A5069990985- Protein Structure and Dynamics
- Enzyme Structure and Function
- Metal complexes synthesis and properties
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Lanthanide and Transition Metal Complexes
- Mass Spectrometry Techniques and Applications
- Bioactive Compounds and Antitumor Agents
- Magnetism in coordination complexes
- Inorganic and Organometallic Chemistry
- Synthesis and Reactions of Organic Compounds
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Synthesis of Organic Compounds
- Chemical Synthesis and Analysis
- Crystallography and molecular interactions
- Asymmetric Synthesis and Catalysis
- Crystallization and Solubility Studies
- Synthesis and Characterization of Heterocyclic Compounds
- Metal-Catalyzed Oxygenation Mechanisms
- Crystal structures of chemical compounds
- Synthesis and biological activity
- Genetics, Bioinformatics, and Biomedical Research
- Ion channel regulation and function
- Oxidative Organic Chemistry Reactions
University of Pavia
2015-2024
Max Perutz Labs
2011-2024
University of Vienna
2013-2024
Vienna Biocenter
2008-2021
In-Q-Tel
2013
International Centre for Genetic Engineering and Biotechnology
2000-2005
AREA Science Park
2003-2005
Istituto Nazionale per la Fisica della Materia
2004
National Center for Genetic Engineering and Biotechnology
2003
University of Oxford
2003
Abstract The degree of similarity two protein three‐dimensional structures is usually measured with the root‐mean‐square distance between equivalent atom pairs. Such a measure depends on dimension proteins, that is, number present communication presents simple procedure to make distances pairs independent their dimensions. This normalization may be useful in evolutionary and fold classification studies as well comparisons different structural models.
The ubiquitous redox cofactors nicotinamide adenine dinucleotides [NAD and NADP] are very similar molecules, despite their participation in substantially different biochemical processes. NADP differs from NAD only the presence of an additional phosphate group esterified to 2′-hydroxyl ribose at end yet is confined with few exceptions reactions reductive biosynthesis, whereas used almost exclusively oxidative degradations. discrimination between therefore impressive example power molecular...
Protein crystal structures are potentially over-interpreted since they routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some their atoms, undetected in electron density maps, allowed to reach extremely large B-factors, even above 100 square Angstroms, and final positions purely speculative not based experimental evidence. A strategy define B-factors limits is described here, analysis protein deposited Data Bank prior 2008, when tendency allow...
Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms sticky sites in biomolecules is underappreciated, and few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures Protein Data Bank (PDB) containing 18 266 selenomethionines found that Se···O commonplace. These findings may help future design functional peptides contribute to understanding Se nature.
In the past 2 decades, structural biology has transformed from a single technique used on proteins to multimodal integrative approach. Recently, protein structure prediction algorithms have opened new avenues address challenging biological questions.
The number of water molecules which are expected to be experimentally located by protein crystallography was determined multiple regression analysis on a test set 873 known crystal structures at room temperature and another 33 low temperature. dependence the included in models as function significant regressors, such resolution, fraction volume occupied solvent, residues asymmetric unit, apolar surface or secondary structure, has been studied. crystallographic depends primarily resolution...
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of and NMR results files Bank, order to find out which extent these information can be aggregated bioinformatics. A non-redundant data set containing 109 - X-ray structure pairs nearly identical proteins was derived from Bank. series comparisons...
Autosomal recessive mutations in the cytolinker protein plectin account for multisystem disorders epidermolysis bullosa simplex (EBS) associated with muscular dystrophy (EBS-MD), pyloric atresia (EBS-PA), and congenital myasthenia (EBS-CMS). In contrast, a dominant missense mutation leads to disease EBS-Ogna, manifesting exclusively as skin fragility. We have exploited this trait study molecular basis of hemidesmosome failure EBS-Ogna reveal contribution homeostasis. generated knock-in mice...
A large fraction of the protein crystal structures deposited in Protein Data Bank are incomplete, since position one or more residues is not reported, despite these part material that was analyzed. This may bias use by molecular biologists. Here we observe majority strings missing. Polar incline to occur missing together with glycine, while apolar and aromatic tend avoid them. Particularly flexible residues, as shown their extremely high B-factors, exposure solvent secondary structures,...
Abstract Motivation: A simple and fast algorithm is described that calculates a measure of protrusion (cx) for atoms in protein structures, directly useable with the common molecular graphics programs. Results: sphere predetermined radius centered around each non-hydrogen atom, volume occupied by free within (internal external volumes, respectively) are calculated. Atoms protruding regions have high ratio between internal volume. The program reads PDB file, writes output same format, cx...
The most popular estimator of structural similarity is the root-mean-square distance (r.m.s.d.) between equivalent atoms, computed after optimal superposition two structures that are compared. It known r.m.s.d. values do not depend only on conformational differences but also other features, for example dimensions An open question how they might accuracy experimentally determined protein structures. Given crystal generally estimated through crystallographic resolution, it important to know...
The copper(I) and copper(II) complexes with the nitrogen donor ligands bis[(1-methylbenzimidazol-2-yl)methyl]amine (1-BB), bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB), N-acetyl-2-BB (AcBB), tris[2-(1-methylbenzimidazol-2-yl)ethyl]nitromethane (TB) have been studied as models for copper nitrite reductase. form adducts azide that isolated characterized. Cu(II)−(1-BB) Cu(II)−AcBB are basically four-coordinated weak axial interaction by solvent or counterion molecules, whereas...
The sodC-encoded Mycobacterium tuberculosis superoxide dismutase (SOD) shows high sequence homology to other members of the copper/zinc-containing SOD family. Its three-dimensional structure is reported here, solved by x-ray crystallography at 1.63-Å resolution. Metal analyses recombinant protein indicate that native form enzyme lacks zinc ion, which has a very important structural and functional role in all known enzymes this class. absence within active site due significant rearrangements...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHemocyanin and tyrosinase models. Synthesis, azide binding, electrochemistry of dinuclear copper(II) complexes with poly(benzimidazole) ligands modeling the met forms proteinsLuigi Casella, Oliviero Carugo, Michele Gullotti, Stefano Garofani, Piero ZanelloCite this: Inorg. Chem. 1993, 32, 10, 2056–2067Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1...
There is indirect evidence that the amino acid composition of proteins depends on their dimension. The a nonredundant set about 550,000 was determined and it observed that, in range 50-200 residues, percentage occurrence most residue types significantly protein This result should prove useful analyzing sequences genomics.
Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of coordination spheres. The analysis non-redundant set (pairwise sequence identity?<?30%) 1739 high resolution (<2 Å) crystal structures that contain at least one shows first spheres chlorides essentially constituted by hydrogen bond donors. Amongst side-chains positively charged, arginine interacts much more frequently than...