Hi, I'm a researcher in molecular biophysics at University of California, San Francisco. Please visit my research page.

About Me

Who is Ignacia Echeverria

I am currently an Assistant Professor at UCSF working on integrative modeling and host-pathogen interactions. Previously I was a postdoctoral researcher UCSF at Prof. Andrej Šali laboratory and at University of Maryland at Prof. Garyk Papoian. I obtained a Ph.D. in Molecular Biophysics at Johns Hopkins University and a bachelors degree in Physics at Pontificia Universidad Católica de Chile.

The overall goal of my research is to obtain rigorous mechanistic insight into the structure and dynamics of macromolecular complexes, with special emphasis on how the interaction between proteins, DNA and carbohydrates determine their biologically relevant function.

On my research I use theoretical and computational methods from molecular biophysics, statistical mechanics, stochastic modeling, molecular modeling and scientific and statistical computing to understand how molecules work.

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Cell Reports paper on Rvb1/Rvb2
June, 2017

Research done in collaboration with the Narlikar lab shows how the Rvb1/Rvb2 complex in regulated by a domain within the INO80 chromatin remodeling complex. More

New Elife paper
October, 2016

Our new Elife paper describes the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. More

New PNAS paper
July, 2016

Using simulations and experiments we have identified new residues necesarry for binding and transport of Na in the Na+/I− symporter (NIS) More

FEBS paper PI3K oncogenic mutations
June, 2015

Our paper describing how oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in PI3K. More


Saltzberg, Daniel J., Shruthi Viswanath, Ignacia Echeverria, Ilan E. Chemmama, Ben Webb, and Andrej Sali. "Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure." Protein Science 30, no. 1 (2021): 250-261.

Braberg, Hannes, Ignacia Echeverria, Stefan Bohn, Peter Cimermancic, Anthony Shiver, Richard Alexander, Jiewei Xu et al. "Genetic interaction mapping informs integrative structure determination of protein complexes." Science 370, no. 6522 (2020).

Kwon, Yonghwa, Robyn Kaake, Ignacia Echeverria, Marissa Suarez, Charlotte Stoneham, Peter W. Ramirez, Jacob Kress et al. "Structural Basis of CD4 Downregulation by HIV-1 Nef." bioRxiv (2020). [PDF]

Gutierrez, Craig, Ilan E. Chemmama, Haibin Mao, Clinton Yu, Ignacia Echeverria, Sarah A. Block, Scott D. Rychnovsky, Ning Zheng, Andrej Sali, and Lan Huang. "Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling." Proceedings of the National Academy of Sciences 117, no. 8 (2020): 4088-4098. [PDF]

Saltzberg, Daniel, Charles H. Greenberg, Shruthi Viswanath, Ilan Chemmama, Ben Webb, Riccardo Pellarin, Ignacia Echeverria, and Andrej Sali. "Modeling biological complexes using integrative modeling platform." In Biomolecular Simulations, pp. 353-377. Humana, New York, NY, 2019.

Kim, Seung Joong, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, J.A. Hogan, Paula Upla. Ilan Chemmama, Riccardo Pellarin, Ignacia Echeverria, et al. "Integrative structure and functional anatomy of a nuclear pore complex." Microscopy and Microanalysis 24, no. S1 (2018): 1212-1213. [PDF]

Kim, Seung Joong, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, J.A. Hogan, Paula Upla. Ilan Chemmama, Riccardo Pellarin, Ignacia Echeverria, et al. "Integrative structure and functional anatomy of a nuclear pore complex." Nature 555, no. 7697 (2018): 475. [PDF]

Zhuo, Coral Y.; Caitlin I. Stoddard; Jonathan B. Johnston; Michael J. Trnka; Ignacia Echeverria; Eugene Palovcak; Andrej Sali; Alma L. Burlingame; Yifan Cheng; Geeta J. Narlikar "Correspondence information about the; Geeta J. Narlikar "Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones" Cell Reports (2017). [PDF]

Schulze-Gahmen, Ursula; Ignacia Echeverria,; Goran Stjepanovic; Yun Bai; Huasong Lu; Dina Schneidman-Duhovny; Jennifer Doudna; Qiang Zhou; Andrej Sali; James Hurley "Insights into HIV-1 proviral transcription from an integrative structure of the P- TEFb:AFF4:Tat:TAR complex" eLife Journal (2016). [PDF]

Ferrandino, Giuseppe; Juan Pablo Nicola; Yuly E. Sánchez; Echeverria, Ignacia; Yunlong Liu; L Mario Amzel; Nancy Carrasco "Na+ coordination at the Na2 site of the Na+/I− symporter" PNAS (2016). [PDF]

Echeverria, Ignacia; Yunlong Liu; Sandra B Gabelli; L Mario Amzel "PI3Kα oncogenic mutations weaken the interactions that stabilize the p110α/p85α heterodimer" FEBS Journal (2015). [PDF]

Winogradoff, David*; Echeverria, Ignacia*; Davit A Potoyan, and Garegin A. Papoian. "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." Journal of the American Chemical Society (2015). [PDF]

Echeverria, Ignacia and Garegin A. Papoian. "DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates." PLoS Comput Biol 11(2): (2015). [LINK]

Echeverria, Ignacia and Garegin A. Papoian. "Perspectives on the coarse-graining models of DNA molecules" in Many-body effects and electrostatics in multi-scale computations of Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly (Book chapter) [LINK]

Echeverria, Ignacia and Garegin A. Papoian. "Structural heterogeneity and dynamics of the unfolded ensemble" Isr. J. Chem. 53 (2014). [PDF]

Echeverria, Ignacia; Dmitrii E. Makarov; and Garegin A. Papoian. "Concerted dihedral rotations give rise to internal friction in unfolded proteins." Journal of the American Chemical Society 136,(2014): 8708–8713. [PDF] Highlighted in JACS select [LINK]

Echeverria, Ignacia, and L. Mario Amzel. "Estimation of Free-Energy Differences from Computed Work Distributions: An Application of Jarzynski’s Equality." The Journal of Physical Chemistry B 116.36 (2012): 10986-10995. [PDF]

Gabelli, Sandra B.; Echeverria, Ignacia et al. "Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects." Biophysical Reviews: 1-7. [LINK]

Echeverria, Ignacia, and L. Mario Amzel. "Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism." Biophysical journal 100.9 (2011): 2283-2292. [PDF]

Echeverria, Ignacia, and L. Mario Amzel. "Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality." Proteins: Structure, Function, and Bioinformatics 78.5 (2010): 1302-1310. [PDF]

Messing, Simon AJ, et al. "Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid." The Plant Cell 22.9 (2010): 2970-2980. [LINK]

Urquiza, Mauricio, et al. "α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide." Amino acids 39.5 (2010): 1507-1519. [LINK]


The Sali Lab homepage

"Computational structural biology and bioinformatic group at the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco"


Integrative Modeling Platform (IMP) homepage

"Open source C++ and Python toolbox for solving complex modeling problems by integrating data from diverse biochemical and biophysical experiments"


The Papoian Lab homepage

"Theoretical physical chemistry group in the Department of Chemistry and Biochemistry at the University of Maryland where I was a postdoc"


The Amzel Lab homepage

"Structural Enzymology and Thermodynamics group in the Department of Biophysics and Biophysical Chemistry at Johns Hopkins University School of Medicine"




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