Ignacia Echeverria Riesco, PhD

Assistant Professor
P_Bioengineering

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

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication.

bioRxiv : the preprint server for biology

Batra J, Rutkowska M, Zhou Y, Ye C, Adavikolanu R, Young JM, Anand D, Verma S, Gordon M, Malpotra S, Cupic A, Kehrer T, Moen JM, Winters DM, Rojc A, Mena I, Aslam S, Martinez-Romero C, Conde Viñas I, Khalil Z, Farrugia K, Banerjee A, Tussia-Cohen D, Santos MD, Maji S, Muralidharan M, Foussard H, Chen IP, Fuchs R, Felipe CS, Zuliani-Alvarez L, Choudhury P, Obernier K, Gracias S, Suryawanshi R, Ibáñez C, Juste J, Pache L, Taha TY, Jouvenet N, Verba KA, Fraser JS, Demeret C, Stroud RM, van Bakel H, Ott M, Hagai T, Polacco B, Swaney DL, Echeverria I, Bouhaddou M, Eckhardt M, Malik HS, Martinez-Sobrido L, Miorin L, García-Sastre A, Krogan NJ

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

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

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

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