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
1B2M 1998-11-27T00:00:00+0000 2.0 THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
1BIR 1996-01-04T00:00:00+0000 1.8 RIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP
1BU4 1998-09-11T00:00:00+0000 1.9 RIBONUCLEASE 1 COMPLEX WITH 2'GMP
1BVI 1998-09-15T00:00:00+0000 1.9 RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP
1CH0 1999-03-30T00:00:00+0000 2.3 RNASE T1 VARIANT WITH ALTERED GUANINE BINDING SEGMENT
1DET 1996-02-20T00:00:00+0000 1.8 RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP
1FYS 2000-10-03T00:00:00+0000 2.0 Ribonuclease T1 V16C mutant
1FZU 2000-10-04T00:00:00+0000 1.8 RNAse T1 V78A mutant
1G02 2000-10-05T00:00:00+0000 1.86 Ribonuclease T1 V16S mutant
1GSP 1997-11-28T00:00:00+0000 2.2 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS, 1 DAY

Relevant UniProtKB Entries

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