Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase

Suwipa Saen-Oon, Mahmoud Ghanem, Vern L. Schramm, Steven D Schwartz

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

It has been found that with mutation of two surface residues (Lys 22 - Glu and His 104 - Arg) in human purine nucleoside phosphorylase (hPNP), there is an enhancement of catalytic activity in the chemical step. This is true although the mutations are quite remote from the active site, and there are no significant changes in crystallographic structure between the wild-type and mutant active sites. We propose that dynamic coupling from the remote residues to the catalytic site may play a role in catalysis, and it is this alteration in dynamics that causes an increase in the chemical step rate. Computational results indicate that the mutant exhibits stronger coupling between promotion of vibrations and the reaction coordinate than that found in native hPNP. Power spectra comparing native and mutant proteins show a correlation between the vibrations of Immucillin-G (ImmG):O5′⋯ImmG: N4′ and H257:Nδ⋯ImmG:O5′ consistent with a coupling of these motions. These modes are linked to the protein promoting vibrations. Stronger coupling of motions to the reaction coordinate increases the probability of reaching the transition state and thus lowers the activation free energy. This motion has been shown to contribute to catalysis. Coincident with the approach to the transition state, the sum of the distances of ImmG:O4′⋯ImmG:O5′-H257:Nδ became smaller, stabilizing the oxacarbenium ion formed at the transition state. Combined results from crystallography, mutational analysis, chemical kinetics, and computational analysis are consistent with dynamic compression playing a significant role in forming the transition state. Stronger coupling of these pairs is observed in the catalytically enhanced mutant enzyme. That motion and catalysis are enhanced by mutations remote from the catalytic site implicates dynamic coupling through the protein architecture as a component of catalysis in hPNP.

Original languageEnglish (US)
Pages (from-to)4078-4088
Number of pages11
JournalBiophysical Journal
Volume94
Issue number10
DOIs
StatePublished - May 15 2008
Externally publishedYes

Fingerprint

Purine-Nucleoside Phosphorylase
Catalysis
Catalytic Domain
Vibration
Mutation
Crystallography
Mutant Proteins
Proteins
Ions
Enzymes
immucillin G

ASJC Scopus subject areas

  • Biophysics

Cite this

Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase. / Saen-Oon, Suwipa; Ghanem, Mahmoud; Schramm, Vern L.; Schwartz, Steven D.

In: Biophysical Journal, Vol. 94, No. 10, 15.05.2008, p. 4078-4088.

Research output: Contribution to journalArticle

Saen-Oon, Suwipa ; Ghanem, Mahmoud ; Schramm, Vern L. ; Schwartz, Steven D. / Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase. In: Biophysical Journal. 2008 ; Vol. 94, No. 10. pp. 4078-4088.
@article{8e017849c94a4757884588df44056cbd,
title = "Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase",
abstract = "It has been found that with mutation of two surface residues (Lys 22 - Glu and His 104 - Arg) in human purine nucleoside phosphorylase (hPNP), there is an enhancement of catalytic activity in the chemical step. This is true although the mutations are quite remote from the active site, and there are no significant changes in crystallographic structure between the wild-type and mutant active sites. We propose that dynamic coupling from the remote residues to the catalytic site may play a role in catalysis, and it is this alteration in dynamics that causes an increase in the chemical step rate. Computational results indicate that the mutant exhibits stronger coupling between promotion of vibrations and the reaction coordinate than that found in native hPNP. Power spectra comparing native and mutant proteins show a correlation between the vibrations of Immucillin-G (ImmG):O5′⋯ImmG: N4′ and H257:Nδ⋯ImmG:O5′ consistent with a coupling of these motions. These modes are linked to the protein promoting vibrations. Stronger coupling of motions to the reaction coordinate increases the probability of reaching the transition state and thus lowers the activation free energy. This motion has been shown to contribute to catalysis. Coincident with the approach to the transition state, the sum of the distances of ImmG:O4′⋯ImmG:O5′-H257:Nδ became smaller, stabilizing the oxacarbenium ion formed at the transition state. Combined results from crystallography, mutational analysis, chemical kinetics, and computational analysis are consistent with dynamic compression playing a significant role in forming the transition state. Stronger coupling of these pairs is observed in the catalytically enhanced mutant enzyme. That motion and catalysis are enhanced by mutations remote from the catalytic site implicates dynamic coupling through the protein architecture as a component of catalysis in hPNP.",
author = "Suwipa Saen-Oon and Mahmoud Ghanem and Schramm, {Vern L.} and Schwartz, {Steven D}",
year = "2008",
month = "5",
day = "15",
doi = "10.1529/biophysj.107.121913",
language = "English (US)",
volume = "94",
pages = "4078--4088",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "10",

}

TY - JOUR

T1 - Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase

AU - Saen-Oon, Suwipa

AU - Ghanem, Mahmoud

AU - Schramm, Vern L.

AU - Schwartz, Steven D

PY - 2008/5/15

Y1 - 2008/5/15

N2 - It has been found that with mutation of two surface residues (Lys 22 - Glu and His 104 - Arg) in human purine nucleoside phosphorylase (hPNP), there is an enhancement of catalytic activity in the chemical step. This is true although the mutations are quite remote from the active site, and there are no significant changes in crystallographic structure between the wild-type and mutant active sites. We propose that dynamic coupling from the remote residues to the catalytic site may play a role in catalysis, and it is this alteration in dynamics that causes an increase in the chemical step rate. Computational results indicate that the mutant exhibits stronger coupling between promotion of vibrations and the reaction coordinate than that found in native hPNP. Power spectra comparing native and mutant proteins show a correlation between the vibrations of Immucillin-G (ImmG):O5′⋯ImmG: N4′ and H257:Nδ⋯ImmG:O5′ consistent with a coupling of these motions. These modes are linked to the protein promoting vibrations. Stronger coupling of motions to the reaction coordinate increases the probability of reaching the transition state and thus lowers the activation free energy. This motion has been shown to contribute to catalysis. Coincident with the approach to the transition state, the sum of the distances of ImmG:O4′⋯ImmG:O5′-H257:Nδ became smaller, stabilizing the oxacarbenium ion formed at the transition state. Combined results from crystallography, mutational analysis, chemical kinetics, and computational analysis are consistent with dynamic compression playing a significant role in forming the transition state. Stronger coupling of these pairs is observed in the catalytically enhanced mutant enzyme. That motion and catalysis are enhanced by mutations remote from the catalytic site implicates dynamic coupling through the protein architecture as a component of catalysis in hPNP.

AB - It has been found that with mutation of two surface residues (Lys 22 - Glu and His 104 - Arg) in human purine nucleoside phosphorylase (hPNP), there is an enhancement of catalytic activity in the chemical step. This is true although the mutations are quite remote from the active site, and there are no significant changes in crystallographic structure between the wild-type and mutant active sites. We propose that dynamic coupling from the remote residues to the catalytic site may play a role in catalysis, and it is this alteration in dynamics that causes an increase in the chemical step rate. Computational results indicate that the mutant exhibits stronger coupling between promotion of vibrations and the reaction coordinate than that found in native hPNP. Power spectra comparing native and mutant proteins show a correlation between the vibrations of Immucillin-G (ImmG):O5′⋯ImmG: N4′ and H257:Nδ⋯ImmG:O5′ consistent with a coupling of these motions. These modes are linked to the protein promoting vibrations. Stronger coupling of motions to the reaction coordinate increases the probability of reaching the transition state and thus lowers the activation free energy. This motion has been shown to contribute to catalysis. Coincident with the approach to the transition state, the sum of the distances of ImmG:O4′⋯ImmG:O5′-H257:Nδ became smaller, stabilizing the oxacarbenium ion formed at the transition state. Combined results from crystallography, mutational analysis, chemical kinetics, and computational analysis are consistent with dynamic compression playing a significant role in forming the transition state. Stronger coupling of these pairs is observed in the catalytically enhanced mutant enzyme. That motion and catalysis are enhanced by mutations remote from the catalytic site implicates dynamic coupling through the protein architecture as a component of catalysis in hPNP.

UR - http://www.scopus.com/inward/record.url?scp=43849102169&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=43849102169&partnerID=8YFLogxK

U2 - 10.1529/biophysj.107.121913

DO - 10.1529/biophysj.107.121913

M3 - Article

C2 - 18234834

AN - SCOPUS:43849102169

VL - 94

SP - 4078

EP - 4088

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 10

ER -