protein backbone and nonpolar side chains, but is accumulated near the basic residues, yielding a nonuniform distribution of betaine molecules at the protein surface. Spatially resolved solvent–protein interaction energies further suggested that betaine behaves in a ligand- rather than solvent-like manner and its exclusion from the protein surface arises mostly from the scarcity of favorable binding sites. Finally, we found that, in the presence of betaine, the reduced ability of water molecules to solvate the protein results in an additional enthalpic contribution to the betaine-induced stabilization.
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18
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Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, Best RB. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J Am Chem Soc 2016. [PMID: 27583687 DOI: 10.1021/jacs.6b05443.probing] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Chemical denaturants are the most commonly used agents for unfolding proteins and are thought to act by better solvating the unfolded state. Improved solvation is expected to lead to an expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of the denaturant action. However, experiments have so far yielded qualitatively different results concerning the effects of chemical denaturation. Studies using Förster resonance energy transfer (FRET) and other methods found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray scattering (SAXS) studies found no change. This discrepancy therefore challenges our understanding of denaturation mechanism and more generally the accuracy of these experiments as applied to unfolded or disordered proteins. Here, we use all-atom molecular simulations to investigate the effect of urea and guanidinium chloride on the structure of the intrinsically disordered protein ACTR, which can be studied by experiment over a wide range of denaturant concentration. Using unbiased molecular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed swells with increasing denaturant concentration. This is due to the favorable association of urea or guanidinium chloride with the backbone of all residues and with the side-chains of almost all residues, with denaturant-water transfer free energies inferred from this association in reasonable accord with experimental estimates. Interactions of the denaturants with the backbone are dominated by hydrogen bonding, while interactions with side-chains include other contributions. By computing FRET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation trajectories are in accord with both experiments on this protein, demonstrating that there is no fundamental inconsistency between the two types of experiment. Agreement with experiment also supports the picture of chemical denaturation described in our simulations, driven by weak association of denaturant with the protein. Our simulations support some assumptions needed for each experiment to accurately reflect changes in protein size, namely, that the commonly used FRET chromophores do not qualitatively alter the results and that possible effects such as preferential solvent partitioning into the interior of the chain do not interfere with the determination of radius of gyration from the SAXS experiments.
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Affiliation(s)
- Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research , Rockville, Maryland 20850, United States
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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19
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Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc 2016; 138:11714-26. [PMID: 27583570 PMCID: PMC5597961 DOI: 10.1021/jacs.6b05917] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.
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Affiliation(s)
- Alessandro Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madeleine B. Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anja Schüler
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Klaus Gast
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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20
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Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, Best RB. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J Am Chem Soc 2016; 138:11702-13. [PMID: 27583687 DOI: 10.1021/jacs.6b05443] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemical denaturants are the most commonly used agents for unfolding proteins and are thought to act by better solvating the unfolded state. Improved solvation is expected to lead to an expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of the denaturant action. However, experiments have so far yielded qualitatively different results concerning the effects of chemical denaturation. Studies using Förster resonance energy transfer (FRET) and other methods found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray scattering (SAXS) studies found no change. This discrepancy therefore challenges our understanding of denaturation mechanism and more generally the accuracy of these experiments as applied to unfolded or disordered proteins. Here, we use all-atom molecular simulations to investigate the effect of urea and guanidinium chloride on the structure of the intrinsically disordered protein ACTR, which can be studied by experiment over a wide range of denaturant concentration. Using unbiased molecular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed swells with increasing denaturant concentration. This is due to the favorable association of urea or guanidinium chloride with the backbone of all residues and with the side-chains of almost all residues, with denaturant-water transfer free energies inferred from this association in reasonable accord with experimental estimates. Interactions of the denaturants with the backbone are dominated by hydrogen bonding, while interactions with side-chains include other contributions. By computing FRET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation trajectories are in accord with both experiments on this protein, demonstrating that there is no fundamental inconsistency between the two types of experiment. Agreement with experiment also supports the picture of chemical denaturation described in our simulations, driven by weak association of denaturant with the protein. Our simulations support some assumptions needed for each experiment to accurately reflect changes in protein size, namely, that the commonly used FRET chromophores do not qualitatively alter the results and that possible effects such as preferential solvent partitioning into the interior of the chain do not interfere with the determination of radius of gyration from the SAXS experiments.
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Affiliation(s)
- Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research , Rockville, Maryland 20850, United States
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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21
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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22
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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.
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23
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Sapir L, Harries D. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions. J Chem Theory Comput 2015; 11:3478-90. [DOI: 10.1021/acs.jctc.5b00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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24
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Holehouse AS, Garai K, Lyle N, Vitalis A, Pappu RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J Am Chem Soc 2015; 137:2984-95. [PMID: 25664638 PMCID: PMC4418562 DOI: 10.1021/ja512062h] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.
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Affiliation(s)
- Alex S. Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
| | - Kanchan Garai
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India
| | - Nicholas Lyle
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, USA
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-5807, Zurich, Switzerland
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25
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Sapir L, Harries D. Is the depletion force entropic? Molecular crowding beyond steric interactions. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2014.12.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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26
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Beneficial effect of sugar osmolytes on the refolding of guanidine hydrochloride-denatured trehalose-6-phosphate hydrolase from Bacillus licheniformis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:806847. [PMID: 25667926 PMCID: PMC4309298 DOI: 10.1155/2015/806847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/23/2014] [Indexed: 11/21/2022]
Abstract
The influence of three sugar osmolytes on the refolding of guanidine hydrochloride- (GdnHCl-) denatured trehalose-6-phosphate hydrolase of Bacillus licheniformis (BlTreA) was studied by circular dichroism (CD) spectra, fluorescence emission spectra, and the recovery of enzymatic activity. These experimental results clearly indicated that sorbitol, sucrose, and trehalose at a concentration of 0.75 M improved the refolding yields of GdnHCl-denatured BlTreA, probably due to the fact that these sugars favored the formation of tertiary architectures. Far-UV CD measurements demonstrated the ability of sugar osmolytes to shift the secondary structure of GdnHCl-denatured enzyme towards near-native conformations. ANS fluorescence intensity measurements revealed a reduction of exposed hydrophobic surfaces upon the treatment of denatured enzyme with sugar osmolytes. These observations suggest that sugar osmolytes possibly play a chaperone role in the refolding of chemically denatured BlTreA.
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27
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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.
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Affiliation(s)
- Jörg Rösgen
- Department of Biochemistry
and Molecular Biology, Penn State University
College of Medicine, Hershey, Pennsylvania 17033, United States
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28
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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]
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29
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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
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30
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Kitevski-LeBlanc JL, Hoang J, Thach W, Larda ST, Prosser RS. 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate. Biochemistry 2013; 52:5780-9. [DOI: 10.1021/bi4010057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julianne L. Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - Joshua Hoang
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - William Thach
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
| | - Sacha Thierry Larda
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
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31
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Tischer A, Auton M. Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding. Protein Sci 2013; 22:1147-60. [PMID: 23813497 PMCID: PMC3776328 DOI: 10.1002/pro.2301] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 11/11/2022]
Abstract
We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
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32
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Lampel A, Bram Y, Levy-Sakin M, Bacharach E, Gazit E. The effect of chemical chaperones on the assembly and stability of HIV-1 capsid protein. PLoS One 2013; 8:e60867. [PMID: 23577173 PMCID: PMC3618117 DOI: 10.1371/journal.pone.0060867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
Chemical chaperones are small organic molecules which accumulate in a broad range of organisms in various tissues under different stress conditions and assist in the maintenance of a correct proteostasis under denaturating environments. The effect of chemical chaperones on protein folding and aggregation has been extensively studied and is generally considered to be mediated through non-specific interactions. However, the precise mechanism of action remains elusive. Protein self-assembly is a key event in both native and pathological states, ranging from microtubules and actin filaments formation to toxic amyloids appearance in degenerative disorders, such as Alzheimer's and Parkinson's diseases. Another pathological event, in which protein assembly cascade is a fundamental process, is the formation of virus particles. In the late stage of the virus life cycle, capsid proteins self-assemble into highly-ordered cores, which encapsulate the viral genome, consequently protect genome integrity and mediate infectivity. In this study, we examined the effect of different groups of chemical chaperones on viral capsid assembly in vitro, focusing on HIV-1 capsid protein as a system model. We found that while polyols and sugars markedly inhibited capsid assembly, methylamines dramatically enhanced the assembly rate. Moreover, chemical chaperones that inhibited capsid core formation, also stabilized capsid structure under thermal denaturation. Correspondingly, trimethylamine N-oxide, which facilitated formation of high-order assemblies, clearly destabilized capsid structure under similar conditions. In contrast to the prevailing hypothesis suggesting that chemical chaperones affect proteins through preferential exclusion, the observed dual effects imply that different chaperones modify capsid assembly and stability through different mechanisms. Furthermore, our results indicate a correlation between the folding state of capsid to its tendency to assemble into highly-ordered structures.
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Affiliation(s)
- Ayala Lampel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Bram
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EB); (EG)
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33
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Toward an atomistic description of the urea-denatured state of proteins. Proc Natl Acad Sci U S A 2013; 110:5933-8. [PMID: 23536295 DOI: 10.1073/pnas.1216589110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.
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34
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Udgaonkar JB. Polypeptide chain collapse and protein folding. Arch Biochem Biophys 2013; 531:24-33. [DOI: 10.1016/j.abb.2012.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 12/11/2022]
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Elam WA, Schrank TP, Campagnolo AJ, Hilser VJ. Temperature and urea have opposing impacts on polyproline II conformational bias. Biochemistry 2013; 52:949-58. [PMID: 23350874 DOI: 10.1021/bi301435p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The native states of globular proteins have been accessed in atomic detail by X-ray crystallography and nuclear magnetic resonance spectroscopy, yet characterization of denatured proteins beyond global metrics has proven to be elusive. Denatured proteins have been observed to exhibit global geometric properties of a random coil polymer. However, this does not preclude the existence of nonrandom, local conformational bias that may be significant for protein folding and function. Indeed, circular dichroism (CD) spectroscopy and other methods have suggested that the denatured state contains considerable local bias to the polyproline II (PII) conformation. Here, we develop predictive models to determine the extent that temperature and the chemical denaturant urea modulate PII propensity. In agreement with our predictive model, PII propensity is observed experimentally to decrease with an increase in temperature. Conversely, urea appears to promote the PII conformation as determined by CD and isothermal titration calorimetry. Importantly, the calorimetric data are in quantitative agreement with a model that predicts the stability of the PII helix relative to other denatured state conformations based upon solvent accessible surface area and experimentally measured Gibbs transfer free energies. The ability of urea to promote the PII conformation can be attributed to the favorable interaction of urea with the peptide backbone. Thus, perturbing denatured states by temperature or cosolutes has subtle, yet opposing, impacts on local PII conformational biases. These results have implications for protein folding as well as for the function of signaling proteins that bind proline-rich targets in globular or intrinsically disordered proteins.
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Affiliation(s)
- W Austin Elam
- T. C. Jenkins Department of Biophysics and Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
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36
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Baldwin RL. The new view of hydrophobic free energy. FEBS Lett 2013; 587:1062-6. [DOI: 10.1016/j.febslet.2013.01.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/29/2022]
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Abstract
The hydrophobic free energy in current use is based on transfer of alkane solutes from liquid alkanes to water, and it has been argued recently that these values are incorrect and should be based instead on gas-liquid transfer data. Hydrophobic free energy is measured here by gas-liquid transfer of hydrocarbon gases from vapor to water. The new definition reduces more than twofold the values of the apparent hydrophobic free energy. Nevertheless, the newly defined hydrophobic free energy is still the dominant factor that drives protein folding as judged by ΔCp, the change in heat capacity, found from the free energy change for heat-induced protein unfolding. The ΔCp for protein unfolding agrees with ΔCp values for solvating hydrocarbon gases and disagrees with ΔCp for breaking peptide hydrogen bonds, which has the opposite sign. The ΔCp values for the enthalpy of liquid-liquid and gas-liquid transfer are similar. The plot of free energy against the apparent solvent-exposed surface area is given for linear alkanes, but only for a single conformation, the extended conformation, of these flexible-chain molecules. The ability of the gas-liquid hydrophobic factor to predict protein stability is tested and reasonable agreement is found, using published data for the dependences on temperature of the unfolding enthalpy of ribonuclease T1 and the solvation enthalpies of the nonpolar and polar groups.
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Shpiruk TA, Khajehpour M. The effect of urea on aqueous hydrophobic contact-pair interactions. Phys Chem Chem Phys 2013; 15:213-22. [DOI: 10.1039/c2cp42759a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Kumar N, Kishore N. Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization. Biophys Chem 2013; 171:9-15. [DOI: 10.1016/j.bpc.2012.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/30/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022]
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40
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Hailu TT, Foit L, Bardwell JCA. In vivo detection and quantification of chemicals that enhance protein stability. Anal Biochem 2012; 434:181-6. [PMID: 23219982 PMCID: PMC3670414 DOI: 10.1016/j.ab.2012.11.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 11/27/2012] [Accepted: 11/27/2012] [Indexed: 11/15/2022]
Abstract
We have devised protein-folding sensors that link protein stability to TEM-1 β-lactamase activity. The addition of osmolytes and other compounds with chemical chaperone activity to the growth medium of bacteria containing these sensors increases β-lactamase activity up to 207-fold in a dose-dependent manner. This enables the rapid detection and sensitive quantification of compounds that enhance in vivo protein stability.
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Affiliation(s)
- Tsinatkeab T Hailu
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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41
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Pazos IM, Gai F. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability. J Phys Chem B 2012; 116:12473-8. [PMID: 22998405 PMCID: PMC3475735 DOI: 10.1021/jp307414s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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42
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Kumar R, McEwan IJ. Allosteric modulators of steroid hormone receptors: structural dynamics and gene regulation. Endocr Rev 2012; 33:271-99. [PMID: 22433123 PMCID: PMC3596562 DOI: 10.1210/er.2011-1033] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Steroid hormones are synthesized from cholesterol primarily in the adrenal gland and the gonads and play vital roles in normal physiology, the control of development, differentiation, metabolic homeostasis, and reproduction. The actions of these small lipophilic molecules are mediated by intracellular receptor proteins. It is just over 25 yr since the first cDNA for steroid receptors were cloned, a development that led to the birth of a superfamily of ligand-activated transcription factors: the nuclear receptors. The receptor proteins share structurally and functionally related ligand binding and DNA-binding domains but possess distinct N-terminal domains and hinge regions that are intrinsically disordered. Since the original cloning experiments, considerable progress has been made in our understanding of the structure, mechanisms of action, and biology of this important class of ligand-activated transcription factors. In recent years, there has been interest in the structural plasticity and function of the N-terminal domain of steroid hormone receptors and in the allosteric regulation of protein folding and function in response to hormone, DNA response element architecture, and coregulatory protein binding partners. The N-terminal domain can exist as an ensemble of conformers, having more or less structure, which prime this region of the receptor to rapidly respond to changes in the intracellular environment through hormone binding and posttranslation modifications. In this review, we address the question of receptor structure and function dynamics with particular emphasis on the structurally flexible N-terminal domain, intra- and interdomain communications, and the allosteric regulation of receptor action.
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Affiliation(s)
- Raj Kumar
- Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18510, USA
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43
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Shao Q, Fan Y, Yang L, Qin Gao Y. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 2012; 136:115101. [DOI: 10.1063/1.3692801] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Li W, Zhou R, Mu Y. Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation. J Phys Chem B 2012; 116:1446-51. [DOI: 10.1021/jp210769q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weifeng Li
- School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights,
New York 10598, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore
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45
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Bandyopadhyay A, Saxena K, Kasturia N, Dalal V, Bhatt N, Rajkumar A, Maity S, Sengupta S, Chakraborty K. Chemical chaperones assist intracellular folding to buffer mutational variations. Nat Chem Biol 2012; 8:238-45. [PMID: 22246401 PMCID: PMC3527004 DOI: 10.1038/nchembio.768] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 11/06/2011] [Indexed: 11/09/2022]
Abstract
Hidden genetic variations harbor potential for the evolution of new traits. Molecular chaperones, that assist protein folding, may conceal genetic variations in protein coding regions. Here, we investigate if the chemical milieu of cells has the potential to alleviate intracellular protein folding; potentially implicating a role of osmolytes in concealing genetic variations. Using the model osmolyte TMAO, we uncover that it can buffer mutations that impose kinetic traps in the folding pathways of two model proteins. Using this information, we rationally designed TMAO-dependent mutants in vivo, starting from a TMAO-independent protein. Strikingly, we delineate different osmolytes to have a unique spectrum of buffered-mutations. Consequently, the chemical milieu of cells may alter the folding pathways of unique mutant variants in polymorphic populations and lead to unanticipated spectra of genetic buffering.
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Affiliation(s)
- Anannya Bandyopadhyay
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi, India
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46
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Rogachev AY, Burger P. Bonding situation and N–O-bond strengths in amine-N-oxides—a combined experimental and theoretical study. Phys Chem Chem Phys 2012; 14:1985-2000. [DOI: 10.1039/c2cp22341d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2011; 22:14-20. [PMID: 22104965 DOI: 10.1016/j.sbi.2011.10.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/25/2022]
Abstract
Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.
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Affiliation(s)
- Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
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48
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Gilman-Politi R, Harries D. Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes. J Chem Theory Comput 2011; 7:3816-28. [PMID: 26598272 DOI: 10.1021/ct200455n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many polyols and carbohydrates serve in different organisms as protective osmolytes that help to stabilize proteins in their native, functional state, even under a variety of environmental stresses. However, despite their important role, much of the molecular mechanism by which these osmolytes exert their action remains elusive. We have recently shown experimentally that, although polyols and carbohydrates are excluded from protein and peptide interfaces, as also expected for the known entropic "crowding" mechanism, the osmolyte folding action can in fact primarily be enthalpic in nature. To follow this newly resolved enthalpically driven stabilization mechanism, we report here on molecular dynamics simulations of a model peptide that can fold in solution into a β-hairpin. In agreement with experiments, our simulations indicate that sorbitol, a representative polyol, promotes peptide folding by preferential exclusion. At the molecular level, simulations further show that peptide stabilization can be explained by sorbitol's perturbation of the solution hydrogen bonding network in the peptide first hydration shells. Consequently, fewer hydrogen bonds between peptide and solvating water are lost upon folding, and additional internal peptide hydrogen bonds are formed in the presence of sorbitol, while internal peptide and water-associated hydrogen bonds are strengthened, resulting in stabilization of the peptide folded state. We further find that changes in water orientational entropy are reduced upon folding in sorbitol solution, reflecting the struggle of water molecules to maintain optimal hydrogen bonding in the presence of competing polyols. By providing first molecular underpinnings for enthalpically driven osmolyte stabilization of peptides and proteins, this mechanism should allow a better understanding of the variety of physical forces by which protective osmolytes act in biologically realistic solutions.
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Affiliation(s)
- Regina Gilman-Politi
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
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49
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Berteotti A, Barducci A, Parrinello M. Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism. J Am Chem Soc 2011; 133:17200-6. [PMID: 21854002 DOI: 10.1021/ja202849a] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite the daily use of urea to influence protein folding and stability, the molecular mechanism with which urea acts is still not well understood. Here the use of combined parallel tempering and metadynamics simulation allows us to study the free-energy landscape associated with the folding/unfolding of β-hairpin GB1 equilibrium in 8 M urea and pure water. The nature of the unfolded state in both solutions has been analyzed: in urea solution the addition of denaturants acts to expand the denatured state, while in pure water solution the unfolded state is noticeably more compact. For what concerns the mechanism by which urea acts as a denaturant, a preferential direct interaction between urea molecules and protein backbone has been found. However, the bias toward urea solvation is largest at intermediate values of the gyration radius.
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Affiliation(s)
- Anna Berteotti
- Computational Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
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50
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Bowler BE. Residual structure in unfolded proteins. Curr Opin Struct Biol 2011; 22:4-13. [PMID: 21978577 DOI: 10.1016/j.sbi.2011.09.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 09/07/2011] [Indexed: 11/27/2022]
Abstract
The denatured state ensemble (DSE) of unfolded proteins, once considered to be well-modeled by an energetically featureless random coil, is now well-known to contain flickering elements of residual structure. The position and nature of DSE residual structure may provide clues toward deciphering the protein folding code. This review focuses on recent advances in our understanding of the nature of DSE collapse under folding conditions, the quantification of the stability of residual structure in the DSE, the determination of the location and types of residues involved in thermodynamically significant residual structure and advances in detection of long-range interactions in the DSE.
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Affiliation(s)
- Bruce E Bowler
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, MT 59812, USA.
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