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Article

Solution NMR and Computer Simulation Studies of Active Site Loop Motion in Triosephosphate Isomerase^†

Francesca Massi, Chunyu Wang,^‡ and Arthur G. Palmer, III*

Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032

Biochemistry, 2006, 45 (36), pp 10787–10794

DOI: 10.1021/bi060764c

Publication Date (Web): August 18, 2006

†

This work was supported by National Institutes of Health grant GM59273 (A.G.P). A.G.P. is a member of the New York Structural Biology Center supported by NIH Grant GM66354.

‡

Current address: Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180-3590.

Corresponding author. Tel: (212) 305-8675. Fax: (212) 305-6949. E-mail: agp6@columbia.edu.

Abstract

Solution NMR spin relaxation experiments and classical MD simulations are used to study the dynamics of triosephosphate isomerase (TIM) in complex with glycerol 3-phosphate (G3P). Three regions in TIM exhibit conformational transitions on the μs−ms time scale as detected by chemical exchange broadening effects in NMR spectroscopy: residue Lys 84 on helix C, located at the dimeric interface; active site loop 6; and helix G. The results indicate that the conformational exchange process affecting the residues of loop 6 is the correlated opening and closing of the loop. Distinct processes are responsible for the chemical exchange linebroadening observed in the other regions of TIM. MD simulations confirm that motions of individual residues within the active site loop are correlated and suggest that the chemical exchange processes observed for residues in helix G arise from transitions between 3₁₀- and α-helical structures. The results of the joint NMR and MD study provide global insight into the role of conformational dynamic processes in the function of TIM.

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