Thermodynamics of denaturant-induced unfolding of a protein that exhibits variable two-state denaturation.


Abstract

Free energy changes (DeltaG(degrees)(N-->D)) obtained by denaturant-induced unfolding using the linear extrapolation method (LEM) are presumed to reflect the stability differences between native (N) and denatured (D) species in the absence of denaturant. It has been shown that with urea and guanidine hydrochloride (GdnHCl) some proteins exhibit denaturant-independent (DeltaG(degrees)(N-->D)). But with several other proteins urea and GdnHCl give different (DeltaG(degrees)(N-->D)) values for the same protein, meaning that the free energy difference between N and D is not the only contribution to one or both (DeltaG(degrees)(N-->D)) values. Using beta1, a mutant form of the protein G B1 domain, we show that both urea- and GdnHCl-induced denaturations are two-state and reversible but that the denaturants give different values for (DeltaG(degrees)(N-->D)). While spectral observables are sensitive to the shift between N and D states (between states effect), they are not sensitive to denaturant-induced changes that occur within the individual N and D states (within state effect). By contrast, nonspectral observables such as Stokes radius and thermodynamic observables such as proton uptake/release are often sensitive to both "between states" and "within state" effects. These observables, along with spectral measurements, provide descriptions of urea- and GdnHCl-induced denaturation of beta1. Our results suggest that in the predenaturation concentration range GdnHCl changes the free energy of the native ensemble in a nonlinear manner but that urea does not. As with RNase A and beta-lactoglobulin, beta1 exhibits variable two-state behavior with GdnHCl-induced denaturation in that the free energy of the native ensemble in the predenaturation zone changes (varies) with GdnHCl concentration in a nonlinear manner. Study holds ProTherm entries: 18232, 18233, 18234, 18235, 18236, 18237, 18238 Extra Details: Fluorescen T 2 Q, I 6 A, T 44 Ace lambda(ex) = 275 nm and lambda(em) = 340 nm free energy change; Stokes radius; non-linear

Submission Details

ID: EZNwsw6e

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:50 p.m.

Version: 1

Publication Details
Ferreon AC;Bolen DW,Biochemistry (2004) Thermodynamics of denaturant-induced unfolding of a protein that exhibits variable two-state denaturation. PMID:15491142
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1MPE 2002-10-30 Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G
5UCF 2017-08-23 Solution NMR-derived model of the minor species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1)
2K0P 2009-03-03 Determination of a Protein Structure in the Solid State from NMR Chemical Shifts
5UB0 2017-08-23 Solution NMR Structure of NERD-C, a natively folded tetramutant of the B1 domain of streptococcal protein G (GB1)
3GB1 1999-06-23 STRUCTURES OF B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
2KLK 2009-10-06 Solution structure of GB1 A34F mutant with RDC and SAXS
1GB1 1993-04-15 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G
2JSV 2008-04-15 Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy
5UCE 2017-08-23 Solution NMR structure of the major species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1)
1GB4 1998-07-22 HYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G, NMR, 47 STRUCTURES
2I2Y 2006-12-12 Solution structure of the RRM of SRp20 bound to the RNA CAUC
2KHU 2010-02-23 Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota
2KHW 2010-02-23 Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex
2RPV 2009-09-15 Solution Structure of GB1 with LBT probe
2NMQ 2006-11-21 Simultaneous determination of protein structure and dynamics using rdcs
2KWD 2010-06-02 Supramolecular Protein Structure Determination by Site-Specific Long-Range Intermolecular Solid State NMR Spectroscopy
1Q10 2003-10-14 Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G
2LUM 2012-08-29 Three-State Ensemble obtained from eNOEs of the Third Immunoglobulin Binding Domain of Protein G (GB3)
2KQ4 2009-11-17 Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy
5UBS 2017-08-23 Solution NMR Structure of NERD-S, a natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) with a solvent-exposed Trp43
2KN4 2010-08-18 The structure of the RRM domain of SC35
1FCL 2001-09-19 DELTA1.5: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
2GB1 1993-04-15 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G
1GJT 2001-08-09 Solution structure of the Albumin binding domain of Streptococcal Protein G
2IGG 1994-01-31 DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR
1LE3 2002-04-24 NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G
2RMM 2007-12-04 Solution structure of GB1 A34F mutant
2IGH 1994-01-31 DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR
1FD6 2001-09-19 DELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
2LGI 2011-10-26 Atomic Resolution Protein Structures using NMR Chemical Shift Tensors
2MBB 2014-06-04 Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex
2KBT 2009-02-03 Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method
2J52 2007-09-25 Solution Structure of GB1 domain Protein G and low and high pressure.
2N9K 2016-12-28 1H, 13C, and 15N Chemical Shift Assignments for in vitro GB1
6HKA 2019-03-27 The solution structure of the micelle-associated FATC domain of the human protein kinase ataxia telangiectasia mutated (ATM)
2N7J 2015-10-14 Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings
1ZXH 2005-11-08 G311 mutant protein
2N9L 2016-12-28 1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1
1PN5 2003-10-07 NMR structure of the NALP1 Pyrin domain (PYD)
1P7E 2003-08-05 GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings
1GJS 2001-08-09 Solution structure of the Albumin binding domain of Streptococcal Protein G
2J53 2007-09-25 Solution Structure of GB1 domain Protein G and low and high pressure.
2PLP 2007-05-08 Ultra high resolution backbone conformation of protein GB1 from residual dipolar couplings alone
2JU6 2007-12-04 Solid-State Protein Structure Determination with Proton-Detected Triple Resonance 3D Magic-Angle Spinning NMR Spectroscopy
1P7F 2003-08-05 GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings
3FIL 2009-08-18 0.88 Structural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution
2QMT 2007-12-25 1.05 Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction
6CHE 2019-07-10 1.1 Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction
2IGD 1998-07-29 1.1 ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION
1IGD 1994-11-01 1.1 THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB
6CPZ 2019-07-10 1.12 Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction
2GI9 2006-04-25 1.14 Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State NMR Spectroscopy
3MP9 2011-02-23 1.2 Structure of Streptococcal protein G B1 domain at pH 3.0
6C9O 2019-07-10 1.2 Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction
6CNE 2019-07-10 1.2 Selenomethionine mutant (L5Sem) of protein GB1 examined by X-ray diffraction
6CTE 2019-07-10 1.2 77Se-NMR probes the protein environment of selenomethionine
6NLA 2019-01-23 1.34 Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc
2ON8 2007-12-04 1.35 Gbeta1 stabilization by in vitro evolution and computational design
6NL7 2019-01-23 1.4 Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)
6NL6 2019-01-23 1.4 Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q)
6NL8 2019-01-23 1.5 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-zinc
5BMH 2016-04-06 1.6 Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form B
1PGX 1992-07-15 1.66 THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN
6NL9 2019-01-23 1.7 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo
2ONQ 2008-01-08 1.7 Gbeta1 stabilization by in vitro evolution and computational design
5HG2 2016-02-24 1.8 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35
4OZB 2014-07-16 1.8 Backbone Modifications in the Protein GB1 Helix: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35
1PGB 1994-04-30 1.92 TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR
1QKZ 2000-02-06 1.95 Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G
4KGS 2013-09-04 1.95 Backbone Modifications in the Protein GB1 Loops: beta-3-Val21, beta-3-Asp40
5HFY 2016-02-24 1.95 Backbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
4KGR 2013-09-04 2.0 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
3V3X 2012-08-29 2.0 Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant
4KGT 2013-09-04 2.0 Backbone Modifications in the Protein GB1 Turns: Aib10, D-Pro47
1EM7 2002-05-08 2.0 HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G
1PGA 1994-04-30 2.07 TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR
5HI1 2016-02-24 2.15 Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35
1UWX 2005-06-15 2.2 P1.2 serosubtype antigen derived from N. meningitidis PorA in complex with Fab fragment
5BMG 2016-04-06 2.2 Nitroxide Spin Labels in Protein GB1: E15 Mutant
4WH4 2015-08-05 2.2 Protein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H
4OZA 2014-07-16 2.2 Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36
6NLB 2019-01-23 2.3 Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo
4OZC 2014-07-16 2.3 Backbone Modifications in the Protein GB1 Helix and Loops: beta-ACPC21, beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35, beta-ACPC40
1MVK 2002-10-30 2.5 X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G
5BMI 2016-04-06 2.5 Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form A
1IGC 1995-06-03 2.6 IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS
3UI3 2012-02-08 2.8 Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity
1FCC 1995-04-20 3.2 CRYSTAL STRUCTURE OF THE C2 FRAGMENT OF STREPTOCOCCAL PROTEIN G IN COMPLEX WITH THE FC DOMAIN OF HUMAN IGG
5LDE 2017-10-04 3.38 Crystal structure of a vFLIP-IKKgamma stapled peptide dimer

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Immunoglobulin G-binding protein G P19909 SPG2_STRSG
100.0 Immunoglobulin G-binding protein G P06654 SPG1_STRSG