Catalytic mechanism of enzymes

Preorganization, short strong hydrogen bond, and charge buffering

Kwang S. Kim, Dongwook Kim, Jin Yong Lee, Tarakeshwar Pilarisetty, Kyung Seok Oh

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

During the past decade, there has been much debate about the enormous catalytic rate enhancement observed in enzymatic reactions involving carbanion intermediates. Our recent theoretical study has demonstrated the importance of the short strong hydrogen bond (SSHB) in the enzymatic reactions. Nevertheless, other recent theoretical studies espouse the role of preorganization over that of the SSHB. To achieve a consensus on this issue and to find the truth, a more clarified explanation must be given. To this end, we have carried out an elaborate analysis of these enzymatic reactions. We here clarify that the catalytic mechanism needs to be explained with three important factors, viz., SSHB, preorganization, and charge buffering/dissipation. Since the charge buffering role is different from the commonly used concepts of the SSHB and preorganization (unless these definitions are expanded), we stress that the charge buffering role of the catalytic residues is an important ingredient of the enzymatic reaction in reducing the level of accumulation of the negative charge on the substrate during the reaction process. This charge reduction is critical to the lowering of activation barriers and the stabilization of intermediates.

Original languageEnglish (US)
Pages (from-to)5300-5306
Number of pages7
JournalBiochemistry
Volume41
Issue number16
DOIs
StatePublished - Apr 23 2002
Externally publishedYes

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Hydrogen
Hydrogen bonds
Enzymes
Theoretical Models
Stabilization
Chemical activation
Substrates

ASJC Scopus subject areas

  • Biochemistry

Cite this

Catalytic mechanism of enzymes : Preorganization, short strong hydrogen bond, and charge buffering. / Kim, Kwang S.; Kim, Dongwook; Lee, Jin Yong; Pilarisetty, Tarakeshwar; Oh, Kyung Seok.

In: Biochemistry, Vol. 41, No. 16, 23.04.2002, p. 5300-5306.

Research output: Contribution to journalArticle

Kim, Kwang S. ; Kim, Dongwook ; Lee, Jin Yong ; Pilarisetty, Tarakeshwar ; Oh, Kyung Seok. / Catalytic mechanism of enzymes : Preorganization, short strong hydrogen bond, and charge buffering. In: Biochemistry. 2002 ; Vol. 41, No. 16. pp. 5300-5306.
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