Rodolfo Ghirlando
National Institutes of Health
Binding siteBiophysicsMolecular biologyChemistryDimerAnalytical UltracentrifugationSedimentation equilibriumProtein structurePlasma protein bindingGeneticsDNABiochemistryHistoneStereochemistryCrystallographyChromatinNucleosomeBiologyDNA-binding proteinCell biology
Publications 194
#1Trang T. Nguyen (Iowa State University)H-Index: 5
#2Rodolfo Ghirlando (NIH: National Institutes of Health)H-Index: 74
Last. Vincenzo Venditti (Iowa State University)H-Index: 18
view all 4 authors...
Enzyme I (EI) is a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate. This reaction initiates a five-step phosphorylation cascade in the bacterial phosphotransferase (PTS) transduction pathway. Under physiological conditions, EI exists in an equilibrium between a functional dimer and an inactive monomer. The monomer–dimer equilibrium is a crucial factor regulating EI activity and the phosphorylation state of the overall PTS. Experimental studies of EI’s...
1 CitationsSource
#1Bing-Rui Zhou (NIH: National Institutes of Health)H-Index: 18
#2Hanqiao Feng (NIH: National Institutes of Health)H-Index: 23
Last. Yawen Bai (NIH: National Institutes of Health)H-Index: 33
view all 9 authors...
Summary The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the fl...
10 CitationsSource
#1Dalibor Kosek (NIH: National Institutes of Health)
#1Dalibor Kosek (NIH: National Institutes of Health)
Last. Fred Dyda (NIH: National Institutes of Health)H-Index: 42
view all 5 authors...
Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathways, it requires both asymmetric and symmetric strand transfer steps. Here, we report the first structural study of a copy-out/paste-in transposase and demonstrate its ability to catalyze all pathway steps in vitro. X-ray structures of ISCth4 transpo...
#1Ruben D. Elias (UCSD: University of California, San Diego)H-Index: 1
#2Wen Ma (UCSD: University of California, San Diego)H-Index: 8
Last. Lalit Deshmukh (UCSD: University of California, San Diego)H-Index: 12
view all 6 authors...
Proline-rich domains (PRDs) are among the most prevalent signaling modules of eukaryotes but often unexplored by biophysical techniques as their heterologous recombinant expression poses significant difficulties. Using a "divide-and-conquer" approach, we present a detailed investigation of a PRD (166 residues; ∼30% prolines) belonging to a human protein ALIX, a versatile adaptor protein involved in essential cellular processes including ESCRT-mediated membrane remodeling, cell adhesion, and apop...
3 CitationsSource
#1Rochelle R. Dotas (Iowa State University)H-Index: 4
#2Trang T. Nguyen (Iowa State University)H-Index: 5
Last. Vincenzo Venditti (Iowa State University)H-Index: 18
view all 6 authors...
Abstract Conformational disorder is emerging as an important feature of biopolymers, regulating a vast array of cellular functions, including signaling, phase separation, and enzyme catalysis. Here we combine NMR, crystallography, computer simulations, protein engineering, and functional assays to investigate the role played by conformational heterogeneity in determining the activity of the C-terminal domain of bacterial Enzyme I (EIC). In particular, we design chimeric proteins by hybridizing E...
1 CitationsSource
#1Eric R. Henry (NIH: National Institutes of Health)H-Index: 38
#2Troy Cellmer (NIH: National Institutes of Health)H-Index: 15
Last. William A. Eaton (NIH: National Institutes of Health)H-Index: 88
view all 14 authors...
The pathology of sickle cell disease is caused by polymerization of the abnormal hemoglobin S upon deoxygenation in the tissues to form fibers in red cells, causing them to deform and occlude the circulation. Drugs that allosterically shift the quaternary equilibrium from the polymerizing T quaternary structure to the nonpolymerizing R quaternary structure are now being developed. Here we update our understanding on the allosteric control of fiber formation at equilibrium by showing how the simp...
5 CitationsSource
#1Alberto Ceccon (NIH: National Institutes of Health)H-Index: 5
#1Alberto Ceccon (NIH: National Institutes of Health)H-Index: 20
Last. G. Marius Clore (NIH: National Institutes of Health)H-Index: 103
view all 4 authors...
Human profilin I reduces aggregation and concomitant toxicity of the polyglutamine-containing N-terminal region of the huntingtin protein encoded by exon 1 (httex1) and responsible for Huntington’s disease. Here, we investigate the interaction of profilin with httex1 using NMR techniques designed to quantitatively analyze the kinetics and equilibria of chemical exchange at atomic resolution, including relaxation dispersion, exchange-induced shifts, and lifetime line broadening. We first show tha...
6 CitationsSource
#1Mukul SherekarH-Index: 1
#2Sae-Won Han (UCSF: University of California, San Francisco)H-Index: 1
Last. Dominic EspositoH-Index: 33
view all 17 authors...
Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS-mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH...
10 CitationsSource
#1Mengli Cai (NIH: National Institutes of Health)H-Index: 21
#2Ying Huang (NIH: National Institutes of Health)H-Index: 47
Last. G. Marius Clore (NIH: National Institutes of Health)H-Index: 103
view all 8 authors...
Bacterial MinD and MinE form a standing oscillatory wave which positions the cell division inhibitor MinC, that binds MinD, everywhere on the membrane except at the midpoint of the cell, ensuring midcell positioning of the cytokinetic septum. During this process MinE undergoes fold switching as it interacts with different partners. We explore the exchange dynamics between major and excited states of the MinE dimer in 3 forms using 15N relaxation dispersion NMR: the full-length protein (6-strande...
5 CitationsSource
#1Rita M. McCall (NIH: National Institutes of Health)H-Index: 2
#2Mary E. Sievers (NIH: National Institutes of Health)H-Index: 1
Last. Stephen H. Leppla (NIH: National Institutes of Health)H-Index: 94
view all 6 authors...
Anthrax toxin activator (AtxA) is the master virulence gene regulator of Bacillus anthracis. It regulates genes on the chromosome as well as the pXO1 and pXO2 plasmids. It is not clear how AtxA regulates these genes, and direct binding of AtxA to its targets has not been shown. It has been previously suggested that AtxA and other proteins in the Mga/AtxA global transcriptional regulators family bind to the curvature of their DNA targets, although this has never been experimentally proven. Using ...
2 CitationsSource