2017 Research Highlights

Physiological Mg2+ conditions significantly alter the inhibition of HIV-1 and HIV-2 reverse transcriptases by nucleoside and non-nucleoside inhibitors in vitro

The efficacy of RT inhibitors is dramatically affected by the level of magnesium, unscoring the need to test inhibitors using physiological conditions.

Achuthan B, Singh K & DeStefano JJ. Biochem. 56, 33-46 (2017).

PubMed PMID: 27936595

PubMedCentral PMCID: PMC5453313

Functional interplay between murine leukemia virus glycogag, Serinc5, and surface glycoprotein governs virus entry, with opposite effects on gammaretroviral and ebolavirus glycoproteins

HIVE Center collaborators examine the effects of a cellular factor, Serinc5, upon the entry of murine leukemia virus

Ahi YS, Zhang S, Thappeta Y, Denman A, Felzpour A, Gummuluru S, Reinhard B, Murlaux D, Fivash MJ & Rein A MBio 7, e01985-16 (2017)

PubMed PMID: 27879338

PubMedCentral PMCID: PMCID5120145

An experimental check of backscattering interferometry

HIVE Center researchers validate BSI, a powerful method for rapid measuring of association constants.

Baksh MM & Finn MG. Sensors Actuators B 243, 9770981 (2017)

PubMed PMID: 28529409

PubMedCentral PMCID: PMC5433263

RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing

A new software package streamlines the analysis of data that probes the structure of RNA.

Cantara WA, Hatterschide J, Wu W & Musier-Forsyth. RNA, 23, 240-249 (2017)

PubMed PMID: 27821510

PMCID: PMC5238798

Analysis of RNA structure using small-angle X-ray scattering

A review of best practices for using SAXS to determine the tertiary structure of RNA under physiological conditions.

Cantara WA, Olson ED & Musier-Forsyth K. Methods , 113, 46-55 (2017)

PubMed PMID: 27777026

PMCID: PMC5253320

Conservation of tRNA mimicry in the 5′-untranslated region of distinct HIV-1 subtypes

HIVE Center researchers discover that part of the HIV genome mimics the shape of cellular transfer RNA

Comandur R, Olson ED & Musier-Forsyth RNA 23, 1850-1859 (2017).

PubMed PMID: 28860303

PubMedCentral: PMCID: PMC5689005

Dissection of specific binding of HIV-1 Gag to the “packaging signal” in viral RNA

HIVE Center collaborators uncover the details of how HIV-1 specifically recognizes its genomic RNA during packaging

Comas-Garcia M, Datta SAK, Baker L, Varma R, Gudla PR & Rein A eLIFE 6, e27055 (2017)

PubMed PMID: 28726630

PubMedCentral PMCID: PMC5531834

Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease

HIVE researchers analyze data from patients to discover how HIV gains resistance to drugs.

Flynn WF, Haldane A, Torbett BE & Levy RM Mol. Biol. Evol. 34, 1291-1306 (2017).

PubMed PMID: 28369521

PubMedCentral PMCID: PMC5435099

Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing

A surprising connection between integrase and maturation of HIV is discovered.

Hoyte AC, Jamin AB, Koneru PC, Kobe MJ, Larue RC, Fuchs JR, Engelman AN & Kvaratskhelia M. J. Biol. Chem. 292, 19814-19825 (2017).

PubMed PMID: 28972144

PubMedCentral PMCID: PMC5712621

Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness

A powerful method for analysis of sequence and structural data is reviewed.

Levy RM, Haldane A & Flynn WF Curr. Op. Struct. Biol. 43, 55-62 (2017).

PubMed PMID: 27870991

Multidimensional SuFEx click chemistry: sequential sulfur(VI) fluoride exchange connection of diverse modules launched from an SOF4 hub.

A new family of transformations allow click chemistry connections between diverse chemical modules, including linkages between small molecules and protein sidechains.

Li S, Wu P, Moses JE & Sharpless KB. Angewandte Chemie 56, 2903-2908 (2017).

PubMed PMID: 28165188

PubMedCentral PMCID: PMC5434761

Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike

Structures of HIV-1 envelope glycoprotein with receptors and antibodies are studied with cryoelectron microscopy

Ozorowski G, Pallesen J, deVal N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA & Ward AB Nature 547 360-363 (2017)

PubMed PMID: 28700571

PubMedCentral PMCID: PMC5538736

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge

Absolute binding free energies are computed for host-guest complexes using a new approach.

Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T & Gallicchio E J. Comput. Aided Mol. Design 31, 29-44 (2017)

PubMed PMID: 27696239

PubMedCentral PMCID: PMC5477994

Multiplex single-cell visualization of nucleic acids and protein during HIV infection

HIVE researchers present a method to observe HIV DNA, RNA and proteins inside infected cells.

Puray-Chavez M, Tedbury PR, Huber AD, Ukah OB, Yapo V, Liu D, Ji J, Wolf JJ, Engelman AN & Sarafianos SG. Nature Comm 8, 1882 (2017)

PubMed PMID: 29292235

PubMedCentral PMCID: PMC5709414

Exposing HIV’s Weaknesses

Commentary on recent research into the viral restriction factor SERINC5.

Tedbury PR & Sarafianos SG (2017) J. Biol. Chem. 292, 6027-6028

PubMed PMID: 28389578

PubMedCentral PMCID: PMC5392592