Enzyme Dynamics During Catalysis

Abstract

Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked to substrate turnover remain largely unknown. We have studied dynamics of an enzyme during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action of the enzyme cyclophilin A, we detect conformational fluctuations of the active site that occur on a time scale of hundreds of microseconds. The rates of conformational dynamics of the enzyme strongly correlate with the microscopic rates of substrate turnover. The present results, together with available structural data, allow a prediction of the reaction trajectory.

Unfolding of CPR3 Gets Initiated at the Active Site and Proceeds via Two Intermediates

“…7, A and C). These regions correlate well with the earlier-reported regions for peptide interaction and catalysis in human CypA (9,16). In this study, the maximal intensity change was observed for N120, and even at low equivalents of the peptide, considerable CSP was measured.…”

“…Eisenmesser and co-workers proposed that the cis conformer of the peptide interacts with residues A101, N102, A103, K82, and R55 of the enzyme; afterward, the enzyme catalyzes rotation of the peptide-prolyl bond by 180 to produce the trans conformation and makes contacts around residues L98 and S99. During isomerization, the C-terminus of the peptide bond is free to rotate, whereas the N-terminus of the bond remains bound at the catalytic site of the enzyme (9). The authors also concluded that R55 is the key player in cis-trans isomerization, which is supported by mutational studies (9,10).…”

“…During isomerization, the C-terminus of the peptide bond is free to rotate, whereas the N-terminus of the bond remains bound at the catalytic site of the enzyme (9). The authors also concluded that R55 is the key player in cis-trans isomerization, which is supported by mutational studies (9,10). Zhao and co-workers proposed the involvement of the guanidino group of the sidechain of R55 in hydrogen bonding with the prolyl nitrogen of the substrate.…”

“…Several efforts to understand the cis-trans isomerization of the peptidyl-prolyl bond have been made using different approaches such as NMR line-shape analysis, monitoring changes in R 2 upon substrate binding, crystal structure studies with different peptides, molecular dynamics simulations, and density functional theory calculations (9)(10)(11)(12)(13). Eisenmesser and co-workers proposed that the cis conformer of the peptide interacts with residues A101, N102, A103, K82, and R55 of the enzyme; afterward, the enzyme catalyzes rotation of the peptide-prolyl bond by 180 to produce the trans conformation and makes contacts around residues L98 and S99.…”

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

“…Flexibilities and dynamics in protein conformation are essential for its function, playing key roles in molecular recognition, rate-limiting conformational transitions, and catalysis (Cole et al, 2002;Eisenmesser et al, 2002). The time scales of these protein conformational motions vary widely, from picoseconds to seconds, making solution NMR a suitable technique for analyzing such motions.…”