Juan Perilla

2019

Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, and Juan R. Perilla (2019): High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities, Journal of Chemical Information and Modeling, American Chemical Society, Vol 59, Num 10, pp4328-4338
Gino Cingolani, Michael McCauley, Anna Lobley, Alexander J. Bryer, Jordan Wesolowski, Deanna L. Greco, Ravi Kumar Lokareddy, Erik Ronzone, Juan R. Perilla, and Fabienne Paumet (2019): Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA, Nature Communications, Springer Nature Publishing AG, Vol 10, Num 1, pp2747

2018

Jodi A. Hadden, Juan R. Perilla, Christopher John Schlicksup, Balasubramanian Venkatakrishnan, Adam Zlotnick, and Klaus Schulten (2018): All-Atom Molecular Dynamics of the HBV Capsid Reveals Insights Into Biological Function and Cryo-EM Resolution Limits, eLife, eLife Sciences Organisation, Ltd., Vol 7

2017

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
Vamseedhar Rayaprolu, Alan Moore, Joseph Che-Yen Wang, Boon Chong Goh, Juan R Perilla, Adam Zlotnick, and Suchetana Mukhopadhyay (2017): Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles, Journal of Physics: Condensed Matter, Vol 29, Num 48, pp484003
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, Journal of Physical Chemistry B, American Chemical Society, 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, Vol 3, Num 9, ppe1701264
Mingzhang Wang, Caitlin M. Quinn, Juan R. Perilla, Huilan Zhang, Randall Shirra, Guangjin Hou, In-Ja Byeon, Christopher L. Suiter, Sherimay Ablan, Emiko Urano, Theodore J. Nitz, Christopher Aiken, Eric O. Freed, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova (2017): Quenching Protein Dynamics Interferes with HIV Capsid Maturation, Nature Communications, Springer Nature, Vol 8, Num 1, pp1779

2016

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, Vol 138, Num 42, pp14066-14075
Katrina J. Heyrana, Boon Chong Goh, Juan R. Perilla, Tam-Linh N. Nguyen, Matthew R. England, Maria C. Bewley, Klaus Schulten, and Rebecca C. Craven (2016): Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly, Journal of Virology, American Society for Microbiology, Vol 90, Num 12, pp5700-5714
Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and Klaus Schulten (2016): All-Atom Molecular Dynamics of Virus Capsids as Drug Targets, Journal of Physical Chemistry Letters, American Chemical Society, Vol 7, Num 10, pp1836-1844
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

2015

Manman Lu, Guangjin Hou, Huilan Zhang, Christopher L. Suiter, Jinwoo Ahn, In-Ja L. Byeon, Juan R. Perilla, Christopher J. Langmead, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William Brey, Christopher Aiken, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova (2015): Dynamic Allostery Governs Cyclophilin A-HIV Capsid Interplay, Proceedings of the National Academy of Sciences, The National Academy of Sciences, Vol 112, Num 47, pp14617-14622
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

2013

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

2019

Juan Perilla (2019): Molecular Mechanisms of Infection by Chlamydia, 2019 Blue Waters Annual Report, pp284-285

2018

Juan R. Perilla, Jodi A. Hadden, Adam Zlotnick, Louis M. Mansky, Peijun Zhang, Tatyana Polenova, Angela M. Gronenborn, Christopher R. Aiken, Tuli Mukhopadhyay (2018): Unveiling the Functions of Virus Capsids through the Computational Microscope, 2018 Blue Waters Annual Report, pp238-239

The Key to Unlock Bacterial Fusion


Jun 18, 2019

Researchers identify how a Chlamydia-produced protein helps bacterial compartments fuse together, thus increasing pathogenicity.


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Biophysics on World Hepatitis Day


Jul 28, 2018

July 28 is World Hepatitis Day. We spoke with Biophysical Society members whose research focuses on viruses, including hepatitis B. Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). It can cause chronic infection and puts people at high risk of death from cirrhosis and liver cancer. According to the World Health Organization, an estimated 257 million people are living with hepatitis B virus infection. In recognition of World Hepatitis Day, Jodi A. Hadden and Juan R. Perilla, both University of Delaware, and JC Gumbart, Georgia Tech, filled us in on their research related to HBV.


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A view of a virus: research reveals new insights into hepatitis B


May 31, 2018

Researchers at the University of Delaware, working with colleagues at Indiana University, have gained new insights into the virus that causes hepatitis B — a life-threatening and incurable infection that afflicts more than 250 million people worldwide. The discovery, which was published April 27 in the journal eLife, reveals previously unknown details about the capsid, or protein shell, that encloses the virus’ genetic blueprint. Scientists believe that the capsid, which drives the delivery of that blueprint to infect a host cell, is a key target in developing drugs to treat hepatitis B. “With hepatitis B, the structure of the capsid has been known for years, but we wanted to study its motion and its influence on its surroundings,” said Jodi A. Hadden, an independent postdoctoral researcher in UD’s Department of Chemistry and Biochemistry and the lead author of the new paper.


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Supercomputer Visualization Shows 1.2 Microseconds in the Life of a 4-Million-Atom HIV Capsid


Jul 21, 2017

While 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.


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Massive Simulation Shows HIV Capsid Interacting with its Environment


Jul 20, 2017

It 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.


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A cure for HIV takes a step closer after supercomputers reveal how the virus moves


Jul 19, 2017

A 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.


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NCSA Grants $2.6M in Blue Waters Awards to Illinois Researchers


Jul 6, 2017

The 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.


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First atomic-scale view of interaction between HIV capsid and host protein cyclophilin A


Mar 7, 2016

A 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.


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Researchers Construct Atomic Model of an Immature Retrovirus


Aug 12, 2015

Using 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.


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Wit, grit and a supercomputer yield chemical structure of HIV capsid


May 29, 2013

Researchers report that they have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus's genetic material and is a key to its virulence. The capsid has become an attractive target for the development of new antiretroviral drugs. ... "This is a big structure, one of the biggest structures ever solved," said U. of I. physics professor Klaus Schulten, who, with postdoctoral researcher Juan R. Perilla, conducted the molecular simulations that integrated data from laboratory experiments performed by colleagues at the University of Pittsburgh and Vanderbilt University. "It was very clear that it would require a huge amount of simulation - the largest simulation ever published - involving 64 million atoms."


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