Energetics of ribonuclease T1 structure.


Abstract

The energetics of thermal denaturation of two isoforms of ribonuclease T1 (Gln25 and Lys25) in various solvents have been studied by differential scanning calorimetry. It has been shown that the thermal transition of both forms of RNase T1 is strongly affected by slow kinetics, which cause an apparent deviation of the transition from a simple two-state model. By decreasing the heating rate or increasing the transition temperature, the denaturation of RNase approaches an equilibrium two-state transition. This permits determination of the thermodynamic parameters characterizing unfolding of the native structure. These thermodynamic parameters were correlated with the structural features of protein. Analysis of different contributions to the stability of RNase T1 shows that van der Waals interactions and hydrogen bonding are the major contributors to the conformational stability of the protein. Study holds ProTherm entries: 2875, 2876, 2877, 2878, 2879, 2880, 2881, 2882, 2883, 2884, 2885, 2886 Extra Details: Ribonuclease T1; conformational stability; hydrogen bonding;,energetics; thermodynamic parameters

Submission Details

ID: MzBMLcYT

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:20 p.m.

Version: 1

Publication Details
Yu Y;Makhatadze GI;Pace CN;Privalov PL,Biochemistry (1994) Energetics of ribonuclease T1 structure. PMID:8136367
Additional Information

Study Summary

Number of data points 54
Proteins Guanyl-specific ribonuclease T1 ; Guanyl-specific ribonuclease T1 ; Guanyl-specific ribonuclease T1
Unique complexes 2
Assays/Quantities/Protocols Experimental Assay: dTm pH:9.7 ; Experimental Assay: dHcal pH:9.7, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: Tm pH:9.7, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dHvH pH:9.7, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dCp pH:9.7, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dTm pH:8.6 ; Experimental Assay: dHcal pH:8.6, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: Tm pH:8.6, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dHvH pH:8.6, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dCp pH:8.6, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dTm pH:7.0 ; Experimental Assay: dHcal buffers:Sodium borate-NaOH: 10 mM, pH:7.0 ; Experimental Assay: Tm buffers:Sodium borate-NaOH: 10 mM, pH:7.0 ; Experimental Assay: dHvH buffers:Sodium borate-NaOH: 10 mM, pH:7.0 ; Experimental Assay: dCp buffers:Sodium borate-NaOH: 10 mM, pH:7.0 ; Experimental Assay: dTm pH:6.5 ; Experimental Assay: dHcal buffers:Sodium borate-NaOH: 10 mM, pH:6.5 ; Experimental Assay: Tm buffers:Sodium borate-NaOH: 10 mM, pH:6.5 ; Experimental Assay: dHvH buffers:Sodium borate-NaOH: 10 mM, pH:6.5 ; Experimental Assay: dCp buffers:Sodium borate-NaOH: 10 mM, pH:6.5 ; Experimental Assay: dTm pH:6.0 ; Experimental Assay: dHcal pH:6.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: Tm pH:6.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dHvH pH:6.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dCp pH:6.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dTm pH:5.0 ; Experimental Assay: dHcal pH:5.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: Tm pH:5.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dHvH pH:5.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dCp pH:5.0, buffers:Sodium borate-NaOH: 10 mM ; Experimental Assay: dCp buffers:glycine-NaOH: 10 mM, pH:9.7 ; Experimental Assay: dHcal buffers:glycine-NaOH: 10 mM, pH:9.7 ; Experimental Assay: Tm buffers:glycine-NaOH: 10 mM, pH:9.7 ; Experimental Assay: dHvH buffers:glycine-NaOH: 10 mM, pH:9.7 ; Experimental Assay: dCp pH:8.6, buffers:Sodium borate-HCl: 10 mM ; Experimental Assay: dHcal pH:8.6, buffers:Sodium borate-HCl: 10 mM ; Experimental Assay: Tm pH:8.6, buffers:Sodium borate-HCl: 10 mM ; Experimental Assay: dHvH pH:8.6, buffers:Sodium borate-HCl: 10 mM ; Experimental Assay: dCp buffers:Sodium cacodylate-HCl: 10 mM, pH:7.0 ; Experimental Assay: dHcal buffers:Sodium cacodylate-HCl: 10 mM, pH:7.0 ; Experimental Assay: Tm buffers:Sodium cacodylate-HCl: 10 mM, pH:7.0 ; Experimental Assay: dHvH buffers:Sodium cacodylate-HCl: 10 mM, pH:7.0 ; Experimental Assay: dCp buffers:Sodium cacodylate-HCl: 10 mM, pH:6.5 ; Experimental Assay: dHcal buffers:Sodium cacodylate-HCl: 10 mM, pH:6.5 ; Experimental Assay: Tm buffers:Sodium cacodylate-HCl: 10 mM, pH:6.5 ; Experimental Assay: dHvH buffers:Sodium cacodylate-HCl: 10 mM, pH:6.5 ; Experimental Assay: dCp pH:6.0, buffers:Sodium cacodylate-HCl: 10 mM ; Experimental Assay: dHcal pH:6.0, buffers:Sodium cacodylate-HCl: 10 mM ; Experimental Assay: Tm pH:6.0, buffers:Sodium cacodylate-HCl: 10 mM ; Experimental Assay: dHvH pH:6.0, buffers:Sodium cacodylate-HCl: 10 mM ; Experimental Assay: dCp buffers:Sodium acetate: 10 mM, pH:5.0 ; Experimental Assay: dHcal buffers:Sodium acetate: 10 mM, pH:5.0 ; Experimental Assay: Tm buffers:Sodium acetate: 10 mM, pH:5.0 ; Experimental Assay: dHvH buffers:Sodium acetate: 10 mM, pH:5.0
Libraries Mutations for sequence ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT

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
1YGW 1997-10-08 NMR STRUCTURE OF RIBONUCLEASE T1, 34 STRUCTURES
1IYY 2003-10-07 NMR STRUCTURE OF Gln25-RIBONUCLEASE T1, 24 STRUCTURES
1I0V 2001-02-14 1.23 Ribonuclease T1 in complex with 2'GMP (form I crystal)
4ODK 2015-01-14 1.4 Structure of SlyD from Thermus thermophilus in complex with T1 peptide
9RNT 1993-01-15 1.5 RIBONUCLEASE T1 WITH FREE RECOGNITION AND CATALYTIC SITE: CRYSTAL STRUCTURE ANALYSIS AT 1.5 ANGSTROMS RESOLUTION
1LOY 2002-08-21 1.55 X-ray structure of the H40A/E58A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate
1LOV 2002-08-21 1.55 X-ray structure of the E58A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate
4GSP 1998-08-12 1.65 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 7 DAYS
1I0X 2001-02-14 1.65 RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL)
4BIR 1998-07-15 1.7 RIBONUCLEASE T1: FREE HIS92GLN MUTANT
1HYF 2001-02-14 1.7 RIBONUCLEASE T1 V16A MUTANT IN COMPLEX WITH SR2+
1Q9E 2004-03-23 1.7 RNase T1 variant with adenine specificity
1RGA 1993-10-31 1.7 CRYSTAL STRUCTURE OF RNASE T1 WITH 3'-GMP AND GUANOSINE: A PRODUCT COMPLEX
1I3I 2001-03-07 1.76 Ribonuclease T1 V78T mutant
5BU4 1998-09-23 1.77 RIBONUCLEASE T1 COMPLEX WITH 2'GMP
3BU4 1998-09-23 1.77 RIBONUCLEASE T1 COMPLEX WITH 2'GMP
5GSP 1998-03-18 1.8 RIBONUCLEASE T1/3'-GMP, 9 WEEKS
4BU4 1998-09-23 1.8 RIBONUCLEASE T1 COMPLEX WITH 2'GMP
8RNT 1993-01-15 1.8 STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH ZINC(II) AT 1.8 ANGSTROMS RESOLUTION: A ZN2+.6H2O.CARBOXYLATE CLATHRATE
1FZU 2000-10-25 1.8 RNAse T1 V78A mutant
1RN4 1993-01-15 1.8 HIS92ALA MUTATION IN RIBONUCLEASE T1 INDUCES SEGMENTAL FLEXIBILITY. AN X-RAY STUDY
3BIR 1997-12-31 1.8 DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 BY ASN AND GLN SUBSTITUTIONS
2GSP 1998-08-12 1.8 RIBONUCLEASE T1/2',3'-CGPS AND 3'-GMP, 2 DAYS
2AAE 1994-01-31 1.8 THE ROLE OF HISTIDINE-40 IN RIBONUCLEASE T1 CATALYSIS: THREE-DIMENSIONAL STRUCTURES OF THE PARTIALLY ACTIVE HIS40LYS MUTANT
1I2E 2001-03-07 1.8 Ribonuclease T1 V16A mutant, form I
1HZ1 2001-01-31 1.8 RIBONUCLEASE T1 V16A MUTANT IN COMPLEX WITH MG2+
1BIR 1996-08-17 1.8 RIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP
3RNT 1989-10-15 1.8 CRYSTAL STRUCTURE OF GUANOSINE-FREE RIBONUCLEASE T1, COMPLEXED WITH VANADATE(V), SUGGESTS CONFORMATIONAL CHANGE UPON SUBSTRATE BINDING
1DET 1996-07-11 1.8 RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP
6RNT 1993-01-15 1.8 CRYSTAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH ADENOSINE 2'-MONOPHOSPHATE AT 1.8-ANGSTROMS RESOLUTION
2RNT 1989-10-15 1.8 THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION
1RN1 1994-01-31 1.84 THREE-DIMENSIONAL STRUCTURE OF GLN 25-RIBONUCLEASE T1 AT 1.84 ANGSTROMS RESOLUTION: STRUCTURAL VARIATIONS AT THE BASE RECOGNITION AND CATALYTIC SITES
1I2G 2001-03-07 1.85 Ribonuclease T1 V16T mutant
1G02 2000-10-25 1.86 Ribonuclease T1 V16S mutant
1RGK 1993-01-15 1.87 RNASE T1 MUTANT GLU46GLN BINDS THE INHIBITORS 2'GMP AND 2'AMP AT THE 3' SUBSITE
3GSP 1998-08-12 1.9 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 4 DAYS
1LRA 1994-01-31 1.9 CRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSINE MONOPHOSPHATE AT 1.9 ANGSTROMS RESOLUTION
1LOW 2002-08-21 1.9 X-ray structure of the H40A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate
2HOH 1998-09-23 1.9 RIBONUCLEASE T1 (N9A MUTANT) COMPLEXED WITH 2'GMP
1BU4 1999-02-16 1.9 RIBONUCLEASE 1 COMPLEX WITH 2'GMP
1RNT 1987-10-16 1.9 RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC ACID COMPLEX AT 1.9 ANGSTROMS RESOLUTION
7RNT 1993-01-15 1.9 CRYSTAL STRUCTURE OF THE TYR45TRP MUTANT OF RIBONUCLEASE T1 IN A COMPLEX WITH 2'-ADENYLIC ACID
1RLS 1994-12-20 1.9 CRYSTAL STRUCTURE OF RNASE T1 COMPLEXED WITH THE PRODUCT NUCLEOTIDE 3'-GMP. STRUCTURAL EVIDENCE FOR DIRECT INTERACTION OF HISTIDINE 40 AND GLUTAMIC ACID 58 WITH THE 2'-HYDROXYL GROUP OF RIBOSE
1BVI 1998-09-23 1.9 RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP
2BU4 1998-09-23 1.95 RIBONUCLEASE T1 COMPLEX WITH 2'GMP
3SYU 2012-03-28 1.95 Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP
1I2F 2001-03-07 1.95 Ribonuclease T1 V16A mutant, form II
3HOH 1998-09-16 1.95 RIBONUCLEASE T1 (THR93GLN MUTANT) COMPLEXED WITH 2'GMP
1RHL 1998-10-14 1.95 RIBONUCLEASE T1 COMPLEXED WITH 2'GMP/G23A MUTANT
1B2M 1999-03-25 2.0 THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
5HOH 1998-09-23 2.0 RIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMP
7GSP 1998-03-18 2.0 RIBONUCLEASE T1/2',3'-CGPS, NON-PRODUCTIVE
1FYS 2000-10-25 2.0 Ribonuclease T1 V16C mutant
1RGL 1993-01-15 2.0 RNASE T1 MUTANT GLU46GLN BINDS THE INHIBITORS 2'GMP AND 2'AMP AT THE 3' SUBSITE
5BIR 1997-12-31 2.0 DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 USING ASN AND GLN MUTATIONS
2AAD 1994-01-31 2.0 THE ROLE OF HISTIDINE-40 IN RIBONUCLEASE T1 CATALYSIS: THREE-DIMENSIONAL STRUCTURES OF THE PARTIALLY ACTIVE HIS40LYS MUTANT
1RGC 1994-01-31 2.0 THE COMPLEX BETWEEN RIBONUCLEASE T1 AND 3'-GUANYLIC ACID SUGGESTS GEOMETRY OF ENZYMATIC REACTION PATH. AN X-RAY STUDY
4HOH 1998-09-23 2.05 RIBONUCLEASE T1 (THR93ALA MUTANT) COMPLEXED WITH 2'GMP
1TTO 2005-09-06 2.1 Crystal structure of the Rnase T1 variant R2
6GSP 1998-03-18 2.2 RIBONUCLEASE T1/3'-GMP, 15 WEEKS
1GSP 1998-02-25 2.2 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS, 1 DAY
4RNT 1992-01-15 2.2 HIS 92 ALA MUTATION IN RIBONUCLEASE T1 INDUCES SEGMENTAL FLEXIBILITY. AN X-RAY STUDY
1TRQ 1994-04-30 2.3 X-RAY CRYSTALLOGRAPHIC AND CALORIMERIC STUDIES OF THE EFFECTS OF THE MUTATION TRP 59 TYR IN RIBONUCLEASE T1
2BIR 1997-06-16 2.3 ADDITIVITY OF SUBSTRATE BINDING IN RIBONUCLEASE T1 (Y42A MUTANT)
1CH0 1999-12-22 2.3 RNASE T1 VARIANT WITH ALTERED GUANINE BINDING SEGMENT
1I3F 2001-03-07 2.35 Ribonuclease T1 V89S mutant
1TRP 1994-04-30 2.4 X-RAY CRYSTALLOGRAPHIC AND CALORIMERIC STUDIES OF THE EFFECTS OF THE MUTATION TRP 59 TYR IN RIBONUCLEASE T1
3URP 2012-03-28 3.19 Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound
5RNT 1993-01-15 3.2 X-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RIBONUCLEASE T1 AND GUANOSINE-3',5'-BISPHOSPHATE

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Guanyl-specific ribonuclease T1 P00651 RNT1_ASPOR