Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease

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• 作者：Theresa Tiefenbrunn ; Stefano Forli ; Michael M. Baksh ; Max W. Chang ; Meaghan Happer ; Ying-Chuan Lin ; Alexander L. Perryman ; Jin-Kyu Rhee ; Bruce E. Torbett ; Arthur J. Olson ; John H. Elder ; M. G. Finn ; C. David Stout
• 刊名：ACS Chemical Biology
• 出版年：2013
• 出版时间：June 21, 2013
• 年：2013
• 卷：8
• 期：6
• 页码：1223-1231
• 全文大小：506K
• 年卷期：v.8,no.6(June 21, 2013)
• ISSN：1554-8937

文摘

The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the T_m of apo-PR by 3.5鈥? 掳C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.