Ignacia Echeverria Riesco, PhD

Assistant Professor

Department of Bioengineering and Therapeutic Sciences

[email protected]

Please update your Location In, Rm 001

UCSF Box 2552

Varies, CA 00001

United States

Links

UCSF Profiles Website

What I do

Our research investigates the structural diversity of protein assemblies by developing integrative modeling methods based on in vivo (in cells), in situ (in their cellular environment), and solution data. Our approach allows us to study difficult-to-isolate protein assemblies in their native environments and understand their full range of structural dynamics. We are particularly interested in applying these methods to understand host-pathogen interactions using proteomics and genetics data.

Professional background

Research keywords

vif Gene Products, Human Immunodeficiency Virus
Histones
Cyclin-Dependent Kinase 9
APOBEC-3G Deaminase
Disaccharides
Molecular Dynamics Simulation
Cyclin T
Thermodynamics
Mammals
Oncogenes
Nuclear Pore Complex Proteins
Molecular Models
Saccharomyces cerevisiae
Nuclear Pore
Galectin 1

Publications

Gupta M, Khandelwal NK, Seka DJ, Balasubramani SG, Dickinson MS, Myasnikov A, Echeverria I, Stroud RM. Molecular mechanism of substrate transport by human peroxisomal ABCD3. bioRxiv. 2025 May 27.

Biswas A, Choudhuri I, Huang K, Sun Q, Sali A, Echeverria I, Haldane A, Levy RM, Lyumkis D. Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV. bioRxiv. 2025 May 02.

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. Multimodal cell maps as a foundation for structural and functional genomics. Nature. 2025 Jun; 642(8066):222-231.

Khandelwal NK, Gupta M, Kumar P, Balasubramani SG, Echeverria I, Stroud RM. Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter. Proc Natl Acad Sci U S A. 2025 Feb 18; 122(7):e2418282122.

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. The molecular architecture of the nuclear basket. Cell. 2024 Sep 19; 187(19):5267-5281.e13.

Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L. Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks. bioRxiv. 2024 Aug 07.

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. The Molecular Architecture of the Nuclear Basket. bioRxiv. 2024 Mar 28.

Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell. 2023 09 21; 83(18):3283-3302.e5.

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. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 10 12; 186(21):4597-4614.e26.

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. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol. 2023 03; 30(3):296-308.

Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Nature. 2023 03; 615(7953):728-733.

Echeverria I, Braberg H, Krogan NJ, Sali A. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J. 2023 05; 290(10):2565-2575.

Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 06; 23(6):342-354.

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. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2022 01 20; 185(2):361-378.e25.

Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. Elife. 2021 11 25; 10.

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. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021; 20:100132.

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. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 12 11; 370(6522).

Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Protein Sci. 2021 01; 30(1):250-261.

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 basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol. 2020 09; 27(9):822-828.

Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proc Natl Acad Sci U S A. 2020 02 25; 117(8):4088-4098.

Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. Modeling Biological Complexes Using Integrative Modeling Platform. Methods Mol Biol. 2019; 2022:353-377.

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. Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018 03 22; 555(7697):475-482.

Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep. 2017 06 06; 19(10):2033-2044.

Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 10 12; 5.

Ferrandino G, Nicola JP, Sánchez YE, Echeverria I, Liu Y, Amzel LM, Carrasco N. Na+ coordination at the Na2 site of the Na+/I- symporter. Proc Natl Acad Sci U S A. 2016 09 13; 113(37):E5379-88.

Echeverria I, Liu Y, Gabelli SB, Amzel LM. Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α. FEBS J. 2015 Sep; 282(18):3528-42.

Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. J Am Chem Soc. 2015 May 20; 137(19):6245-53.

Echeverria I, Papoian GA. DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates. PLoS Comput Biol. 2015 Feb; 11(2):e1003980.

Echeverria I, Makarov DE, Papoian GA. Concerted dihedral rotations give rise to internal friction in unfolded proteins. J Am Chem Soc. 2014 Jun 18; 136(24):8708-13.

Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM. Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects. Biophys Rev. 2014 Mar 01; 6(1):89-95.

Echeverria I, Amzel LM. Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality. J Phys Chem B. 2012 Sep 13; 116(36):10986-95.

Echeverria I, Amzel LM. Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism. Biophys J. 2011 May 04; 100(9):2283-92.

Messing SA, Gabelli SB, Echeverria I, Vogel JT, Guan JC, Tan BC, Klee HJ, McCarty DR, Amzel LM. Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid. Plant Cell. 2010 Sep; 22(9):2970-80.

Urquiza M, Melo-Cardenas J, Guevara T, Echeverria I, Rodriguez IC, Vanegas M, Amzel M, Patarroyo ME. α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide. Amino Acids. 2010 Nov; 39(5):1507-19.

Echeverria I, Amzel LM. Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality. Proteins. 2010 Apr; 78(5):1302-10.