News


Congrats to Guangfeng on a successful PhD defense!

posted Nov 3, 2017, 5:37 PM by Vincent Voelz

Dr. Guangfeng Zhou has successfully defended his thesis work, earning himself a Ph.D. in Chemistry.  After submitting his dissertation "Statistical models and their applications in studying biomolecular conformational dynamics", Guangfeng is off to postdoctoral work with Frank DiMaio at the Institute for Protein Design at the University of Washington in Seattle.  Congrats Guangfeng!




Happy Halloween from the Voelz Lab

posted Nov 3, 2017, 5:22 PM by Vincent Voelz

With our second annual Halloween-themed group meeting behind us, it appears we have started a new spook-tacular tradition.   Happy Halloween 2017 from the Voelz group!

New paper on peptoid-porphyrin conjugates

posted Oct 31, 2017, 3:36 PM by Vincent Voelz

Our collaborative work with the Jiwon Seo group has just been published!  The new manuscript, "Control of porphyrin interactions via structural change of peptoid scaffold", describes a helical peptoid scaffold that can be functionalized by conjugating porphyrin groups at specific positions.  Using a combination of experiment and molecular modeling, we show that a more rigid peptoid-porphyrin linker results in improved conformational properties.   These studies move a step closer to designing foldameric molecules that can mimic the light-harvesting photosynthetic complexes found in nature. 

Woojin Yang, Boyeong Kang, Vincent A. Voelz, Jiwon Seo, Org. Biomol. Chem. (2017) doi:10.1039/C7OB02398G

Sara wins Honorable Mention at the URP Research Symposium

posted Oct 10, 2017, 9:19 AM by Vincent Voelz

Congratulations to Sara Dornblaser, whose poster won Honorable Mention at Undergraduate Research Program (URP) Fall Research Symposium.  Her presentation, entitled "Molecular simulations reveal the importance of disulfide bridging in PrgW, a putative redox switch for plasmid replication", is a collaboration between the Voelz Lab and Bettina Buttaro's group in the Department of Microbiology and Immunology at Temple School of Medicine.


 

New BiophysJ paper on p53-MDM2 binding

posted Aug 22, 2017, 9:21 AM by Vincent Voelz   [ updated Aug 22, 2017, 9:24 AM ]

Congrats to Guangfeng Zhou on his first-author paper just published in Biophysical Journal!  This work is currently featured on the front webpage of the Aug. 22 issue.

In this work, we analyzed over 800 µs of explicit-solvent  ab initio binding simulations of the p53 TAD peptide to MDM2, to obtain a detailed picture of the binding mechanism.  Kinetic network models built from the trajectory data reveal a binding-then-folding mechanism, which we further connect to macroscopic binding flux models, enabling physiological insight into the binding of intrinsically disordered peptides (IDPs) like p53 TAD.

New JCIM paper on Designed Beta-Cap Hairpins

posted Aug 18, 2017, 7:24 PM by Vincent Voelz   [ updated Aug 18, 2017, 7:25 PM ]

Congratulations to Yunhui on his first-author paper!  In this work, a collaboration with the Andersen lab at UW, we compare simulation predictions against experimental NMR and CD data for a series of designed beta-hairpins stabilized by a Trp-Trp capping motifs.  You can read the full paper here



Eigenspikers rally, beating A-team

posted Aug 14, 2017, 8:18 AM by Vincent Voelz

The Eigenspikers (Voelz/Matsika lab), continued their unprecedented winning streak, rallying to defeat the A-team (Andrade Lab16-18, 6-15, 8-15.  The Eigenspikers now advance in the playoffs, facing off against the Killa Grahams (Dobereiner Lab) later this week. Go Eigenspikers!

Eigenspikers normalize the Plasmonsters

posted Jul 27, 2017, 4:04 PM by Vincent Voelz   [ updated Jul 28, 2017, 10:25 AM ]

In breaking sports news, the Eigenspikers (Voelz/Matsika labs) defeated the Plasmonsters (Willets lab), handing the unbeaten team their first loss of the season. Congratulations on a fantastic win!

  • Game 1: 15-6 Plasmonsters
  • Game 2: 14-16 Eigenspikers
  • Game 3: 7-15 Eigenspikers

The Eigenspikers are now 5-5 for the season.  For now, there is little time to bask in the glow this incredible upset, as a rematch in the final tournament almost certainly awaits these two teams. To the playoffs!



A new XSEDE award for supercomputing resources

posted Mar 15, 2017, 8:24 AM by Vincent Voelz

Good news: our renewal request for the XSEDE supercomputing allocation was renewed March 2017!  The allocation, comprising over 6.2 million processor-hours on TACC Stampede, PSC Bridges and SDSC Comet supports our continuing work on "Molecular simulation and kinetic network modeling of protein folding mechanisms", funded through the NSF (MCB140270), and new work on simulating protein binding pathways and kinetics.   The estimated value of the allocation is over $222K, and represents a significant investment by the NSF in advances computing infrastructure for the U.S.

New JCTC paper on MaxCal modeling of protein mutations

posted Nov 28, 2016, 3:31 PM by Vincent Voelz   [ updated Nov 28, 2016, 4:10 PM ]

Congrats to Hongbin Wan and Guangfeng Zhou on their new paper published in the Journal of Chemical Theory and Computation!  

This new work describes a new statistical mechanical technique to compute changes in folding kinetics directly from changes in equilibrium state populations.  Our current approach to modeling folding kinetics for different protein sequences is to perform large-scale simulations, from which we construct transition network models of folding called Markov State Models.  In the future, this new method could be used to infer how mutations and other perturbations affect folding, and avoid the expense of having to do so many simulations for each sequence.


Wan, H., Zhou, G., & Voelz, V. A. (2016). A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations. Journal of Chemical Theory and Computation, Article ASAP. http://doi.org/10.1021/acs.jctc.6b00938

 


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