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
1BVI 1998-09-15T00:00:00+0000 1.9 RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP
8RNT 1991-09-23T00:00:00+0000 1.8 STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH ZINC(II) AT 1.8 ANGSTROMS RESOLUTION: A ZN2+.6H2O.CARBOXYLATE CLATHRATE
4HOH 1998-09-14T00:00:00+0000 2.05 RIBONUCLEASE T1 (THR93ALA MUTANT) COMPLEXED WITH 2'GMP
3GSP 1997-12-02T00:00:00+0000 1.9 RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 4 DAYS
1I0V 2001-01-30T00:00:00+0000 1.23 Ribonuclease T1 in complex with 2'GMP (form I crystal)
3BU4 1998-09-14T00:00:00+0000 1.77 RIBONUCLEASE T1 COMPLEX WITH 2'GMP
5GSP 1997-12-09T00:00:00+0000 1.8 RIBONUCLEASE T1/3'-GMP, 9 WEEKS
4BIR 1998-01-13T00:00:00+0000 1.7 RIBONUCLEASE T1: FREE HIS92GLN MUTANT
1I0X 2001-01-30T00:00:00+0000 1.65 RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL)
5RNT 1991-03-28T00:00:00+0000 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