Steve Artandi | Robert Baldwin | Phil Beachy | Paul Berg | Doug Brutlag | Gil Chu | Rhiju Das | Ron Davis | James Ferrell | Pehr Harbury | Dan Herschlag | Dale Kaiser | Chaitan Khosla | Peter Kim | Mark Krasnow | Robert Lehman | Sharon Long | Suzanne Pfeffer | Rajat Rohatgi | Julia Salzman | James Spudich | Aaron Straight | Julie Theriot | Ellen Yeh
Comparative genetic screens in human cells reveal new regulatory mechanisms in WNT signaling
Lebensohm, A. - Rohatgi Lab
The comprehensive understanding of cellular signaling pathways remains a challenge due to multiple layers of regulation that may become evident only when the pathway is probed at different levels or critical nodes are eliminated. To discover regulatory mechanisms in canonical WNT signaling, we conducted a systematic forward genetic analysis through reporter-based screens in haploid human cells. . . .
Inhibiting HIV-1 Entry: Discovery of D-Peptide Inhibitors that Target the gp41 Coiled-Coill Pocket
Eckert, D. - Kim Lab
The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibit HIV-1 entry. We designed a peptide, IQN17, which properly presents this pocket. . . .
Vaccination with peptide mimetics of the gp41 prehairpin fusion intermediate yields neutralizing antisera against HIV-1 isolates
Bianchi, E. - Kim Lab
Eliciting a broadly neutralizing polyclonal antibody response against HIV-1 remains a major challenge.One approach to vaccine development is prevention of HIV-1 entry into cells by blocking the fusion of viral and cell membranes. More speciﬁcally, our goal is to elicit neutralizing antibodies that target a transient viral entry intermediate (the prehairpin intermediate) formed by the HIV-1 gp41 protein. Because this intermediate is transient, a stable mimetic required to elicit a immune response. . .
Protein Design of an HIV-1 Entry Inhibitor
Root, M. - Kim Lab
Human immunodeficiency virus type-1 (HIV-1) membrane fusion is promoted by the formation of a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 envelope glycoprotein ectodomain into close proximity. Peptides derived from the carboxyl-terminal region (called C-peptides) potently inhibit HIV-1 entry by binding to the gp41 amin0-terminal region. . .
The Solution Structural Ensembles of RNA and RNA·Protein Complexes
She, XS - Harbury Lab
RNAs play many functional roles in biology, from non-coding RNAs directly regulating gene expressions to structured RNAs acting as molecular machines essential to chromosome maintenance, alternative pre-mRNA splicing, protein synthesis, and protein export. RNA function typically involves a series of conformational steps, which can be considered as different conformational states that can be adopted by the same RNA. . . .
The peptidergic control circuit for sighing
Li, P - Krasnow Lab
Sighs are long, deep breaths expressing sadness, relief or exhaustion. Sighs also occur spontaneously every few minutes to reinflate alveoli, and sighing increases under hypoxia, stress, and certain psychiatric conditions. Here we use molecular, genetic, and pharmacologic approaches to identify a peptidergic sigh control circuit in murine brain. Small neural subpopulations in a key breathing control . . . .
Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development
Szabo, L - Salzman Lab
The pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover . . .
Extensive Site-directed Mutagenesis Reveals Interconnected Functional Units in the Alkaline Phosphatase Active Site
Sunden, F - Herschlag Lab
Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively . . . .
Protein flexibility is required for vesicle tethering at the Golgi
Cheung PY - Pfeffer Lab
The Golgi is decorated with coiled-coil proteins that may extend long distances to help vesicles find their targets. GCC185 is a trans Golgi-associated protein that captures vesicles inbound from late endosomes. Although predicted to be relatively rigid and highly extended, we show that flexibility in a central region is required for GCC185’s ability to function in a vesicle tethering cycle . . . .
A Turnstile Mechanism for the Controlled Growth of Biosynthetic Intermediates on Assembly Line Polyketide Synthases
Lowry, B - Khosla Lab
Vectorial polyketide biosynthesis on an assembly line polyketide synthase is the most distinctive property of this family of biological machines, while providing the key conceptual tool for the bioinformatic decoding of new antibiotic pathways. We now show that the action of the entire assembly line is synchronized by a previously unrecognized turnstile mechanism that prevents the . . . .
Thresholds and ultrasensitivity from negative cooperativity
Ha, SH - Ferrell Lab
Negative cooperativity is a phenomenon in which the binding of one or more molecules of a ligand to a multimeric receptor makes it more difficult for subsequent ligand molecules to bind. Negative cooperativity can make a . . . .
Consistent global structures of complex RNA states through multidimensional chemical mapping
Cheng, CY - Das Lab
Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end . . . .
A cell-free CENP-A assembly system defines the chromatin requirements for centromere maintenance
Westhorpe, FG - Straight Lab
Centromeres are defined by the presence of CENP-A nucleosomes in chromatin and are essential for accurate chromosome segregation. Centromeric chromatin epigenetically seeds new CENP=A nucleosome formation . . . .
Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis
Gao, W - Davis Lab
Wearable sensor technologies are essential to the realization of personalized medicine through continuously monitoring an individual’s state of health. Sampling human sweat, which is rich in physiological information, could enable non-invasive monitoring. Previously reported sweat-based and other non-invasive biosensors either can only monitor a single analyte at a time or lack on-site signal processing . . . .