Ignacia Echeverria Riesco, PhD

Assistant Professor
Bioengineering
[email protected]

My research is focused on building integrative, computational, and theoretical models to describe the structure and dynamics of proteins, nucleic acids, and carbohydrates to understand their function and evolution. My scientific background is molecular biophysics, computational modeling, and statistical physics. My research experience is computational structural biology, biophysics, and integrative structure determination of macromolecular assemblies. I have developed methods for integrative structure determination, molecular dynamics (MD) simulations, free energy calculations, and coarse-graining.

I have applied these methods to a variety of biological problems, such as (1) structure determination of host-pathogen macromolecular complexes, with emphasis is HIV (Kaake*, Echeverria* et al. MCP 2021), (2) structure determination of large protein assemblies using integrative methods, including the Nuclear Pore Complex (Akey*, Singh*, Ouch*, Echeverria* et al. Cell 2022), (3) converting genetic interactions data into structural models (Braberg*, Echeverria* et al. Science 2020),  (4) characterization of the dynamics of unfolded proteins and (5) the effects of post-translational modifications, and (6) free energy calculations of protein folding, protein-DNA, and protein-carbohydrate interactions.

Publications: 

Multimodal cell maps as a foundation for structural and functional genomics.

Nature

Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T

Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter.

Proceedings of the National Academy of Sciences of the United States of America

Khandelwal NK, Gupta M, Kumar P, Balasubramani SG, Echeverria I, Stroud RM

The molecular architecture of the nuclear basket.

Cell

Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E

Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks.

bioRxiv : the preprint server for biology

Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L

The Molecular Architecture of the Nuclear Basket.

bioRxiv : the preprint server for biology

Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E

Implications of a multiscale structure of the yeast nuclear pore complex.

Molecular cell

Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP

SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

Cell

Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.

Nature structural & molecular biology

Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM

The structural basis for HIV-1 Vif antagonism of human APOBEC3G.

Nature

Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD

Integrative structure determination of histones H3 and H4 using genetic interactions.

The FEBS journal

Echeverria I, Braberg H, Krogan NJ, Sali A

From systems to structure - using genetic data to model protein structures.

Nature reviews. Genetics

Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ

Comprehensive structure and functional adaptations of the yeast nuclear pore complex.

Cell

Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP

Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb.

eLife

Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K

Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.

Molecular & cellular proteomics : MCP

Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ

Genetic interaction mapping informs integrative structure determination of protein complexes.

Science (New York, N.Y.)

Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.

Protein science : a publication of the Protein Society

Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A

Structural basis of CD4 downregulation by HIV-1 Nef.

Nature structural & molecular biology

Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X

Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.

Proceedings of the National Academy of Sciences of the United States of America

Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L

Modeling Biological Complexes Using Integrative Modeling Platform.

Methods in molecular biology (Clifton, N.J.)

Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A

Integrative structure and functional anatomy of a nuclear pore complex.

Nature

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP

Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.

Cell reports

Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.

eLife

Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH

Na+ coordination at the Na2 site of the Na+/I- symporter.

Proceedings of the National Academy of Sciences of the United States of America

Ferrandino G, Nicola JP, Sánchez YE, Echeverria I, Liu Y, Amzel LM, Carrasco N

The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects.

Journal of the American Chemical Society

Winogradoff D, Echeverria I, Potoyan DA, Papoian GA

Concerted dihedral rotations give rise to internal friction in unfolded proteins.

Journal of the American Chemical Society

Echeverria I, Makarov DE, Papoian GA

Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects.

Biophysical reviews

Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM

Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid.

The Plant cell

Messing SA, Gabelli SB, Echeverria I, Vogel JT, Guan JC, Tan BC, Klee HJ, McCarty DR, Amzel LM

α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide.

Amino acids

Urquiza M, Melo-Cardenas J, Guevara T, Echeverria I, Rodriguez IC, Vanegas M, Amzel M, Patarroyo ME