A5017845863- Enzyme Production and Characterization
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Epigenetics and DNA Methylation
- Microbial Metabolic Engineering and Bioproduction
- Genomic variations and chromosomal abnormalities
- Fetal and Pediatric Neurological Disorders
- Synthetic Organic Chemistry Methods
- Microtubule and mitosis dynamics
- Congenital heart defects research
- Gene Regulatory Network Analysis
- Microbial Metabolites in Food Biotechnology
- Single-cell and spatial transcriptomics
- Enzyme Catalysis and Immobilization
- Computational Drug Discovery Methods
- DNA Repair Mechanisms
- Evolution and Genetic Dynamics
- Biofuel production and bioconversion
- Chemical Synthesis and Analysis
- Bioinformatics and Genomic Networks
- Protein Kinase Regulation and GTPase Signaling
- Chromatin Remodeling and Cancer
- Product Development and Customization
- Advanced Proteomics Techniques and Applications
- Genomics and Rare Diseases
German Cancer Research Center
2023-2024
Heidelberg University
2023-2024
European Molecular Biology Laboratory
2019
Howard Hughes Medical Institute
2003-2012
Boston Children's Hospital
2012
Broad Institute
2011
Beth Israel Deaconess Medical Center
2007-2009
Harvard University
2007-2009
University of Minnesota
2008
Iowa State University
2005-2008
We describe a new method of describing the pucker an N-member monocyclic ring using N − 3 parameters. To accomplish this, three atoms define reference plane, and remainder is decomposed into triangular flaps. The angle incidence for each flap upon plane then measured. combination these angles characteristic ring's pucker. This puckering coordinate system compared to existing reduced parameter systems rings cyclohexane molecule. show that this has same descriptive power previous while...
Abstract Summary: SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation synthetic genetic constructs. utilizes registry standard biological parts, database kinetic parameters, both graphical command-line interfaces to multiscale algorithms. Availability: available under GNU General Public License at http://synbioss.sourceforge.net. Contact: yiannis@cems.umn.edu Supplementary information: Tutorials documentation are web site:
Abstract Patients with distal deletions of chromosome 1q have a recognizable syndrome that includes microcephaly, hypoplasia or agenesis the corpus callosum, and psychomotor retardation. Although these symptoms been attributed to 1q42‐1q44, minimal chromosomal region involved has not identified. Using microsatellite single nucleotide polymorphism (SNP) markers, we mapped deleted regions in seven patients terminal define 2.0‐Mb microcephaly critical including 1q43‐1q44 boundary no more than...
To describe a novel form of pontocerebellar hypoplasia (PCH) and map its genetic locus.PCH is heterogeneous group disorders that are characterized by abnormally small cerebellum brainstem. Autosomal recessive inheritance has been implied in many cases, but no loci have mapped to date.The authors studied consanguineous family from the Sultanate Oman with three siblings PCH. The performed clinical studies linkage analysis this pedigree.The features affected children include developmental...
Abstract Glycoside hydrolase family 1 consists of β‐glucosidases, β‐galactosidases, 6‐phospho‐β‐galactosidases, myrosinases, and other enzymes having similar primary tertiary structures but diverse specificities. Among these enzymes, β‐glucosidases hydrolyze cellobiose to glucose, therefore they are key players in any cellulose glucose process. All members attack β‐glycosidic bonds between a pyranosyl glycon an aglycon, most have little specificity for the aglycon or bond configuration....
Abstract Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. While tens of thousands sites have been identified human cells to date, the extent and functional importance phosphoproteome remains largely unknown. Here, we analyzed 6,801 publicly available phospho-enriched mass spectrometry proteomics experiments, creating state-of-the-art containing 119,809 phosphosites. To prioritize sites, 59 features indicative...
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large data set has been assembled literature. The contains 262 unique protein-carbohydrate crystal structures for which experimental is known. Hydrogen atoms were added and training conformations generated with automated docking program AutoDock 3.06, resulting in 225,920 all-atom conformations. In all, 288 formulations 3.0 free energy...
Abstract Cellooligosaccharides were computationally docked using AutoDock into the active sites of glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly Trichoderma reesei ) cellobiohydrolase and Thermobifida fusca endoglucanase. Subsite –2 exerts greatest intermolecular energy in binding β‐glucosyl residues, with energies progressively decreasing to either side. Cumulative forces imparting processivity exerted by these two are significantly less than equivalent 7 studied...
Abstract Multiple sequence alignment separates members of glycoside hydrolase Family 6 into eight subfamilies: one mainly actinobacterial endoglucanases (EGs), ascomycotal EGs, chytridiomycotal EGs and cellobiohydrolases (CBHs), proteobacterial CBHs, two basidiomycotal CBHs. Each also has some proteins unknown function. extends to all the observation that lengths loops form active‐site tunnel in CBHs vary among subfamilies, along with loop conformations, determine enzyme © 2005 Wiley...
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ABSTRACT Combination treatment–the mainstay of cancer therapy–often fails because treatment interactions evoke complex resistance mechanisms that are hard to predict. Designing combination therapy prevent is especially challenging for rare cancers. Here, we introduce REsistance through COntext DRift (RECODR): a computational pipeline tracks how genes change their transcriptome context across development and drug conditions. By applying RECODR genetically modified mouse model choroid plexus...
Centrosomes are the major microtubule organizing centers of animal cells. Supernumerary centrosomes a common feature human tumors and associated with karyotype abnormalities aggressive disease, but whether they cause or consequence cancer remains controversial. Here, we analyzed consequences centrosome amplification by generating transgenic mice in which numbers can be increased overexpression structural protein STIL. We show that STIL induces aneuploidy, leading to senescence, apoptosis,...
Abstract Different programs and methods were employed to superimpose protein structures, using members of four very different families as test subjects, the results these efforts compared. Algorithms based on human identification key amino acid residues which base superpositions nearly always more successful than that used automated techniques identify residues. Among those automatically identifying residues, MASS could not all some families, but was efficient with other families. MODELLER,...
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