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Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 12 11; 370(6522).
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. PMID: 33303586.
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PubMed Mentions:
3 Fields:
Translation:
AnimalsCells
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Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Protein Sci. 2021 01; 30(1):250-261.
Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. PMID: 33166013.
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PubMed Mentions:
4 Fields:
Translation:
Cells
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Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol. 2020 09; 27(9):822-828.
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. PMID: 32719457.
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PubMed Mentions:
7 Fields:
Translation:
HumansCells
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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.
Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. PMID: 32034103.
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PubMed Mentions:
9 Fields:
Translation:
HumansCells
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Modeling Biological Complexes Using Integrative Modeling Platform. Methods Mol Biol. 2019; 2022:353-377.
Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. PMID: 31396911.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018 03 22; 555(7697):475-482.
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. PMID: 29539637.
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PubMed Mentions:
93 Fields:
Translation:
AnimalsCells
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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.
Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. PMID: 28591576.
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PubMed Mentions:
22 Fields:
Translation:
AnimalsCells
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Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 10 12; 5.
Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. PMID: 27731797.
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PubMed Mentions:
13 Fields:
Translation:
HumansCells
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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.
Ferrandino G, Nicola JP, Sánchez YE, Echeverria I, Liu Y, Amzel LM, Carrasco N. PMID: 27562170.
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PubMed Mentions:
7 Fields:
Translation:
HumansCells
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Oncogenic mutations weaken the interactions that stabilize the p110a-p85a heterodimer in phosphatidylinositol 3-kinase a. FEBS J. 2015 Sep; 282(18):3528-42.
Echeverria I, Liu Y, Gabelli SB, Amzel LM. PMID: 26122737.
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PubMed Mentions:
11 Fields:
Translation:
HumansCells
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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.
Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. PMID: 25905561.
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PubMed Mentions:
27 Fields:
Translation:
Cells
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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, Papoian GA. PMID: 25675216.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Concerted dihedral rotations give rise to internal friction in unfolded proteins. J Am Chem Soc. 2014 Jun 18; 136(24):8708-13.
Echeverria I, Makarov DE, Papoian GA. PMID: 24844314.
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PubMed Mentions:
25 Fields:
Translation:
Cells
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Activation of PI3Ka by physiological effectors and by oncogenic mutations: structural and dynamic effects. Biophys Rev. 2014 Mar 01; 6(1):89-95.
Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM. PMID: 25309634.
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PubMed Mentions:
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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. PMID: 22849340.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism. Biophys J. 2011 May 04; 100(9):2283-92.
Echeverria I, Amzel LM. PMID: 21539798.
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PubMed Mentions:
6 Fields:
Translation:
AnimalsCells
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Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid. Plant Cell. 2010 Sep; 22(9):2970-80.
Messing SA, Gabelli SB, Echeverria I, Vogel JT, Guan JC, Tan BC, Klee HJ, McCarty DR, Amzel LM. PMID: 20884803.
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PubMed Mentions:
52 Fields:
Translation:
AnimalsCells
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a-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.
Urquiza M, Melo-Cardenas J, Guevara T, Echeverria I, Rodriguez IC, Vanegas M, Amzel M, Patarroyo ME. PMID: 20473772.
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PubMed Mentions: Fields:
Translation:
HumansAnimalsCells
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Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality. Proteins. 2010 Apr; 78(5):1302-10.
Echeverria I, Amzel LM. PMID: 20014024.
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PubMed Mentions:
4 Fields:
Translation:
Cells