1
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Cui M, Li Y, Li J, Jia N, Cao W, Li Z, Li X, Chu X. Construction of various lipid carriers to study the transdermal penetration mechanism of sinomenine hydrochloride. J Microencapsul 2024; 41:157-169. [PMID: 38451031 DOI: 10.1080/02652048.2024.2324810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
OBJECTIVE To investigate the transdermal mechanisms and compare the differences in transdermal delivery of Sinomenine hydrochloride (SN) between solid lipid nanoparticles (SLN), liposomes (LS), and nanoemulsions (NE). METHODS SN-SLN, SN-LS and SN-NE were prepared by ultrasound, ethanol injection and spontaneous emulsification, respectively. FTIR, DSC, in vitro skin penetration, activation energy (Ea) analysis were used to explore the mechanism of drug penetration across the skin. RESULTS The particle size and encapsulation efficiency were 126.60 nm, 43.23 ± 0.48%(w/w) for SN-SLN, 224.90 nm, 78.31 ± 0.75%(w/w) for SN-LS, and 83.22 nm, 89.01 ± 2.16%(w/w) for SN-LS. FTIR and DSC showed the preparations had various levels of impacts on the stratum corneum's lipid structure which was in the order of SLN > NE > LS. Ea values of SN-SLN, SN-LS, and SN-NE crossing the skin were 2.504, 1.161, and 2.510 kcal/mol, respectively. CONCLUSION SLN had a greater degree of alteration on the skin cuticle, which allows SN to permeate skin more effectively.
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Affiliation(s)
- Mengyao Cui
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yaqing Li
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Li
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Nini Jia
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Wenxuan Cao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zhengguang Li
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiang Li
- Anhui Province Institute for Food and Drug Control, Hefei, China
| | - Xiaoqin Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Pharmaceutical Preparation Technology and Application, Hefei, China
- Anhui Education Department (AUCM), Engineering Technology Research Center of Modernized Pharmaceutics, Hefei, China
- Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei, China
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2
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Wermter FC, Bock C, Dreher W. Characterization of amine proton exchange for analyzing the specificity and intensity of the CEST effect: from humans to fish. NMR IN BIOMEDICINE 2022; 35:e4622. [PMID: 34605080 DOI: 10.1002/nbm.4622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Chemical exchange saturation transfer (CEST) at about 2.8 ppm downfield from water is characterized besides other compounds by exchanging amine protons of relatively high concentration amino acids and is determined by several physiological (pH, T) and experimental (B0 , B1 , tsat ) parameters. Although the weighting of the CEST effect observed in vivo can be attributed mainly to one compound depending on the organism and organ, there are still several other amino acids, proteins and molecules that also contribute. These contributions in turn exhibit dependences and thus can lead to possible misinterpretation of the measured changes in the CEST effect. With this in mind, this work aimed to determine the exchange rates of six important amino acids as a function of pH and temperature, and thus to create multi-pool models that allow the accurate analysis of the CEST effect concerning different physiological and experimental parameters for a wide variety of organisms. The results show that small changes in the above parameters have a significant impact on the CEST effect at about 2.8 ppm for the chosen organisms, i.e. the human brain (37 °C) and the brain of polar cod (1.5 °C), furthermore, the specificity of the CEST effect observed in vivo can be significantly affected. Based on the exchange rates ksw (pH, T) determined for six metabolites in this study, it is possible to optimize the intensity and the specificity for the CEST effect of amino acids at about 2.8 ppm for different organisms with their specific physiological characteristics. By adjusting experimental parameters accordingly, this optimization will help to avoid possible misinterpretations of CEST measurements. Furthermore, the multi-pool models can be utilized to further optimize the saturation.
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Affiliation(s)
- Felizitas C Wermter
- Department of Chemistry, in-vivo-MR group, University Bremen, Bremen, Germany
| | - Christian Bock
- Integrative Ecophysiology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wolfgang Dreher
- Department of Chemistry, in-vivo-MR group, University Bremen, Bremen, Germany
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3
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Green AR, Li K, Lockard B, Young RP, Mueller LJ, Larive CK. Investigation of the Amide Proton Solvent Exchange Properties of Glycosaminoglycan Oligosaccharides. J Phys Chem B 2019; 123:4653-4662. [PMID: 31067054 DOI: 10.1021/acs.jpcb.9b01794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
One-dimensional 1H NMR experiments were conducted for aqueous solutions of glycosaminoglycan oligosaccharides to measure the amide proton temperature coefficients and activation energy barriers for solvent exchange and evaluate the effect of pH on the solvent exchange properties. A library of mono- and oligosaccharides was prepared by enzymatic depolymerization of amide-containing polysaccharides and by chemical modification of heparin and heparan sulfate saccharides including members that contain a 3- O-sulfated glucosamine residue. The systematic evaluation of this saccharide library facilitated assessment of the effects of structural characteristics, such as size, sulfation number and site, and glycosidic linkage, on amide proton solvent exchange rates. Charge repulsion by neighboring negatively charged sulfate and carboxylate groups was found to have a significant impact on the catalysis of amide proton solvent exchange by hydroxide. This observation leads to the conclusion that solvent exchange rates must be interpreted within the context of a given chemical environment. On their own, slow exchange rates do not conclusively establish the involvement of a labile proton in a hydrogen bond, and additional supporting experimental evidence such as reduced temperature coefficients is required.
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Affiliation(s)
- Andrew R Green
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Kecheng Li
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States.,Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
| | - Blake Lockard
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Robert P Young
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States.,Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Leonard J Mueller
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Cynthia K Larive
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
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4
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Payliss BJ, Vogel J, Mittermaier AK. Side chain electrostatic interactions and pH-dependent expansion of the intrinsically disordered, highly acidic carboxyl-terminus of γ-tubulin. Protein Sci 2019; 28:1095-1105. [PMID: 30968464 DOI: 10.1002/pro.3618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 11/09/2022]
Abstract
Intramolecular electrostatic attraction and repulsion strongly influence the conformational sampling of intrinsically disordered proteins and domains (IDPs). In order to better understand this complex relationship, we have used nuclear magnetic resonance to measure side chain pKa values and pH-dependent translational diffusion coefficients for the unstructured and highly acidic carboxyl-terminus of γ-tubulin (γ-CT), providing insight into how the net charge of an IDP relates to overall expansion or collapse of the conformational ensemble. Many of the pKa values in the γ-CT are shifted upward by 0.3-0.4 units and exhibit negatively cooperative ionization pH profiles, likely due to the large net negative charge that accumulates on the molecule as the pH is raised. pKa shifts of this magnitude correspond to electrostatic interaction energies between the affected residues and the rest of the charged molecule that are each on the order of 1 kcal mol-1 . Diffusion of the γ-CT slowed with increasing net charge, indicative of an expanding hydrodynamic radius (rH ). The degree of expansion agreed quantitatively with what has been seen from comparisons of IDPs with different charge content, yielding the general trend that every 0.1 increase in relative charge (|Q|/res) produces a roughly 5% increase in rH . While γ-CT pH titration data followed this trend nearly perfectly, there were substantially larger deviations for the database of different IDP sequences. This suggests that other aspects of an IDP's primary amino acid sequence beyond net charge influence the sensitivity of rH to electrostatic interactions.
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Affiliation(s)
- Brandon J Payliss
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Jackie Vogel
- Department of Biology, McGill University, Montreal, Quebec, Canada.,The School of Computer Science, McGill University, Montreal, Quebec, Canada
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5
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Wermter FC, Maus B, Pörtner HO, Dreher W, Bock C. CO 2 induced pH i changes in the brain of polar fish: a TauCEST application. NMR IN BIOMEDICINE 2018; 31:e3955. [PMID: 29932479 DOI: 10.1002/nbm.3955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Chemical exchange saturation transfer (CEST) from taurine to water (TauCEST) can be used for in vivo mapping of taurine concentrations as well as for measurements of relative changes in intracellular pH (pHi ) at temperatures below 37°C. Therefore, TauCEST offers the opportunity to investigate acid-base regulation and neurological disturbances of ectothermic animals living at low temperatures, and in particular to study the impact of ocean acidification (OA) on neurophysiological changes of fish. Here, we report the first in vivo application of TauCEST imaging. Thus, the study aimed to investigate the TauCEST effect in a broad range of temperatures (1-37°C) and pH (5.5-8.0), motivated by the high taurine concentration measured in the brains of polar fish. The in vitro data show that the TauCEST effect is especially detectable in the low temperature range and strictly monotonic for the relevant pH range (6.8-7.5). To investigate the specificity of TauCEST imaging for the brain of polar cod (Boreogadus saida) at 1.5°C simulations were carried out, indicating a taurine contribution of about 65% to the in vivo expected CEST effect, if experimental parameters are optimized. B. saida was acutely exposed to three different CO2 concentrations in the sea water (control normocapnia; comparatively moderate hypercapnia OAm = 3300 μatm; high hypercapnia OAh = 4900 μatm). TauCEST imaging of the brain showed a significant increase in the TauCEST effect under the different CO2 concentrations of about 1.5-3% in comparison with control measurements, indicative of changes in pHi or metabolite concentration. Consecutive recordings of 1 H MR spectra gave no support for a concentration induced change of the in vivo observed TauCEST effect. Thus, the in vivo application of TauCEST offers the possibility of mapping relative changes in pHi in the brain of polar cod during exposure to CO2 .
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Affiliation(s)
- Felizitas C Wermter
- University of Bremen, Department of Chemistry, in-vivo-MR Group, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Bastian Maus
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Hans-O Pörtner
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Wolfgang Dreher
- University of Bremen, Department of Chemistry, in-vivo-MR Group, Bremen, Germany
| | - Christian Bock
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
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6
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Basharat M, deSouza NM, Parkes HG, Payne GS. Determining the chemical exchange saturation transfer (CEST) behavior of citrate and spermine under in vivo conditions. Magn Reson Med 2016; 76:742-6. [PMID: 26467055 PMCID: PMC5042183 DOI: 10.1002/mrm.25997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 08/20/2015] [Accepted: 08/29/2015] [Indexed: 11/11/2022]
Abstract
PURPOSE To estimate the exchange rates of labile (1) H in citrate and spermine, metabolites present in prostatic secretions, to predict the size of the citrate and spermine CEST effects in vivo. METHODS CEST z-spectra were acquired at high-field [11.7 Tesla (T)] from citrate and spermine solutions at physiological pH (6.5) using saturation power 6 μT. CEST was performed at different temperatures to determine exchange regimes (slow, intermediate or fast). For low pH solutions of spermine, exchange rates were estimated from resonance line width, fitting z-spectra using the Bloch equations incorporating exchange, and using quantifying exchange using saturation time experiments (QUEST). These rates were extrapolated to physiological pH. RESULTS Citrate showed little CEST effect at pH 6.5 and temperature (T) = 310 K (maximum 0.001% mM(-1) ), indicating fast exchange, whereas spermine showed greater CEST effects (maximum 0.2% mM(-1) ) indicating intermediate-to-fast exchange. Extrapolating data acquired from low pH spermine solutions predicts exchange rates at pH 6.5 and T of 310 K of at least 2 × 10(4) s(-1) . CONCLUSION Citrate and spermine show minimal CEST effects at 11.7T even using high saturation power. These effects would be much less than 2% at clinical field-strengths due to relatively faster exchange and would be masked by CEST from proteins. Magn Reson Med 76:742-746, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Affiliation(s)
- Meer Basharat
- CRUK Cancer Imaging Centre, Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, United Kingdom
| | - Nandita M deSouza
- CRUK Cancer Imaging Centre, Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, United Kingdom
| | - Harold G Parkes
- CRUK Cancer Imaging Centre, Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, United Kingdom
| | - Geoffrey S Payne
- CRUK Cancer Imaging Centre, Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, United Kingdom
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7
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Wermter FC, Bock C, Dreher W. Investigating GluCEST and its specificity for pH mapping at low temperatures. NMR IN BIOMEDICINE 2015; 28:1507-17. [PMID: 26412088 DOI: 10.1002/nbm.3416] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 05/17/2023]
Abstract
Chemical exchange saturation transfer (CEST) from glutamate to water (GluCEST) is a powerful tool for mapping glutamate concentration and intracellular pH. GluCEST could also be helpful to understand the physiology of lower aquatic vertebrates and invertebrates. Therefore, this study aimed to investigate the GluCEST effect and the exchange rate ksw from amine protons of glutamate to water in a broad range of temperatures (1-37°C) and pH (5.5-8.0). Z-spectra were measured from glutamate solutions at different pH values and temperatures and analysed by numerically solving the Bloch-McConnell equation. As expected, a strong dependence of the GluCEST effect and the determined ksw values on pH and temperature was observed. In addition, a strong dependence of the GluCEST effect on phosphate buffer concentration was confirmed. The in vitro data show that GluCEST is detectable in the whole temperature range, even at 1°C. An interpolation function for the exchange rate ksw was determined for the considered range of temperatures and pH values, showing a bijective relation between the exchange rate and pH at a given temperature. To investigate the specificity of GluCEST imaging at low temperatures, the CEST effect was investigated for several metabolites relevant for CEST imaging of the brain. As an example, the contribution of GluCEST to the total CEST effect at 3 ppm was estimated for zebrafish (Danio rerio). It is shown that also at lower temperatures glutamate is the major contributor to the total CEST effect, particularly if the experimental parameters are optimized.
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Affiliation(s)
- Felizitas C Wermter
- University of Bremen, Department of Chemistry, in-vivo-MR Group, Bremen, Germany
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Department of Integrative Ecophysiology, Bremerhaven, Germany
| | - Christian Bock
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Department of Integrative Ecophysiology, Bremerhaven, Germany
| | - Wolfgang Dreher
- University of Bremen, Department of Chemistry, in-vivo-MR Group, Bremen, Germany
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8
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Keppel TR, Weis DD. Mapping residual structure in intrinsically disordered proteins at residue resolution using millisecond hydrogen/deuterium exchange and residue averaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:547-554. [PMID: 25481641 DOI: 10.1007/s13361-014-1033-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/16/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
Measurement of residual structure in intrinsically disordered proteins can provide insights into the mechanisms by which such proteins undergo coupled binding and folding. The present work describes an approach to measure residual structure in disordered proteins using millisecond hydrogen/deuterium (H/D) exchange in a conventional bottom-up peptide-based workflow. We used the exchange mid-point, relative to a totally deuterated control, to quantify the rate of H/D exchange in each peptide. A weighted residue-by-residue average of these midpoints was used to map the extent of residual structure at near single-residue resolution. We validated this approach both by simulating a disordered protein and experimentally using the p300 binding domain of ACTR, a model disordered protein already well-characterized by other approaches. Secondary structure elements mapped in the present work are in good agreement with prior nuclear magnetic resonance measurements. The new approach was somewhat limited by a loss of spatial resolution and subject to artifacts because of heterogeneities in intrinsic exchange. Approaches to correct these limitations are discussed.
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Affiliation(s)
- Theodore R Keppel
- Department of Chemistry, The University of Kansas, 1251 Wescoe Hall Drive, Lawrence, KS, 66045, USA
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9
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Brock A. Fragmentation hydrogen exchange mass spectrometry: A review of methodology and applications. Protein Expr Purif 2012; 84:19-37. [DOI: 10.1016/j.pep.2012.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 01/19/2023]
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10
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Percy AJ, Rey M, Burns KM, Schriemer DC. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal Chim Acta 2012; 721:7-21. [PMID: 22405295 DOI: 10.1016/j.aca.2012.01.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure-function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure-function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in "dynamic topography" and thus represents a powerful means of monitoring protein structure-function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.
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Affiliation(s)
- Andrew J Percy
- Department of Chemistry, University of Calgary, Alberta, Canada
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11
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Keppel TR, Howard BA, Weis DD. Mapping Unstructured Regions and Synergistic Folding in Intrinsically Disordered Proteins with Amide H/D Exchange Mass Spectrometry. Biochemistry 2011; 50:8722-32. [DOI: 10.1021/bi200875p] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Theodore R. Keppel
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - Brent A. Howard
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - David D. Weis
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
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12
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Danielsson J, Kurnik M, Lang L, Oliveberg M. Cutting off functional loops from homodimeric enzyme superoxide dismutase 1 (SOD1) leaves monomeric β-barrels. J Biol Chem 2011; 286:33070-83. [PMID: 21700707 DOI: 10.1074/jbc.m111.251223] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Demetallation of the homodimeric enzyme Cu/Zn-superoxide dismutase (SOD1) is known to unleash pronounced dynamic motions in the long active-site loops that comprise almost a third of the folded structure. The resulting apo species, which shows increased propensity to aggregate, stands out as the prime disease precursor in amyotrophic lateral sclerosis (ALS). Even so, the detailed structural properties of the apoSOD1 framework have remained elusive and controversial. In this study, we examine the structural interplay between the central apoSOD1 barrel and the active-site loops by simply cutting them off; loops IV and VII were substituted with short Gly-Ala-Gly linkers. The results show that loop removal breaks the dimer interface and leads to soluble, monomeric β-barrels with high structural integrity. NMR-detected nuclear Overhauser effects are found between all of the constituent β-strands, confirming ordered interactions across the whole barrel. Moreover, the breathing motions of the SOD1 barrel are overall insensitive to loop removal and yield hydrogen/deuterium protection factors typical for cooperatively folded proteins (i.e. the active-site loops act as a "bolt-on" domain with little dynamic influence on its structural foundation). The sole exceptions are the relatively low protection factors in β-strand 5 and the turn around Gly-93, a hot spot for ALS-provoking mutations, which decrease even further upon loop removal. Taken together, these data suggest that the cytotoxic function of apoSOD1 does not emerge from its folded ground state but from a high energy intermediate or even from the denatured ensemble.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University S-106 91 Stockholm, Sweden
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13
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Sheridan RP, Levy RM, Englander SW. Normal mode paths for hydrogen exchange in the peptide ferrichrome. Proc Natl Acad Sci U S A 2010; 80:5569-72. [PMID: 16593367 PMCID: PMC384299 DOI: 10.1073/pnas.80.18.5569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Possible paths for exposure to solvent and hydrogen exchange of the amide protons of ferrichrome, a cyclic hexapeptide, are examined. The paths are obtained from calculations of the vibrational normal modes of ferrichrome and correspond to low energy atomic displacements away from the local minimum in the multidimensional conformational space of the molecule. Exposure of exchangeable groups along the normal modes was determined by using the solvent accessible surface area algorithm of Lee and Richards. Three of the exchangeable protons (Gly(1,2,3,)) are largely exposed to solvent in the x-ray structure while the remaining three exchangeable protons of the ornithines are totally shielded from solvent. A very small number of normal mode displacements are found to expose the Orn(2) and Orn(3) amide groups while the Orn(1) amide proton remains shielded from solvent for all the paths studied. The effective paths for exposure of Orn(2) and Orn(3) correspond to the lowest frequency ( approximately 18 cm(-1)) motions. The paths are characterized in terms of the magnitude and energy of atomic displacements, correlated changes in dihedral angles, and the resulting changes in exposure and hydrogen bonding of exchangeable groups.
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Affiliation(s)
- R P Sheridan
- Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08903
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14
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Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange. Biophys J 2010; 96:169-79. [PMID: 18835891 DOI: 10.1529/biophysj.108.142448] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 09/15/2008] [Indexed: 11/18/2022] Open
Abstract
The exchange rates for the amide hydrogens of beta(2)-microglobulin, the protein responsible for dialysis-related amyloidosis, were measured under native conditions at different temperatures ranging from 301 to 315 K. The pattern of protection factors within different regions of the protein correlates well with the hydrogen-bonding pattern of the deposited structures. Analysis of the exchange rates indicates the presence of mixed EX1- and EX2-limit mechanisms. The measured parameters are consistent with a two-process model in which two competing pathways, i.e., global unfolding in the core region and partial openings of the native state, determine the observed exchange rates. These findings are analyzed with respect to the amyloidogenic properties of the protein.
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15
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NMR analysis of native-state protein conformational flexibility by hydrogen exchange. Methods Mol Biol 2009; 490:285-310. [PMID: 19157088 DOI: 10.1007/978-1-59745-367-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The rate of hydrogen exchange for the most protected amides of a protein is widely used to provide an estimate of global conformational stability by analyzing the exchange kinetics in the unfolded state in terms of model peptide exchange rates. The exchange behavior of the other amides of the protein which do not exchange via a global unfolding mechanism can provide insight into the smaller-scale conformational transitions that facilitate access to solvent as required for the exchange reaction. However, since the residual tertiary structure in the exchange-competent conformation can modulate the chemistry of the exchange reaction, equilibrium values estimated from normalization with model peptide rates are open to question. To overcome this limitation, the most robust approaches utilize differential analyses as a function of experimental variables such as denaturant concentration, temperature, pH, and mutational variation. Practical aspects of these various differential analysis techniques are considered with illustrations drawn from the literature.
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17
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Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ. Residue-level interrogation of macromolecular crowding effects on protein stability. J Am Chem Soc 2008; 130:6826-30. [PMID: 18459780 DOI: 10.1021/ja8005995] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Theory predicts that macromolecular crowding affects protein behavior, but experimental confirmation is scant. Herein, we report the first residue-level interrogation of the effects of macromolecular crowding on protein stability. We observe up to a 100-fold increase in the stability, as measured by the equilibrium constant for folding, for the globular protein chymotrypsin inhibitor 2 (CI2) in concentrations of the cosolute poly(vinylpyrrolidone) (PVP) that mimic the protein concentration in cells. We show that the increased stability is caused by the polymeric nature of PVP and that the degree of stabilization depends on both the location of the individual residue in the protein structure and the PVP concentration. Our data reinforce the assertion that macromolecular crowding stabilizes the protein by destabilizing its unfolded states.
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Affiliation(s)
- Lisa M Charlton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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18
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Tartaglia GG, Cavalli A, Vendruscolo M. Prediction of Local Structural Stabilities of Proteins from Their Amino Acid Sequences. Structure 2007; 15:139-43. [PMID: 17292832 DOI: 10.1016/j.str.2006.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 12/05/2006] [Accepted: 12/28/2006] [Indexed: 11/24/2022]
Abstract
Hydrogen exchange experiments provide detailed information about the local stability and the solvent accessibility of different regions of the structures of folded proteins, protein complexes, and amyloid fibrils. We introduce an approach to predict protection factors from hydrogen exchange in proteins based on the knowledge of their amino acid sequences without the inclusion of any additional structural information. These results suggest that the propensity of different regions of the structures of globular proteins to undergo local unfolding events can be predicted from their amino acid sequences with an accuracy of 80% or better.
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Affiliation(s)
- Gian Gaetano Tartaglia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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19
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20
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Barksdale AD, Rosenberg A. Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. METHODS OF BIOCHEMICAL ANALYSIS 2006; 28:1-113. [PMID: 7048016 DOI: 10.1002/9780470110485.ch1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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21
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Liang X, Lee GI, Van Doren SR. Partially unfolded forms and non-two-state folding of a beta-sandwich: FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. J Mol Biol 2006; 364:225-40. [PMID: 17007879 PMCID: PMC2020856 DOI: 10.1016/j.jmb.2006.08.090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 08/30/2006] [Indexed: 11/21/2022]
Abstract
FHA domains adopt a beta-sandwich fold with 11 strands. The first evidence of partially unfolded forms of a beta-sandwich is derived from native-state hydrogen exchange (NHX) of the forkhead-associated (FHA) domain from kinase-associated protein phosphatase from Arabidopsis. The folding kinetics of this FHA domain indicate that EX2 behavior prevails at pH 6.3. In the chevron plot, rollover in the folding arm and bends in the unfolding arm suggest folding intermediates. NHX of this FHA domain suggests a core of six most stable beta-strands and two loops, characterized by rare global unfolding events. Flanking this stable core are beta-strands and recognition loops with less stability, termed subglobal motifs. These suggest partially unfolded forms (near-native intermediates) with two levels of stability. The spatial separation of the subglobal motifs on the flanks suggests possible parallelism in their folding as additional beta-strands align with the stable core of six strands. Intermediates may contribute to differences in stabilities and m-values suggested by NHX or kinetics relative to chemical denaturation. Residual structure in the unfolded regime is suggested by superprotection of beta-strand 6 and by GdmCl-dependence of adjustments in amide NMR spectra and residual optical signal. The global folding stability depends strongly on pH, with at least 3 kcal/mol more stability at pH 7.3 than at pH 6.3. This FHA domain is hypothesized to fold progressively with initial hydrophobic collapse of its stable six-stranded core followed by addition of less stable flanking beta-strands and ordering of recognition loops.
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Affiliation(s)
| | | | - Steven R. Van Doren
- *To whom correspondence should be addressed. E-mail: ., Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812
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22
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Abstract
Peptides corresponding to excised alpha-helical segments of natural proteins can spontaneously form helices in solution. However, peptide helices are usually substantially less stable in solution than in the structural context of a folded protein, because of the additional interactions possible between helices in a protein. Such interactions can be thought of as coupling helix formation and tertiary contact formation. The relative energetic contributions of the two processes to the total energy of the folded state of a protein is a matter of current debate. To investigate this balance, an extended helix-coil model (XHC) that incorporates both effects has been constructed. The model treats helix formation with the Lifson-Roig formalism, which describes helix initiation and propagation through cooperative local interactions. The model postulates an additional parameter representing participation of a site in a tertiary contact. In the model, greater helix stability can be achieved through combinations of these short-range and long-range interactions. For instance, stronger tertiary contacts can compensate for helices with little intrinsic stability. By varying the strength of the nonlocal interactions, the model can exhibit behavior consistent with a variety of qualitative models describing the relative importance of secondary and tertiary structure. Moreover, the model is explicit in that it can be used to fit experimental data to individual peptide sequences, providing a means to quantify the two contributions on a common energetic basis.
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Affiliation(s)
- Andrew C Hausrath
- Department of Biochemistry and Molecular Physics, University of Arizona, Arizona 85721, USA.
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23
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Best RB, Vendruscolo M. Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2. Structure 2006; 14:97-106. [PMID: 16407069 DOI: 10.1016/j.str.2005.09.012] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 09/20/2005] [Accepted: 09/21/2005] [Indexed: 11/30/2022]
Abstract
Protection factors obtained from equilibrium hydrogen exchange experiments are an important source of structural information on both native and nonnative states of proteins. We present a method for determining ensembles of protein structures by using hydrogen exchange data as restraints in molecular dynamics simulations in conjunction with an empirical force-field. The method is applied to determine the ensemble of structures representing the native state of chymotrypsin inhibitor 2 (CI2), including the rare, large fluctuations responsible for hydrogen exchange.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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24
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Bollen YJM, Kamphuis MB, van Mierlo CPM. The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates. Proc Natl Acad Sci U S A 2006; 103:4095-100. [PMID: 16537490 PMCID: PMC1449652 DOI: 10.1073/pnas.0509133103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many native proteins occasionally form partially unfolded forms (PUFs), which can be detected by hydrogen/deuterium exchange and NMR spectroscopy. Knowledge about these metastable states is required to better understand the onset of folding-related diseases. So far, not much is known about where PUFs reside within the energy landscape for protein folding. Here, four PUFs of the relatively large apoflavodoxin (179 aa) are identified. Remarkably, at least three of them are partially misfolded conformations. The misfolding involves side-chain contacts as well as the protein backbone. The rates at which the PUFs interconvert with native protein have been determined. Comparison of these rates with stopped-flow data positions the PUFs in apoflavodoxin's complex folding energy landscape. PUF1 and PUF2 are unfolding excursions that start from native apoflavodoxin but do not continue to the unfolded state. PUF3 and PUF4 could be similar excursions, but their rates of formation suggest that they are on a dead-end folding route that starts from unfolded apoflavodoxin and does not continue all of the way to native protein. All PUFs detected thus are off the protein's productive folding route.
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Affiliation(s)
- Yves J. M. Bollen
- *Department of Structural Biology, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands; and
| | - Monique B. Kamphuis
- Laboratory of Biochemistry, Wageningen University, 6703 HA, Wageningen, The Netherlands
| | - Carlo P. M. van Mierlo
- Laboratory of Biochemistry, Wageningen University, 6703 HA, Wageningen, The Netherlands
- To whom correspondence should be addressed. E-mail:
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25
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Huang SW, Hwang JK. Computation of conformational entropy from protein sequences using the machine-learning method-Application to the study of the relationship between structural conservation and local structural stability. Proteins 2005; 59:802-9. [PMID: 15828008 DOI: 10.1002/prot.20462] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A complete protein sequence can usually determine a unique conformation; however, the situation is different for shorter subsequences--some of them are able to adopt unique conformations, independent of context; while others assume diverse conformations in different contexts. The conformations of subsequences are determined by the interplay between local and nonlocal interactions. A quantitative measure of such structural conservation or variability will be useful in the understanding of the sequence-structure relationship. In this report, we developed an approach using the support vector machine method to compute the conformational variability directly from sequences, which is referred to as the sequence structural entropy. As a practical application, we studied the relationship between sequence structural entropy and the hydrogen exchange for a set of well-studied proteins. We found that the slowest exchange cores usually comprise amino acids of the lowest sequence structural entropy. Our results indicate that structural conservation is closely related to the local structural stability. This relationship may have interesting implications in the protein folding processes, and may be useful in the study of the sequence-structure relationship.
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Affiliation(s)
- Shao-Wei Huang
- Institute of Bioinformatics, National Chiao Tung University, Taiwan, Republic of China
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26
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Kaya H, Chan HS. Explicit-chain model of native-state hydrogen exchange: Implications for event ordering and cooperativity in protein folding. Proteins 2004; 58:31-44. [PMID: 15468168 DOI: 10.1002/prot.20286] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Native-state hydrogen exchange experiments on several proteins have revealed partially unfolded conformations with diverse stabilities. These equilibrium observations have been used to support kinetic arguments that folding proceeds via a sequential "pathway." This interpretative logic is evaluated here by analyzing the relationship between thermodynamic behavior and folding kinetics in a class of simplified lattice protein models. The chain models studied have varying degrees of cooperative interplay (coupling) between local helical conformational preference and favorable nonlocal interactions. When model cooperativity is high, as native conditions are weakened, "isotherms" of free energy of exchange for residues belonging to the same helix merge together before global unfolding. The point of merger depends on the model energetic favorability of the helix. This trend is similar to the corresponding experimental observations. Kinetically, we find that the ordering of helix formation in the very last stage of native core assembly tends to follow the stabilities of their converged isotherms. In a majority (but not all) of folding trajectories, the final assembly of helices that are thermodynamically more stable against exchange precedes that of helices that are less stable against exchange. These model features are in partial agreement with common experimental interpretations. However, the model results also underscore the ensemble nature of the folding process: the kinetics of helix formation is not a discrete, strictly "all-or-none" process as that envisioned by certain non-explicit-chain models. Helices generally undergo many cycles of partial formation and dissolution before their conformations are fixed in the final assembly stage of folding, a kinetic stage that takes up only approximately 2% of the average folding time in the present model; and the ordering of the helices' final assembly in some trajectories can be different from the dominant ordering stipulated by the exchange isotherms.
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Affiliation(s)
- Hüseyin Kaya
- Department of Biochemistry, Faculty of Medicine, Protein Engineering Network of Centres of Excellence, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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27
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Cliff MJ, Higgins LD, Sessions RB, Waltho JP, Clarke AR. Beyond the EX1 limit: probing the structure of high-energy states in protein unfolding. J Mol Biol 2004; 336:497-508. [PMID: 14757061 DOI: 10.1016/j.jmb.2003.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hydrogen exchange kinetics in native solvent conditions have been used to explore the conformational fluctuations of an immunoglobulin domain (CD2.domain1). The global folding/unfolding kinetics of the protein are unaltered between pH 4.5 and pH 9.5, allowing us to use the pH-dependence of amide hydrogen/deuterium exchange to characterise conformational states with energies up to 7.2kcal/mol higher than the folded ground state. The study was intended to search for discreet unfolding intermediates in this region of the energy spectrum, their presence being revealed by the concerted exchange behaviour of subsets of amide groups that become accessible at a given free energy, i.e. the spectrum would contain discreet groupings. Protection factors for 58 amide groups were measured across the pH range and the hydrogen-exchange energy profile is described. More interestingly, exchange behaviour could be grouped into three categories; the first two unremarkable, the third unexpected. (1) In 33 cases, amide exchange was dominated by rapid fluctuation, i.e. the free energy difference between the ground state and the rapidly accessed open state is sufficiently low that the contribution from crossing the unfolding barrier is negligible. (2) In 18 cases exchange is dominated by the global folding transition barrier across the whole pH range measured. The relationship between hydroxyl ion concentration and observed exchange rate is hyperbolic, with the limiting rate being that for global unfolding; the so-called EX1 limit. For these, the free energy difference between the folded ground state and any rapidly-accessed open state is too great for the proton to be exchanged through such fluctuations, even at the highest pH employed in this study. (3) For the third group, comprising five cases, we observe a behaviour that has not been described. In this group, as in category 2, the rate of exchange reaches a plateau; the EX1 limit. However, as the intrinsic exchange rate (k(int)) is increased, this limit is breached and the rate begins to rise again. This unintuitive behaviour does not result from pH instability, rather it is a consequence of amide groups experiencing two processes; rapid fluctuation of structure and crossing the global barrier for unfolding. The boundary at which the EX1 limit is overcome is determined by the equilibrium distribution of the fluctuating open and closed states (K(O/C)) and the rate constant for unfolding (k(u)). This critical boundary is reached when k(int)K(O/C)=k(u). Given that, in a simple transition state formalism: k(u)=K(#)k' (where K(#) describes the equilibrium distribution between the transition and ground state and k' describes the rate of a barrierless rearrangement), it follows that if the pH is raised to a level where k(int)=k', then the entire free energy spectrum from ground state to transition state could be sampled.
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Affiliation(s)
- Matthew J Cliff
- The Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, BS8 1TD, Bristol, UK.
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28
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Abstract
Slow amide hydrogen exchange is an increasingly popular tool for investigating structure and function in proteins. The kinetic model for slow hydrogen exchange has two limits, called EX2 and EX1, wherein the thermodynamics and kinetics of protein motions, respectively, are reported by the exchange data. While many laboratories have demonstrated that EX2 exchange can indeed provide accurate results regarding the thermodynamics of protein stability, the potential of EX1 exchange to follow the kinetics of protein unfolding and folding is only beginning to be realized. EX1 hydrogen exchange has advantages over more traditional folding experiments: it provides single-residue resolution, as well as whole-molecule information, the latter of which can be interpreted in terms of the cooperativity of unfolding. However, key questions remain regarding the interpretation of EX1 hydrogen exchange.
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Affiliation(s)
- Debra M Ferraro
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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29
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Woodward C, Carulla N, Barany G. Native state hydrogen-exchange analysis of protein folding and protein motional domains. Methods Enzymol 2004; 380:379-400. [PMID: 15051346 DOI: 10.1016/s0076-6879(04)80017-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Clare Woodward
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, St. Paul 55108, USA
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30
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Bhutani N, Udgaonkar JB. Folding subdomains of thioredoxin characterized by native-state hydrogen exchange. Protein Sci 2003; 12:1719-31. [PMID: 12876321 PMCID: PMC2323958 DOI: 10.1110/ps.0239503] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 05/02/2003] [Accepted: 05/02/2003] [Indexed: 10/26/2022]
Abstract
Native-state hydrogen exchange (HX) studies, used in conjunction with NMR spectroscopy, have been carried out on Escherichia coli thioredoxin (Trx) for characterizing two folding subdomains of the protein. The backbone amide protons of only the slowest-exchanging 24 amino acid residues, of a total of 108 amino acid residues, could be followed at pH 7. The free energy of the opening event that results in an amide hydrogen exchanging with solvent (DeltaG(op)) was determined at each of the 24 amide hydrogen sites. The values of DeltaG(op) for the amide hydrogens belonging to residues in the helices alpha(1), alpha(2), and alpha(4) are consistent with them exchanging with the solvent only when the fully unfolded state is sampled transiently under native conditions. The denaturant-dependences of the values of DeltaG(op) provide very little evidence that the protein samples partially unfolded forms, lower in energy than the unfolded state. The amide hydrogens belonging to the residues in the beta strands, which form the core of the protein, appear to have higher values of DeltaG(op) than amide hydrogens belonging to residues in the helices, suggesting that they might be more stable to exchange. This apparently higher stability to HX of the beta strands might be either because they exchange out their amide hydrogens in a high energy intermediate preceding the globally unfolded state, or, more likely, because they form residual structure in the globally unfolded state. In either case, the central beta strands-beta(3,) beta(2), and beta(4)-would appear to form a cooperatively folding subunit of the protein. The native-state HX methodology has made it possible to characterize the free energy landscape that Trx can sample under equilibrium native conditions.
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Affiliation(s)
- Nidhi Bhutani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, University of Agricultural Sciences at the Gandhi Krishi Vigyan Kendra Campus, Bangalore 560065, India
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31
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Abstract
A key paradigm in the biology of adaptation holds that urea affects protein function by increasing the fluctuations of the native state, while trimethylamine N-oxide (TMAO) affects function in the opposite direction by decreasing the normal fluctuations of the native ensemble. Using urea and TMAO separately and together, hydrogen exchange (HX) studies on RNase A at pH* 6.35 were used to investigate the basic tenets of the urea:TMAO paradigm. TMAO (1 M) alone decreases HX rate constants of a select number of sites exchanging from the native ensemble, and low urea alone increases the rate constants of some of the same sites. Addition of TMAO to urea solutions containing RNase A also suppresses HX rate constants. The data show that urea and TMAO independently or in combination affect the dynamics of the native ensemble in opposing ways. The results provide evidence in support of the counteraction aspect of the urea:TMAO paradigm linking structural dynamics with protein function in urea-rich organs and organisms. RNase A is so resistant to urea denaturation at pH* 6.35 that even in the presence of 4.8 M urea, the native ensemble accounts for >99.5% of the protein. An essential test, devised to determine the HX mechanism of exchangeable protons, shows that over the 0-4.8 M urea concentration range nearly 80% of all observed sites convert from EX2 to EX1. The slow exchange sites are all EX1; they do not exhibit global exchange even at urea concentrations (5.8 M) well into the denaturation transition zone, and their energetically distinct activated complexes leading to exchange gives evidence of residual structure. Under these experimental conditions, the use of DeltaG(HX) as a basis for HX analysis of RNase A urea denaturation is invalid.
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Affiliation(s)
- Youxing Qu
- Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, 5.154 MRB, Galveston, Texas 77555-1052, USA
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32
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Hespenheide BM, Rader AJ, Thorpe MF, Kuhn LA. Identifying protein folding cores from the evolution of flexible regions during unfolding. J Mol Graph Model 2002; 21:195-207. [PMID: 12463638 DOI: 10.1016/s1093-3263(02)00146-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The unfolding of a protein can be described as a transition from a predominantly rigid, folded structure to an ensemble of denatured states. During unfolding, the hydrogen bonds and salt bridges break, destabilizing the secondary and tertiary structure. Our previous work shows that the network of covalent bonds, salt bridges, hydrogen bonds, and hydrophobic interactions forms constraints that define which regions of the native protein are flexible or rigid (structurally stable). Here, we test the hypothesis that information about the folding pathway is encoded in the energetic hierarchy of non-covalent interactions in the native-state structure. The incremental thermal denaturation of protein structures is simulated by diluting the network of salt bridges and hydrogen bonds, breaking them one by one, from weakest to strongest. The structurally stable and flexible regions are identified at each step, providing information about the evolution of flexible regions during denaturation. The folding core, or center of structure formation during folding, is predicted as the region formed by two or more secondary structures having the greatest stability against denaturation. For 10 proteins with different architectures, we show that the predicted folding cores from this flexibility/stability analysis are in good agreement with those identified by native-state hydrogen-deuterium exchange experiments.
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Affiliation(s)
- Brandon M Hespenheide
- Department of Biochemistry and Molecular Biology Michigan State University East Lansing MI 48824, USA
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33
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Rodriguez HM, Robertson AD, Gregoret LM. Native state EX2 and EX1 hydrogen exchange of Escherichia coli CspA, a small beta-sheet protein. Biochemistry 2002; 41:2140-8. [PMID: 11841204 DOI: 10.1021/bi011347x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli CspA is a small all-beta-sheet protein that folds fast (tau = 4 ms) via an apparent two-state mechanism. Our previous studies have shown that a large aromatic cluster on the surface of the protein participates in the rate-limiting step of folding and thus may be part of the folding nucleus of this protein. To obtain a more detailed picture of molecular events at the peptide backbone during unfolding and folding of CspA, we used native state hydrogen exchange and nuclear magnetic resonance spectroscopy (NMR). The experiments with native CspA were performed over a range of pH values from low pH, where exchange is governed by a rapid equilibrium before chemical exchange (EX2 exchange), to high pH, where exchange is dictated by the rate of unfolding (EX1 exchange). Rates of folding and unfolding were determined for 11 residues. The distribution of rates of folding within the structure of CspA suggests that hairpin turns, including one near the aromatic cluster, may nucleate the folding of CspA.
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Affiliation(s)
- Hector M Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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34
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Murphy OJ, Yi X, Weis RM, Thompson LK. Hydrogen exchange reveals a stable and expandable core within the aspartate receptor cytoplasmic domain. J Biol Chem 2001; 276:43262-9. [PMID: 11553619 DOI: 10.1074/jbc.m105585200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intensive study of bacterial chemoreceptors has not yet revealed how receptor methylation and ligand binding alter the interactions between the receptor cytoplasmic domain and the CheA kinase to control kinase activity. Both monomeric and dimeric forms of an Asp receptor cytoplasmic fragment have been shown to be highly dynamic, with a small core of slowly exchanging amide hydrogens (Seeley, S. K., Weis, R. M., and Thompson, L. K. (1996) Biochemistry 35, 5199-5206). Hydrogen exchange studies of the wild-type cytoplasmic fragment and an S461L mutant thought to mimic the kinase-inactivating state are used to investigate the relationship between the stable core and dimer dissociation. Our results establish that (i) decreasing pH stabilizes the dimeric state, (ii) the stable core is present also in the transition state for dissociation, and (iii) this core is expanded significantly by small changes in electrostatic and hydrophobic interactions. These kinase-inactivating changes stabilize both the monomeric and the dimeric states of the protein, which has interesting implications for the mechanism of kinase activation. We conclude that the cytoplasmic domain is a flexible region poised for stabilization by small changes in electrostatic and hydrophobic interactions such as those caused by methylation of glutamate residues and by ligand-induced conformational changes during signaling.
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Affiliation(s)
- O J Murphy
- Graduate Program in Molecular and Cellular Biology, and the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003-4510, USA
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35
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Neira JL, Mateu MG. Hydrogen exchange of the tetramerization domain of the human tumour suppressor p53 probed by denaturants and temperature. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:4868-77. [PMID: 11559355 DOI: 10.1046/j.1432-1327.2001.02414.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have analysed the hydrogen/deuterium exchange of the tetramerization domain of human tumour suppressor p53 under mild chemical denaturation conditions, and at different temperatures. Exchange behaviour has been measured for 16 amide protons in the chemical-denaturation studies and for seven protons in the temperature-denaturation studies. The exchange rates are in the range observed for other proteins with similar elements of secondary structure. The slowest-exchange core includes contributions from residues in the alpha helix and the beta sheet. However, only some of the slowest-exchanging protons correspond to residues involved in native interactions in the transient intermediate detected during the folding of this domain. The guanidinium-chloride denaturation curves of all residues seem to merge together, although they are well below the main isotherm of global unfolding. Thus, there is no evidence for several subglobal unfolding units. The activation parameters obtained from the temperature-denaturation experiments are similar to those obtained for monomeric proteins, and well below the global unfolding enthalpy obtained by circular dichroism measurements. Thus, the exchange studies at different denaturant concentrations and temperatures indicate that no particular folding intermediate is populated under those conditions.
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Affiliation(s)
- J L Neira
- Centro de Biología Molecular y Celular, Universidad Miguel Hernández, Alicante, Spain.
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36
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Bhattacharyya A, Mandal AK, Banerjee R, Roy S. Dynamics of compact denatured states of glutaminyl-tRNA synthetase probed by bis-ANS binding kinetics. Biophys Chem 2000; 87:201-12. [PMID: 11099182 DOI: 10.1016/s0301-4622(00)00192-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Bis-ANS binds to native glutaminyl-tRNA synthetase (GlnRS) with a fast and a slow phase. The rate constant of the slow phase is independent of bis-ANS concentration suggesting a slow conformational change in the pathway of bis-ANS binding. Aging of GlnRS causes a large decrease of the slow phase amplitude with concomitant increase of the fast phase amplitude. Several other large, multi-domain proteins show similar patterns upon aging. The near UV-CD spectra of the native and the aged GlnRS remain similar. Significant changes in far UV-CD, acrylamide quenching and sulfhydryl reactivity, are seen upon aging, suggesting disruptions in native interactions. Refolding of GlnRS from the urea-denatured state rapidly produces a state that is very similar to the equilibrium molten globule state. Bis-ANS binds to the molten globule state with kinetics similar to that of the aged state and unlike that of the native state. This suggests that the slow binding phase of bis-ANS, seen in native proteins, originate from relatively high energy barriers between the native and the more open states. Thus bis-ANS can be used as a powerful probe for large amplitude, low-frequency motions of proteins.
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37
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Cota E, Hamill SJ, Fowler SB, Clarke J. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability. J Mol Biol 2000; 302:713-25. [PMID: 10986129 DOI: 10.1006/jmbi.2000.4053] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As part of a systematic study of the folding of protein structural families we compare the effect of mutation in two closely related fibronectin type III (fnIII) domains, the tenth fnIII domain of human fibronectin (FNfn10) and the third fnIII domain of human tenascin (TNfn3). This comparison of the two related proteins allows us to distinguish any anomalous response to mutation. Although they have very similar structures, the effect of mutation is very different. TNfn3 behaves like a "typical" protein, with changes in free energy correlated to the number of contacts lost on mutation. The loss of free energy upon mutation is significantly lower for FNfn10, particularly mutations of residues in the A, B and G strands. Remarkably, some of the residues involved are completely buried and closely packed in the core. In FNfn10 the regions of the protein that can accommodate mutation have previously been shown to be mobile. We propose that there is a "plasticity" in the peripheral regions of FNfn10 that allows it to rearrange to minimise the effect of mutations. This study emphasises the difficulties that might arise when making generalisations from a single member of a protein family.
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Affiliation(s)
- E Cota
- Cambridge University Chemical Laboratory, MRC Centre for Protein Engineering, Lensfield Road, Cambridge, CB2 1EW, UK
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38
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Abstract
The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure.
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Affiliation(s)
- D P Kharakoz
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, 142290 Pushchino, Moscow, Russia.
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39
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Arrington CB, Robertson AD. Microsecond to minute dynamics revealed by EX1-type hydrogen exchange at nearly every backbone hydrogen bond in a native protein. J Mol Biol 2000; 296:1307-17. [PMID: 10698635 DOI: 10.1006/jmbi.2000.3536] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A previous comprehensive analysis of the pH dependence of native-state amide hydrogen (NH) exchange in turkey ovomucoid third domain (OMTKY3) yielded apparent opening and closing rate constants (k(op) and k(cl)) at 14 NH groups involved in global conformational changes. This analysis has been extended to 18 additional slowly exchanging NH groups. Quench-flow experiments were performed to monitor NH exchange in native OMTKY3 from neutral to very alkaline pH ( approximately 12) conditions. Above pH 10 the mechanism of exchange switched from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e. EX2 exchange), to one where exchange was limited by the rate of opening (i.e. EX1 exchange). Kinetics of solvent exposure are now known for nearly all backbone NH groups in native OMTKY3, yielding rate constants that span five orders of magnitude, 0.004 to 200 s(-1).
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Affiliation(s)
- C B Arrington
- Department of Biochemistry, the University of Iowa, Iowa City 52242, USA
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40
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Dixon ME, Hitchens TK, Bryant RG. Comparisons of pressure and temperature activation parameters for amide hydrogen exchange in T4 lysozyme. Biochemistry 2000; 39:248-54. [PMID: 10625500 DOI: 10.1021/bi991718y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activation enthalpies and entropies are reported for proton-deuteron exchange at 42 amide sites in T4 lysozyme and compared with activation volumes for the same residues obtained earlier [Hitchens, T. K., and Bryant, R. G. (1998) Biochemistry 37, 5878-5887]. There is no correlation found between activation volume and activation entropy or activation enthalpy. The activation enthalpy is linearly related to the activation entropy in part as a consequence of a relatively narrow sampling window for the rate constants that corresponds to a narrow range of activation free energy. A consequence of the entropy-enthalpy compensation is preservation of rank order of proton exchange. Variations in DeltaH, DeltaS, and DeltaV for residues that are structurally close together in the folded protein suggest that there may be a variety of energetically distinct pathways for the access of solvent to these structurally related exchange sites.
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Affiliation(s)
- M E Dixon
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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41
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Yuan C, Li J, Selby TL, Byeon IJ, Tsai MD. Tumor suppressor INK4: comparisons of conformational properties between p16(INK4A) and p18(INK4C). J Mol Biol 1999; 294:201-11. [PMID: 10556039 DOI: 10.1006/jmbi.1999.3231] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The INK4 (inhibitor of cyclin-dependent kinase 4) family consists of four tumor-suppressor proteins: p15(INK4B), p16(INK4A), p18(INK4C), and p19(INK4D). While their sequences and structures are highly homologous, they show appreciable differences in conformational flexibility, stability, and aggregation tendency. Here, p16 and p18 were first compared directly by NMR for line broadening and disappearance, then investigated by three different approaches in search of the causes of these differences. From denaturation experiments it was found that both proteins are marginally stable with low denaturation stability (1.94 and 2.98 kcal/mol, respectively). Heteronuclear (1)H-(15)N nuclear Overhauser enhancement measurements revealed very limited conformational flexibility on the pico- to nanosecond time-scale for both p16 and p18. H/(2)H exchange of amide protons monitored by NMR on three proteins (p16, p18 as well as p15), however, revealed markedly different rates in the order p18<p16</=p15. A subset of very slowly exchanging residues (about 19 in total) was identified in p18, including 16 residues in the region of the fourth ankyrin repeat, probably as a result of a stabilizing effect by the extra ankyrin repeat. Thus, while INK4 proteins may have similar low thermodynamic stability as well as limited flexibility on the pico- to nanosecond time-scale, they display pronounced differences in the conformational flexibility on the time-scale of minutes to hours. Further analyses suggested that differences in H/(2)H exchange rates reflect differences in the kinetic stability of the INK4 proteins, which in turn is related to differences in the aggregation tendency.
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Affiliation(s)
- C Yuan
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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42
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Abstract
A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered.
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Affiliation(s)
- R Li
- Department of Biochemistry, University of Minnesota, St. Paul 55108, USA
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43
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Qian H, Chan SI. Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process model. J Mol Biol 1999; 286:607-16. [PMID: 9973574 DOI: 10.1006/jmbi.1998.2484] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recent progress in measurements on the amide hydrogen exchange (HX) in proteins under varying denaturing conditions, both at equilibrium and in transient relaxation, necessitates the development of a unifying theory which quantitatively relates the HX rates to the conformational energetics of the proteins. We present here a comprehensive kinetic model for the site-specific HX of proteins under varying solvent denaturing conditions based on the two-state protein folding model. The generalized two-process model considers both conformational fluctuations and residual protections, respectively, within the folded and unfolded states of a protein, as well as a global kinetic folding-unfolding transition between the two states. The global transition can be either rapid or slow, depending on the solvent condition for the protein. This novel model is applicable to the traditional equilibrium HX measurements in both EX2 and EX1 regimes, and also the recently introduced transient pulse-labeling HX experiments. A set of simple analytical equations is provided for quantitative interpretation of experimental data. The model emphasizes the use of full time-course of bi-exponential HX kinetics, rather than fitting time-course data to single rate constants, to obtain quantitative information about fluctuating conformers within the folded and unfolded states of proteins. This HX kinetic model naturally unfolds into a simple two-state and two-stage kinetic interpretation for protein folding. It suggests that the various observed intermediates of a protein can be interpreted as dominant isomers of either the folded or the unfolded state under different solvent conditions. This simple, minimalist's view of protein folding is consistent with various recent experimental observations on folding kinetics by HX.
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Affiliation(s)
- H Qian
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA.
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44
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Neira JL, Sevilla P, Menéndez M, Bruix M, Rico M. Hydrogen exchange in ribonuclease A and ribonuclease S: evidence for residual structure in the unfolded state under native conditions. J Mol Biol 1999; 285:627-43. [PMID: 9878434 DOI: 10.1006/jmbi.1998.2365] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two-dimensional NMR spectroscopy has been used to monitor the exchange of backbone amide protons in ribonuclease A (RNase A) and its subtilisin-cleaved form, ribonuclease S (RNase S). Exchange measurements at two different pH values (5.4 and 6.0) show that the exchange process occurs according to the conditions of the EX2 limit. Differential scanning calorimetry measurements have been carried out in 2H2O under conditions analogous to those used in the NMR experiments in order to determine the values of DeltaCp, DeltaHu and Tm, corresponding to the thermal denaturation of both proteins. For the amide protons of a large number of residues in RNase A, the free energies at 25 degreesC for exchange competent unfolding processes are much lower than the calorimetric denaturation free energies, thus showing that exchange occurs through local fluctuations in the native state. For 20 other protons, the cleavage reaction had approximately the same effect on the exchange rate constants than on the equilibrium constant for unfolding, indicating that those protons exchange by global unfolding. There is a good agreement between the residues to which these protons belong and those involved in the putative folding nucleation site identified by quench-flow NMR studies. The unfolding free energies of the slowest exchanging protons, DeltaGex, as evaluated from exchange data, are much larger than the calorimetric free energies of unfolding, DeltaGu. Given the agreement between DeltaDeltaGex(A-S), the difference in free energy from exchange for a given proton of the two proteins, and DeltaDeltaGu(A-S), the difference in the calorimetric free energy of the two proteins, the discrepancy indicates that the intrinsic exchange rates in the unfolded state of those protons cannot be approximated by those measured in short unstructured peptides and, consequently, exchange for those protons in RNase A and S must occur through a rather structured denatured state.
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Affiliation(s)
- J L Neira
- Instituto de Estructura de la Materia, CSIC, Serrano 119, Madrid, E-28006, Spain
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45
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Bhuyan AK, Udgaonkar JB. Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochromec under strongly destabilizing conditions. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19980801)32:2<241::aid-prot10>3.0.co;2-d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Hitchens TK, Bryant RG. Pressure dependence of amide hydrogen-deuterium exchange rates for individual sites in T4 lysozyme. Biochemistry 1998; 37:5878-87. [PMID: 9558321 DOI: 10.1021/bi972950b] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report measurements of the pressure dependence of rate constants for the exchange of amide residue protons with solvent deuterium for T4 lysozyme. Data obtained at nine pressures from 0.1 to 200 MPa are analyzed using an elementary kinetic model and the formalism of transition state theory which yield activation volumes for the exchange process. Resolution of individual amide sites was accomplished using the HSQC two-dimensional (2D) NMR experiment on uniformly (15)N-labeled protein. The observed activation volumes span the range from 2.75 to -25.1 mL/mol at 22 degreesC and pH* 7.5. When corrected for the pressure dependence of the ionic product for water and for the reported activation volume for the amide exchange reaction in model compounds, the portion of the activation volume associated with the accessibility of the solvent or catalyst to the amide sites ranges from -15.1 to 12.8 mL/mol. There is no simple correlation between the activation volumes and the protection factors for amide hydrogen exchange. The activation volumes for residues in close proximity in either the primary sequence or the folded structure may differ considerably. There is no trivial correlation between the activation volume and the secondary structural unit in which a residue is located, and activation volumes for residues that are apparently structurally coupled may be very different. The modest sizes of the activation volumes obtained under these conditions are in contrast to large values reported for bovine pancreatic trypsin inhibitor at more extreme conditions of 60 degreesC and pH* 8 where major unfolding events or structural rearrangements may dominate the mechanism [Wagner, G. (1983) Q. Rev. Biophys. 16, 1-57].
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Affiliation(s)
- T K Hitchens
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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47
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Fuentes EJ, Wand AJ. Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange. Biochemistry 1998; 37:3687-98. [PMID: 9521687 DOI: 10.1021/bi972579s] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cytochrome b562 is a heme-binding protein consisting of four helices folded into a classic helix bundle motif. Though retaining much of the topology of the holoprotein, apocytochrome b562 displays physical features commonly associated with so-called protein molten globules. Here, the stability and dynamics of this "structured" molten globule are probed by examination of the dependence of its hydrogen exchange behavior upon the presence of a chemical denaturant. Compared to other systems studied in this manner, apocytochrome b562 displays a limited dynamic range of hydrogen exchange rates and the analysis required the development of a quantitative approach. The protein is found to have three regions of subglobal cooperative stability. The most stable region, or core, is composed of the central two helices of the bundle, with the N- and C-terminal helices being of independent and lower stability. The dependence of the global unfolding free energy upon denaturant concentration indicates the applicability of a binding model and explains the observed difference between global unfolding free energies obtained by the linear extrapolation method and those obtained by calorimetry and hydrogen exchange. These observations place a significant restraint upon the type of folding pathway that is operative for this protein and suggest that that the N- and C-terminal helices fold and unfold independently of the core of the molecule.
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Affiliation(s)
- E J Fuentes
- Department of Chemistry, State University of New York at Buffalo 14260-3000, USA
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48
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49
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Abstract
Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.
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Affiliation(s)
- J Clarke
- Centre for Protein Engineering, MRC Unit for Protein Function and Design, MRC Centre, Cambridge, UK.
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50
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Bahar I, Wallqvist A, Covell DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 1998; 37:1067-75. [PMID: 9454598 DOI: 10.1021/bi9720641] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the conformational fluctuations of proteins in their folded state. This so-called Gaussian network model (GNM) is applied here to the interpretation of experimental hydrogen exchange (HX) behavior of proteins in their native state or under weakly denaturing conditions. Calculations are performed for five proteins: bovine pancreatic trypsin inhibitor, cytochrome c, plastocyanin, staphylococcal nuclease, and ribonuclease H. The results are significant in two respects. First, a good agreement is reached between calculated fluctuations and experimental measurements of HX despite the simplicity of the model and within computational times 2 or 3 orders of magnitude faster than earlier, more complex simulations. Second, the success of a theory, based on the coupled conformational fluctuations of residues near the native state, to satisfactorily describe the native-state HX behavior indicates the significant contribution of local, but cooperative, fluctuations to protein conformational dynamics. The correlation between the HX data and the unfolding kinetics of individual residues further suggests that local conformational susceptibilities as revealed by the GNM approach may have implications relevant to the global dynamics of proteins.
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Affiliation(s)
- I Bahar
- Molecular Structure Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5677, USA
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