Physical Sciences and Mathematics Commons^™

Prediction And Confirmation Of A Switch-Like Region Within The N-Terminal Domain Of Hsirt1, Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig, Ningkun Wang

Faculty Research, Scholarly, and Creative Activity

Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch- like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

University Scholar Series: Marc D'Alarcao, Marc D'Alarcao

University Scholar Series

Synthetic Organic Chemistry to Shed Light on Type II Diabetes and Cancer

On March 16, 2011 Marc d'Alarcao spoke in the University Scholar Series hosted by Provost Gerry Selter at the Dr. Martin Luther King, Jr. Library. Marc d'Alarcao is a Professor in the Chemistry Department at SJSU. In this seminar, he gives a progress report on his work aimed at developing and synthesizing new compounds that are designed to take advantage of this metabolic difference. His hope is that these compounds will be selectively toxic to cancer cells and may provide a new strategy for treating this major threat …

Chemistry–Climate Model Simulations Of Twenty-First Century Stratospheric Climate And Circulation Changes, Neal Butchart, I. Cionni, V. Eyring, T. G. Shepherd, D. W. Waugh, H. Akiyoshi, J. Austin, C. Brühl, M. P. Chipperfield, Eugene C. Cordero, M. Dameris, R. Deckert, S. Dhomse, S. M. Frith, R. R. Garcia, A. Gettelman, M. A. Giorgetta, D. E. Kinnison, F. Li, E. Mancini, S. Pawson, G. Pitari, D. A. Plummer, E. Rozanov, F. Sassi, J. F. Scinocca, K. Shibata, B. Steil, W. Tian

Faculty Publications, Meteorology and Climate Science

The response of stratospheric climate and circulation to increasing amounts of greenhouse gases (GHGs) and ozone recovery in the twenty-first century is analyzed in simulations of 11 chemistry–climate models using near-identical forcings and experimental setup. In addition to an overall global cooling of the stratosphere in the simulations (0.59 ± 0.07 K decade⁻¹ at 10 hPa), ozone recovery causes a warming of the Southern Hemisphere polar lower stratosphere in summer with enhanced cooling above. The rate of warming correlates with the rate of ozone recovery projected by the models and, on average, changes from 0.8 to 0.48 K decade …

Chemistry–Climate Model Simulations Of Twenty-First Century Stratospheric Climate And Circulation Changes, Neal Butchart, I. Cionni, V. Eyring, T. G. Shepherd, D. W. Waugh, H. Akiyoshi, J. Austin, C. Brühl, M. P. Chipperfield, Eugene C. Cordero, M. Dameris, R. Deckert, S. Dhomse, S. M. Frith, R. R. Garcia, A. Gettelman, M. A. Giorgetta, D. E. Kinnison, F. Li, E. Mancini, S. Pawson, G. Pitari, D. A. Plummer, E. Rozanov, F. Sassi, J. F. Scinocca, K. Shibata, B. Steil, W. Tian

Eugene C. Cordero

The response of stratospheric climate and circulation to increasing amounts of greenhouse gases (GHGs) and ozone recovery in the twenty-first century is analyzed in simulations of 11 chemistry–climate models using near-identical forcings and experimental setup. In addition to an overall global cooling of the stratosphere in the simulations (0.59 ± 0.07 K decade⁻¹ at 10 hPa), ozone recovery causes a warming of the Southern Hemisphere polar lower stratosphere in summer with enhanced cooling above. The rate of warming correlates with the rate of ozone recovery projected by the models and, on average, changes from 0.8 to 0.48 K decade …