University of Illinois at Urbana-Champaign
Unveiling the functions of the HIV-1 and hepatitis B virus capsids through the computational microscope(balb)
Jun 2017 - May 2018
John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten (2017): GPU-Accelerated Molecular Dynamics Clustering Analysis with OpenACC, Elsevier, Parallel Programming with OpenACC, pp215--240
Juan R. Perilla, and Klaus Schulten (2017): Physical Properties of the HIV-1 Capsid from All-Atom Molecular Dynamics Simulations, Nature Communications, Springer Nature, Vol 8, pp15959
Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L. Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang (2017): CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp3853--3863
Frances J. D. Alvarez, Shaoda He, Juan R. Perilla, Sooin Jang, Klaus Schulten, Alan N. Engelman, Sjors H. W. Scheres, and Peijun Zhang (2017): CryoEM Structure of MxB Reveals a Novel Oligomerization Interface Critical for HIV Restriction, Science Advances, American Association for the Advancement of Science (AAAS), Vol 3, Num 9, ppe1701264
Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon, Christopher J. Langmead, Juan R. Perilla, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William W. Brey, David A. Case, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova (2016): HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD, Journal of the American Chemical Society, American Chemical Society (ACS), Vol 138, Num 42, pp14066--14075
Chuang Liu and Juan R. Perilla and Jiying Ning and Manman Lu and Guangjin Hou and Ruben Ramalho and Benjamin A. Himes and Gongpu Zhao and Gregory J. Bedwell and In-Ja Byeon and Jinwoo Ahn and Angela M. Gronenborn and Peter E. Prevelige and Itay Rousso and Christopher Aiken and Tatyana Polenova and Klaus Schulten and Peijun Zhang (2016): Cyclophilin a Stabilizes the HIV-1 Capsid Through a Novel Non-Canonical Binding Site, Nature Communications, Nature Publishing Group, Vol 7, pp10714
Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, and Klaus Schulten (2015): Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis, Structure, Elsevier BV, Vol 23, Num 8, pp1414--1425
C Keith Cassidy, Benjamin A Himes, Frances J Alvarez, Jun Ma, Gongpu Zhao, Juan R Perilla, Klaus Schulten, and Peijun Zhang (2015): CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling, eLife, eLife Sciences Organisation, Ltd., Vol 4
Juan R Perilla, Boon Chong Goh, C Keith Cassidy, Bo Liu, Rafael C Bernardi, Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten (2015): Molecular Dynamics Simulations of Large Macromolecular Complexes, Current Opinion in Structural Biology, Elsevier BV, Vol 31, pp64--74
Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang (2013): Mature HIV-1 Capsid Structure by Cryo-Electron Microscopy and All-Atom Molecular Dynamics, Nature, Nature Publishing Group, Vol 497, Num 7451, pp643--646
NCSA Grants $2.6M in Blue Waters Awards to Illinois ResearchersThe National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign has awarded 3,697,000 node hours (NH) of time on the Blue Waters supercomputer to Illinois researchers from Spring 2017 proposal submissions.The combined value of these awards is over $2.6 million dollars, and through the life of the Blue Waters program, NCSA has awarded over 43 million node hours to UI researchers—a value of nearly $27 million. Some of the time allocated for Blue Waters will go to projects that focus on HIV research, Laser Interferometer Gravitational-Wave Observatory (LIGO) simulations, genomics and global warming research..
Supercomputer Visualization Shows 1.2 Microseconds in the Life of a 4-Million-Atom HIV CapsidWhile some researchers look for drugs to treat HIV, other scientists delve deep into the virus itself for answers on how it causes infections. Using two supercomputers, University of Illinois research scientist Juan R. Perilla and late physics professor Klaus Schulten simulated 1.2 microseconds of the life of the HIV capsid, the structure that contains the virus's genetic material. The simulation, which took two years to complete, gives us a view of the virus on a molecular level and provides us with insight into how HIV senses its environment and becomes infective..
A cure for HIV takes a step closer after supercomputers reveal how the virus movesA brief glimpse into how HIV travels through the body has been simulated for the first time on supercomputers in the US. For two years, multiple supercomputers at the University of Illinois modelled the behaviour of 64 million atoms to capture 1.2 microseconds of the life of an HIV capsid, a protein cage that transports the HIV virus to the nucleus of a human cell. The capsid simulation was performed on the Department of Energy's Titan supercomputer, while analysis was made using the Blue Waters supercomputer at the National Center for Supercomputing Applications at the university..
Massive Simulation Shows HIV Capsid Interacting with its EnvironmentIt took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle. The findings are reported in the journal Nature Communications. "We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment," said University of Illinois research scientist Juan R. Perilla, who led the study with U. of I. physics professor Klaus Schulten. Such details could help scientists find new ways to defeat the virus, Perilla said..
First atomic-scale view of interaction between HIV capsid and host protein cyclophilin AA new study offers the first atomic-scale view of an interaction between the HIV capsid - the protein coat that shepherds HIV into the nucleus of human cells - and a host protein known as cyclophilin A. This interaction is key to HIV infection, researchers say. A paper describing the research appears in the journal Nature Communications. ... "We have known for some time that cyclophilin A plays a role in HIV infection," said University of Illinois physics professor Klaus Schulten, who led the new study with postdoctoral researcher Juan R. Perilla and University of Pittsburgh professor Peijun Zhang and postdoctoral researcher Chuang Liu..
Researchers Construct Atomic Model of an Immature RetrovirusUsing molecular modeling and large-scale molecular dynamic simulation, University of Illinois researchers constructed an atomic model of an immature retrovirus. The researchers, from the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at Illinois, published their work in the journal Structure..