News & Highlights

Regeneron Science Talent Search

Annie Chang, a high school student from the Simmerling lab, was selected as one of the top 300 scholars in the prestigious national Regeneron Science Talent Search. Annie's project involved understanding the different effect that strong and weak inhibitors have on the dynamics of HIV protease's flaps. For her achievement, she was awarded $2000, a one-year subscription to Science News, and a certificate. Congratulations Annie

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New publication alert

"Congratulations to Haoquan for his first-author JACS article! Even though he has gone on to other things since being in our group, he did a really impressive job at continuing to move this project forward and finish another really strong paper." - Prof. Simmerling

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"Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base eversion pathway. TheMD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site, but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions." - excerpt from the Abstract.

Check out the paper below

DNA deformation-coupled recognition of 8-oxoguanine: conformational kinetic gating in human DNA glycosylase.
Li, Haoquan; Endutkin, Anton; Bergonzo, Christina; Lin, Fu; Grollman, Arthur P.; Zharkov, Dmitry O.; Simmerling, Carlos, Journal of the American Chemical Society, 2016 accepted

A new doctor in the house

Dr. Kevin Hauser defended his thesis with an exciting talk that shed light on how a transcription factor, MTERF, search and recognize a specific sequence on DNA. His research focused on developing a model of protein-DNA search and recognition which described a sliding mechanism of MTERF on DNA.

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There is always time to celebrate after a great defense talk!

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Siemens Science competition semi-finalists

The Siemens Science Competition semi-finalists list is out [1] and Annie Chang is on it. Annie is a high school student that participated in the Siemens Science Research Program at SBU, this summer. She performed research in the Simmerling lab on understanding the effect of various drugs on HIV-1 PR flap dynamics. Congratulations on making it to the semi-finals.

New publication

Junjie Zou, a graduate student in the Simmerling and Raleigh lab, published his first paper in the lab. Outstanding job Junjie, congratulations!


Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects
Zou, Junjie; Song, Benben; Simmerling, Carlos; Raleigh, Daniel, Journal of the American Chemical Society, 2016 accepted

Congratulations Kevin Hauser!

Kevin Hauser started a post-doctoral position at Schrödinger. All the best Kevin, we know you will shine in your new position.

Congratulations Professor Simmerling!

Professor Carlos Simmerling was selected to the 2016 class of ACS fellows, an elite group of 57 distinguished scientists who have made outstanding achievements in chemistry and contributed to the profession, science and ACS organization. Professor Simmerling was recognized at a ceremony on August 22, during the 252nd National ACS Meeting and Exposition in Philadelphia.

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Check out Professor Simmerling and the other 57 members of the 2016 class of ACS fellows:

Congratulations to Gabriela and Victoria!

Victoria and Gabriela (Undergraduates in the Simmerling lab) got accepted to the PhD program at University of Florida and University of Pennsylvania respectively. All the best ladies on your future endeavors.

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Recently Published Manuscripts

Base flipping by MTERF1 can accommodate multiple conformations and occurs in a stepwise fashion
Byrnes, J.; Hauser, K.; Mejia, E.,; Norona, L.; Simmerling, C.; Garcia-Diaz, M.,J. Mol. Biol., 2016, 428 (12), 2542–2556

Advances in free-energy-based simulations of protein folding and ligand binding
Perez, A., Morrone, J. A., Simmerling, C., Dill, A.,Current opinion in structural biology 2016, 36, 25–31

A Dynamic Checkpoint in Oxidative Lesion Discrimination by Formamidopyrimidine–DNA Glycosylase
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los Santos, C., Zharkov, D., Simmerling, C.,Nucleic Acids Research, 44 (2), 683–694

A human transcription factor in search mode
Hauser, K.; Essuman, B.; He, Y.; Coutsias, E.; Garcia-Diaz, M.; Simmerling, C., Nucleic Acids Research, 44 (1), 63–74

A grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations
Perez, A., MacCallum, JL., Brini, E., Simmerling, C., Dill, KA, J. Chem. Theor. Comput., 2015, 11 (10), 4770–4779
DOI: 10.1021/acs.jctc.5b00662