Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks.
bioRxiv : the preprint server for biology, 2024
Clinton Yu, Eric Novitsky, Xiaorong Wang, Ignacia Echeverria, Scott Rychnovsky, Lan Huang
The Molecular Architecture of the Nuclear Basket.
Cell, 2024
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, 2023
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, 2023
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
Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α.
The FEBS journal
Echeverria I, Liu Y, Gabelli SB, Amzel LM
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
DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.
PLoS computational biology
Echeverria I, 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
Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality.
The journal of physical chemistry. B
Echeverria I, Amzel LM
Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism.
Biophysical journal
Echeverria I, 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
Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality.
Proteins
Echeverria I, Amzel LM