Now : Assistant professor at University of Delaware
Perilla @ UDelaware

Home Department: Beckman Institute

Office Address: Beckman Institute, Room 3143

Office Phone: (217) 244-7403

Home Page: perilla.me

Email Address: juan [at] ks [dot] uiuc [dot] edu

Education

• Ph.D. in Biophysics
  Johns Hopkins University - School of Medicine, 2011
• B.S. Physics
  Universidad Nacional de Colombia, 2005

Research

• The molecular architecture of HIV
• Molecular mechanisms of cell-signaling processes.
• Mechanisms of folding and signaling function by membrane receptors.
• Conformational and phase changes in biomolecules.
• Protein-protein interactions in biological membranes.
• Theoretical and computational methods.
• Medical imaging for treatment and diagnosis

Selected Publications

• Length of encapsidated cargo impacts stability and structure of in vitro assembled Alphavirus core-like particles. Vamseedhar Rayaprolu, Alan Moore, Joseph Wang, Boon Chong Goh, Juan R. Perilla, Adam Zlotnick, Suchetana Mukhopadhyay
  Journal of Physics: Condensed Matter, 2017
• CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction Frances J. D. Alvarez, Shaoda He, Juan R. Perilla ,Sooin Jang, Klaus Schulten, Alan N. Engelman, Sjors H. W. Scheres, Peijun Zhang
  Science Advances, 2017 , 9 , Pages: e1701264
• Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations.
Juan R. Perilla and Klaus Schulten
Nature Communications, 2017, doi:10.1038/ncomms15959
• CryoEM structure refinement by integrating NMR chemical shifts with molecular dynamics simulations
Juan R. Perilla*, Gongpu Zhao*, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja Byeon, Angela M. Gronenborn, Tatyana Polenova and Peijun Zhang
* Equal contribution authors
Journal of Physical Chemistry B, 2017, 10.1021/acs.jpcb.6b13105
• GPU-accelerated molecular dynamics clustering analysis with openACC.
  John E. Stone, Juan R. Perilla, C. Keith Cassidy and Klaus Schulten
  In Parallel Programming with openACC, Elsevier, 2016; ISBN: 9780124103979
• HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD
  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
  Journal of the American Chemical Society, 2016, doi: 10.1021/jacs.6b08744
• All-Atom Molecular Dynamics of Virus Capsids as Drug Targets
  Juan R. Perilla#, Jodi A. Hadden, Boon Chong Goh, Christopher Mayne and Klaus Schulten#
  # Corresponding authors
  Journal of Physical Chemistry Letters, 2016, doi: 10.1021/acs.jpclett.6b00517
• Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly
  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#
  # Corresponding authors
  Journal of Virology, 2016, doi: 10.1128/JVI.00378-16
• Molecular architecture of the retroviral capsid.
  Juan R. Perilla and Angela M. Gronenborn
  Trends in Biochemical Sciences, 2016, 41, 410-420
• Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site.
  Chuang Liu*, Juan R. Perilla*, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Benjamin A. Himes, Gongpu Zhao, Gregory J. Bedwell, In-Ja Byeon, Jinwoo Ahn, Angela M. Gronenborn, Peter E. Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klaus Schulten and Peijun Zhang
  * Equal contribution authors
  Nature Communications , 2016, 10.1038/ncomms10714
• CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling.
  C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten and Peijun Zhang
  eLife, 2015, 10.7554/eLife.08419
• Dynamic allostery governs cyclophilin A-HIV capsid interplay.
  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
  Proceedings of the National Academy of Sciences USA, 2015, 47,14617-14622
• Chemical Visualization of Human Pathogens : The Retroviral Capsids.
  Juan R. Perilla*, Boon Chong Goh*, John Stone and Klaus Schulten
  * Equal contribution authors
  Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SuperComputing'15. IEEE Press, 2015
• Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis.
  Boon Chong Goh*, Juan R. Perilla*, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven and Klaus Schulten.
  * Co-first authors
  Structure, 2015, 23,1414-1425
• Molecular dynamics simulations of large macromolecular complexes.
  Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi, Till Rudack, Hang Yu, Zhe Wu and Klaus Schulten
  Current Opinion in Structural Biology, 2015, 31, 64-74
• Computing ensembles of transitions with molecular dynamics simulations.
  Juan R. Perilla and Thomas B. Woolf
  In Molecular Modeling of Proteins - Methods in Molecular Biology, Springer, 2015; ISBN: 978-1-4939-1464-7
• Ictal propagation of high frequency activity is recapitulated in interictal recordings: Effective connectivity of epileptogenic networks recorded with intracranial EEG.
  A. Korzeniewskaa, M.C. Cervenkaa, C.C. Jounya, J.R. Perilla, J. Harezlakc, G.K. Bergeya, P.J. Franaszczuka, N.E. Crone.
  Neuroimage, 2014, 101, 96-113
• Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
  Gongpu Zhao* , Juan R. Perilla*, Ernest L. Yufenyuy*, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang.
  * Equal contribution authors
  Nature, 2013, 497 , 643-646
• Molecular dynamics simulations of transitions for ECD Epidermal Growth Factor Receptors show key differences between human and drosophila forms of the receptors
  Juan R. Perilla, Daniel Leahy, and Thomas Woolf.
  Proteins: Structure, Function, and Bioinformatics, 2013, 81, 1113-1126
• Towards the prediction of order parameters from molecular dynamics simulations in proteins
  Juan R. Perilla and Thomas B. Woolf.
  Journal of Chemical Physics , 2012, 136 , 164101
• Computing ensembles of transitions from stable states: Dynamic importance sampling
  Juan R. Perilla#; Oliver Beckstein; Elizabeth J. Denning; Thomas B. Woolf#.
  # Corresponding authors
  Journal of Computational Chemistry, 2011, 32, 196-209
• Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open <-> Closed Transitions
  Oliver Beckstein#; Elizabeth J. Denning#; Juan R. Perilla#; Thomas B. Woolf#.
  # Corresponding authors
  Journal of Molecular Biology, 2009, 394, 160-176
• Del socavón a la vida (From the cave to life). Baseline to the eradication and prevention of child labor in artisan minery in Colombia.
  United Nations Development Programme, 2003, ISBN: 958-701-350-6.

Journal Covers

Protein Data Bank Entries

News Coverage

CHARMM (Chemistry at HARvard Macromolecular Mechanics)

Lectures and Presentations

• Structure, Dynamics, and Function of the HIV Capsid at the All-atom Level. 2014 FASEB virus assembly and structure conference.
• Unveiling the structure of the HIV-1 capsid. 2013 GPU Technology Conference.
• Structural Analysis of Supramolecular Assemblies by Hybrid Methods. 2013 Keystone Symposia, Lake Tahoe, CA
• CUDA Research Fast Forward. NVIDIA Booth, SuperComputing 2011, Seattle, WA
• Towards finding a better reaction coordinate: NtrC and DIMS. Biophysical Society 55th Annual Meeting, 2011. Baltimore, MD
• Dynamic importance sampling calculations on ECD Epidermal Growth Factor Receptor conformational changes. Biophysical Society 55th Annual Meeting, 2011. Baltimore, MD
• Computing Transitions in Macromolecular Systems: Dynamic Importance Sampling. Biophysical Society 53th Annual Meeting, 2009. Boston, MA
• Understanding the conformational changes in Ca-ATPase using Coarse-grained and All-atom simulations with Dynamic Importance Sampling. Biophysical Society 53th Annual Meeting, 2009. Boston, MA

Medical imaging


• Language Mapping in Multilingual Patients: Electrocorticography and Cortical Stimulation During Naming.
  Mackenzie C. Cervenka, Dana F. Boatman-Reich, Julianna Ward, Piotr J. Franaszczuk, and Nathan E. Crone. Frontiers in human neuroscience, 2011, 5:13
• Choices of references used for EEG measures of effective connectivity to localize seizure foci. American Epilepsy Society, 2011. Baltimore, MD
• Propagation of Intracranial Electroencephalographic Activity between Neocortex and Subcortical Structures as an Indicator of Seizure Onset. American Epilepsy Society, 2010. San Antonio, TX

Legacy

• Quark top production and detection in ATLAS(LHC). Revista Colombiana de Física, 2006, 38, 1276-1280

Funded by a grant from
the National Institute of
General Medical Sciences
of the National Institutes
of Health

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at University of Illinois at Urbana-Champaign

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