Xabier Agirrezabala, Eduard Schreiner, Leonardo G. Trabuco, Jianlin Lei, Rodrigo F. Ortiz‐Meoz, Klaus Schulten, Rachel Green, Joachim Frank,
... for more papers by this author Leonardo G Trabuco Leonardo G Trabuco Beckman Institute for Advanced Science and Technology, University ... for more papers by this author Leonardo G Trabuco Leonardo G Trabuco Beckman Institute for Advanced Science and Technology, University ... maps using molecular dynamics-based flexible fitting (MDFF) (Trabuco et al, 2008) (described in the Materials and ...
Tópico(s): Machine Learning in Bioinformatics
2011 - Springer Nature | The EMBO Journal
... probably marine. The red lower part, named the "Trabuco formation" by E. L. Packard, was interpreted as ... are believed due to differences in weathering. The Trabuco conglomerate is interpreted as a flood-plain deposit ... deposition of the gray marine conglomerate overlying. The Trabuco conglomerate is thus recognized as a valid formation, ...
Tópico(s): Geological and Geophysical Studies Worldwide
1941 - University of Chicago Press | The Journal of Geology
Daniel Roca‐Sanjuán, Mickaël G. Delcey, Isabelle Navizet, Nicolas Ferré, Ya‐Jun Liu, Roland Lindh,
... Ribeirão Preto, São Paulo, Brazil E‐mail: danilo.trabuco@gmail.com Bioluminescence in Coleoptera is found mainly ... of Sorocaba, Sorocaba, SP, Brazil E‐mail: danilo.trabuco@gmail.com Bioluminescent click‐beetles (Elateridae) produce one ...
Tópico(s): bioluminescence and chemiluminescence research
2012 - Wiley | Luminescence
Richard A. Henderson, Andrej Šali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, Catherine L. Lawson,
... Full Text PDF PubMed Scopus (125) Google Scholar, Trabuco et al., 2008Trabuco L.G. Villa E. Mitra ... Full Text PDF PubMed Scopus (235) Google Scholar, Trabuco et al., 2011Trabuco L.G. Schreiner E. Gumbart ...
Tópico(s): Force Microscopy Techniques and Applications
2012 - Elsevier BV | Structure
... N. Gartmann M. Armache J.P. Villa E. Trabuco L.G. Becker T. Mielke T. Schulten K. ... N. Gartmann M. Armache J.P. Villa E. Trabuco L.G. Becker T. Mielke T. Schulten K. ...
Tópico(s): Bacterial Genetics and Biotechnology
2011 - Elsevier BV | Molecular Cell
Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean‐Paul Armache, Elizabeth Villa, Leonardo G. Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A. Steitz, Roland Beckmann,
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal ...
Tópico(s): Bacteriophages and microbial interactions
2009 - American Association for the Advancement of Science | Science
Jiantao Guo, Charles E. Melançon, Hyun Soo Lee, Dan Groff, Peter G. Schultz,
... Eargle, A. A. Black, A. Sethi, L. G. Trabuco, Z. Luthey-Schulten, J. Mol. Biol. 2008, 377, ...
Tópico(s): Genomics and Phylogenetic Studies
2009 - Wiley | Angewandte Chemie International Edition
Roberta E. Blandon, John B. Gebhart, Emanuel C. Trabuco, Christopher J. Klingele,
Tópico(s): Pelvic and Acetabular Injuries
2009 - Springer Science+Business Media | International Urogynecology Journal
Produção Nacional
Revisado por pares
Lucas Novaes Teixeira, Grasiele Edilaine Crippa, Amanda Cristina Trabuco, Rossano Gimenes, M.A. Zaghete, Daniela Bazan Palioto, Paulo Tambasco de Oliveira, Adalberto Luiz Rosa, Márcio Mateus Beloti,
The aim of this work was to evaluate the biocompatibility of poly(vinylidene fluoride–trifluoroethylene)/barium titanate (P(VDF-TrFE)/BT) membrane to be used in guided tissue regeneration (GTR). Fibroblasts from human periodontal ligament (hPDLF) and keratinocytes (SCC9) were plated on P(VDF-TrFE)/BT and polytetrafluorethylene membranes at a cell density of 20,000 cells well−1 and cultured for up to 21 days. Cell morphology, adhesion and proliferation were evaluated in hPDLF and keratinocytes, while ...
Tópico(s): Bone Tissue Engineering Materials
2009 - Elsevier BV | Acta Biomaterialia
Jen Hsin, James C. Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Qian Pu, C. Neil Hunter, Klaus Schulten,
In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-LH1-PufX dimers aggregate into tubular vesicles with a radius of ∼250–550 Å, making RC-LH1-PufX one of the few integral membrane proteins known to actively induce membrane curvature. Recently, ...
Tópico(s): Spectroscopy and Quantum Chemical Studies
2009 - Elsevier BV | Biophysical Journal
Elizabeth Villa, Jayati Sengupta, Leonardo G. Trabuco, Jamie LeBarron, William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen, Måns Ehrenberg, Klaus Schulten, Joachim Frank,
In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-Å cryo-electron microscopy map of the aminoacyl-tRNA·EF-Tu·GDP·kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. ...
Tópico(s): RNA Research and Splicing
2009 - National Academy of Sciences | Proceedings of the National Academy of Sciences
Emanuel C. Trabuco, Christopher J. Klingele, Amy L. Weaver, Michaela E. McGree, Deborah J. Lightner, John B. Gebhart,
The purpose of this study was to compare continence rates after placement of rectus fascia or midurethral slings.We performed a retrospective cohort study of 242 women who underwent rectus fascia (n = 79) or midurethral (n = 163) sling procedures to treat urinary incontinence. Outcome was based on responses to validated questionnaires and need for interim treatment for incontinence. Survival free of incontinence was estimated using the Kaplan-Meier method. Associations between patient factors and survival ...
Tópico(s): Urinary Bladder and Prostate Research
2009 - Elsevier BV | American Journal of Obstetrics and Gynecology
Melih Şener, Jen Hsin, Leonardo G. Trabuco, Elizabeth Villa, Qian Pu, C. Neil Hunter, Klaus Schulten,
The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes ...
Tópico(s): Spectroscopy and Quantum Chemical Studies
2009 - Elsevier BV | Chemical Physics
James C. Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, Klaus J Schulten,
During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, ...
Tópico(s): RNA modifications and cancer
2009 - Elsevier BV | Structure
Leonardo G. Trabuco, Elizabeth Villa, Eduard Schreiner, Christopher B. Harrison, Klaus Schulten,
Hybrid computational methods for combining structural data from different sources and resolutions are becoming an essential part of structural biology, especially as the field moves toward the study of large macromolecular assemblies. We have developed the molecular dynamics flexible fitting (MDFF) method for combining high-resolution atomic structures with cryo-electron microscopy (cryo-EM) maps, that results in atomic models representing the conformational state captured by cryo-EM. The method has ...
Tópico(s): Advanced Electron Microscopy Techniques and Applications
2009 - Elsevier BV | Methods
Rosebud O. Roberts, Debra J. Jacobson, Cynthia J. Girman, Thomas Rhodes, Michael M. Lieber, Steven J. Jacobsen,
... publication date: 1-Dec-2008. Bharucha A and Trabuco E (2008) Functional and Chronic Anorectal and Pelvic ...
Tópico(s): Pelvic floor disorders treatments
2002 - Lippincott Williams & Wilkins | The Journal of Urology
Produção Nacional
Revisado por pares
Jamary Oliveira‐Filho, S.C.S. Silva, Carolina C. Trabuco, Bruno B. Pedreira, E.U. Sousa, Andreza Mourão Lopes Bacellar,
Background: High blood pressure, although the main modifiable risk factor for stroke, may have a beneficial effect in maintaining brain perfusion after acute ischemia. The authors assessed the effects of blood pressure variation in the first 24 hours of stroke onset. Methods: The authors prospectively studied consecutive patients admitted in the first 24 hours after stroke onset. Patients were classified according to the NIH Stroke Scale (NIHSS) and Oxfordshire Stroke Classification Scale (OSCS). Stroke etiology ...
Tópico(s): Cerebrovascular and Carotid Artery Diseases
2003 - Lippincott Williams & Wilkins | Neurology
Produção Nacional
Revisado por pares
D Cancherini, Leonardo G. Trabuco, Nancy Amaral Rebouças, Alicia J. Kowaltowski,
Isolated kidney mitochondria swell when incubated in hyposmotic solutions containing K + salts in a manner inhibited by ATP, ADP, 5-hydroxydecanoate, and glibenclamide and stimulated by GTP and diazoxide. These results suggest the existence of ATP-sensitive K + channels in these mitochondria, similar to those previously described in heart, liver, and brain. Renal mitochondrial ATP-sensitive K + uptake rates are ∼140 nmol·min –1 ·mg protein –1 . This K + transport results in a slight increase in respiration and ...
Tópico(s): ATP Synthase and ATPases Research
2003 - American Physical Society | AJP Renal Physiology
... Google Scholar , 5 Oliveira-Filho J Silva SC Trabuco CC Pedreira BB Sousa EU Bacellar A Detrimental ...
Tópico(s): Cerebrovascular and Carotid Artery Diseases
2008 - Elsevier BV | The Lancet Neurology
Produção Nacional
Revisado por pares
Denise Pinheiro Soncini da Costa, Pedro Fernando Romanelli, Elizeu Trabuco,
No presente trabalho, estudou-se o processamento das vísceras de frango (Gallus domesticus) e das ratitas avestruz (Struthio camellus) e ema (Rhea americana), processadas da mesma forma, com o objetivo de elaborar farinhas. A qualidade e controle de produção dessas farinhas foram avaliados por meio de parâmetros tecnológicos exigidos pela legislação vigente. Basicamente, a matéria-prima foi cozida e esterilizada, filtrada em peneira (para a separação do óleo), moída, seca em estufa e analisada. Foram ...
Tópico(s): Sensory Analysis and Statistical Methods
2008 - Sociedade Brasileira de Ciência e Tecnologia de Alimentos | Food Science and Technology
Adil E. Bharucha, E manuel Trabuco,
Several organic and functional disorders of the urinary bladder, reproductive tract, anorectum, and the pelvic floor musculature cause pelvic pain. This article describes functional disorders in which chronic pelvic and anorectal pain cannot be explained by a structural or other specified pathology. Currently, these functional disorders are classified into urogynecologic conditions or cystitis and painful bladder syndrome, anorectal disorders, and the levator ani syndrome. Although nomenclature ...
Tópico(s): Gastrointestinal motility and disorders
2008 - Elsevier BV | Gastroenterology Clinics of North America
John Eargle, Alexis A. Black, Anurag Sethi, Leonardo G. Trabuco, Zaida Luthey‐Schulten,
Elongation factor Tu (EF-Tu) binds to all standard aminoacyl transfer RNAs (aa-tRNAs) and transports them to the ribosome while protecting the ester linkage between the tRNA and its cognate amino acid. We use molecular dynamics simulations to investigate the dynamics of the EF-Tu·guanosine 5′-triphosphate·aa-tRNACys complex and the roles played by Mg2+ ions and modified nucleosides on the free energy of protein·RNA binding. Individual modified nucleosides have pronounced effects on the structural ...
Tópico(s): Protein Structure and Dynamics
2008 - Elsevier BV | Journal of Molecular Biology
Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, Klaus Schulten,
Tópico(s): Force Microscopy Techniques and Applications
2008 - Elsevier BV | Structure
Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter V. Cornish, Taekjip Ha, Zaida Luthey‐Schulten, Klaus Schulten,
The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk–tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment ...
Tópico(s): RNA Research and Splicing
2010 - Elsevier BV | Journal of Molecular Biology
Malcolm A. Paine, Jeffrey R. Harnsberger, James L. Whiteside,
... functional outcomes.3Blandon R.E. Gebhart J.B. Trabuco E.C. Klingele C.J. Complications from vaginally ...
Tópico(s): Anorectal Disease Treatments and Outcomes
2010 - Elsevier BV | American Journal of Obstetrics and Gynecology
Leonardo G. Trabuco, Eduard Schreiner, James C. Gumbart, Jen Hsin, Elizabeth Villa, Klaus Schulten,
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing ...
Tópico(s): RNA and protein synthesis mechanisms
2010 - Elsevier BV | Journal of Structural Biology
Leonardo G. Trabuco, Christopher B. Harrison, Eduard Schreiner, Klaus Schulten,
Regulatory nascent chains interact with the ribosomal exit tunnel and modulate their own translation. To characterize nascent chain recognition by the ribosome at the atomic level, extensive molecular dynamics simulations of TnaC, the leader peptide of the tryptophanase operon, inside the exit tunnel were performed for an aggregate time of 2.1 μs. The simulations, complemented by quantum chemistry calculations, suggest that the critical TnaC residue W12 is recognized by the ribosome via a cation- ...
Tópico(s): RNA modifications and cancer
2010 - Elsevier BV | Structure
Anna Kicińska, Aleksandra Świda-Barteczka, Piotr Bednarczyk, Izabela Koszela-Piotrowska, Katarzyna Choma, Krzysztof Dołowy, Adam Szewczyk, Wiesława Jarmuszkiewicz,
... Scopus (89) Google Scholar), kidney (10Cancherini D.V. Trabuco L.G. Reboucas N.A. Kowaltowski A.J. ...
Tópico(s): Ion channel regulation and function
2007 - Elsevier BV | Journal of Biological Chemistry
Emanuel C. Trabuco, Mark E. Zobitz, Christopher J. Klingele, John B. Gebhart,
Objective The objective of the study was to determine whether the elicited histologic response to synthetic and xenograft materials affected the tensile strength of mesh-reinforced repairs in the rat ventral hernia model. Study Design Hernias were repaired with Gynemesh, Pelvicol, Pelvisoft, or Surgisis (representing incorporation, encapsulation, mixed incorporation and encapsulation, or resorption responses) and were compared with a suture-plicated control. Six animals per group were killed at 1 ...
Tópico(s): Intestinal and Peritoneal Adhesions
2007 - Elsevier BV | American Journal of Obstetrics and Gynecology
John E. Stone, J. C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten,
Abstract Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State‐of‐the‐art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In ...
Tópico(s): Enzyme Structure and Function
2007 - Wiley | Journal of Computational Chemistry