A5089062316- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Cell Adhesion Molecules Research
- Computational Drug Discovery Methods
- Photoreceptor and optogenetics research
- Receptor Mechanisms and Signaling
- Glycosylation and Glycoproteins Research
- Biotin and Related Studies
- Bacterial Genetics and Biotechnology
- Monoclonal and Polyclonal Antibodies Research
- Neuroscience and Neuropharmacology Research
- Cell Image Analysis Techniques
- Hemoglobin structure and function
- Cellular transport and secretion
- HER2/EGFR in Cancer Research
- Photosynthetic Processes and Mechanisms
- Machine Learning in Bioinformatics
- Lung Cancer Treatments and Mutations
- Click Chemistry and Applications
- Protist diversity and phylogeny
- Gene expression and cancer classification
- Lipid Membrane Structure and Behavior
- Biochemical and Structural Characterization
- Genomics and Phylogenetic Studies
Åbo Akademi University
2016-2025
University of Turku
1997-2023
Loma Linda University
2005-2021
Chelsea and Westminster Hospital NHS Foundation Trust
2020
U.S. Army Center for Health Promotion and Preventive Medicine
2019
University of Eastern Finland
2008
Turku Centre for Computer Science
2007
Hebei Normal University
2006
Kōchi University
2006
Chinese Academy of Sciences
2006
A computer analysis of the amino acid sequences from putative gene products retroviral pol genes has revealed a 150-residue segment that is homologous with ribonuclease H Escherichia coli. The occurs at carboxyl terminus region assigned to 90-kDa reverse transcriptase polypeptide. In contrast, section nearer this sequence can be aligned nonretroviral polymerases. order activities in thus: polymerase-ribonuclease-endonuclease. On another note, all endonuclease contain consensus zinc-binding...
Retinal transducin, a guanine nucleotide regulatory protein (referred to as G protein) that activates cGMP phosphodiesterase in photoreceptor cells, is comprised of three subunits. We have identified and analyzed cDNA clones the bovine transducin beta subunit may be highly conserved or identical other proteins. From sequence entire coding region, primary structure 340-amino acid was deduced. The encoded has Mr 37,375 repetitive homologous segments arranged tandem. Furthermore, significant...
The task of generating a nonredundant set low-energy conformations for small molecules is fundamental importance many molecular modeling and drug-design methodologies. Several approaches to conformer generation have been published. Exhaustive searches suffer from the exponential growth search space with increasing degrees conformational freedom (number rotatable bonds). Stochastic algorithms do not as much increase provide good coverage energy minima. Here, use multiobjective genetic...
Abstract MOTIVATION: JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed display 3D information in alignment and help understand the conservation of amino acids their specific local environments. RESULTS:: The representation now constitutes an essential part two databases structure alignments: HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/homstrad ) CAMPASS (http://www-cryst.bioc.cam.ac. uk/campass). has also been...
Abstract The local environment of an amino acid in a folded protein determines the acceptability mutations at that position. In order to characterize and quantify these structural constraints, we have made comparative analysis families homologous proteins. Residues each structure are classified according type, secondary structure, accessibility side chain, existence hydrogen bonds from chain. Analysis pattern observed substitutions as function shows there distinct patterns, especially for...
We identified a protein, Aer, as signal transducer that senses intracellular energy levels rather than the external environment and transduces signals for aerotaxis (taxis to oxygen) other energy-dependent behavioral responses in Escherichia coli . Domains Aer are similar signaling domain chemotaxis receptors putative oxygen-sensing of some transcriptional activators. A FAD-binding site N-terminal shares consensus sequence with NifL, Bat, Wc-1 signal-transducing proteins regulate gene...
Four integrins, namely α1β1, α2β1, α10β1, and α11β1, form a special subclass of cell adhesion receptors. They are all collagen receptors, they recognize their ligands with an inserted domain (I domain) in α subunit. We have produced the human integrin α10I as recombinant protein to reveal its ligand binding specificity. In general, did types I–VI laminin-1 Mg2+-dependent manner, whereas tenascin was only slightly better than albumin. When tested together α1I α2I domains, three I domains...
The pattern of residue substitution in divergently evolving families globular proteins is highly variable. At each position a fold there are constraints on the identities amino acids from both three-dimensional structure and function protein. To characterize quantify structural constraints, we have made comparative analysis homologous proteins. Residues classified according to acid type, secondary structure, accessibility sidechain, existence hydrogen bonds sidechain other sidechains or...
ShaEP is a tool for rigid-body superimposition and similarity evaluation of ligand-sized molecules. Molecular overlay methods traditionally work on either substructures, molecular surfaces or interaction fields, atom-centered Gaussian functions representing the volume. While substructure searches are unlikely to reveal hits that chemically different from template structure, other capable "scaffold hopping". Methods match characteristic points in fields can find alignments situations where...
The inferred amino acid sequences of 10 specific gene products from nine retroviruses were aligned by computer, all evolutionary distances between them calculated, and trees constructed. Not unexpectedly, the various are changing at different rates, reverse transcriptase being least envelope proteins most one retrovirus to another. For part, based on retroviral enzyme congruent, indicating that extensive genetic recombination has not been a major factor in evolution central part genome. In...
The integrins alpha(1)beta(1), alpha(2)beta(1), alpha(10)beta(1), and alpha(11)beta(1) are referred to as a collagen receptor subgroup of the integrin family. Recently, both alpha(1)beta(1) alpha(2)beta(1) have been shown recognize triple-helical GFOGER (where single letter amino acid nomenclature is used, O = hydroxyproline) or GFOGER-like motifs found in collagens, despite their distinct binding specificity for various subtypes. In present study we investigated mechanism whereby latest...
The caspase-8 inhibitor c-FLIP exists as two splice variants, c-FLIPL and c-FLIPS, with distinct roles in death receptor signaling. mechanisms determining their turnover have not been established. We found that differentiating K562 erythroleukemia cells both isoforms were inducibly degraded by the proteasome, but c-FLIPS was more prone to ubiquitylation had a considerably shorter half-life. Analysis of c-FLIPS-specific revealed lysines, 192 195, C-terminal effector domains, principal...
Abstract Adenosine triphosphate (ATP) plays an essential role in energy transfer within the cell. In form of NAD, adenine participates multiple redox reactions. Phosphorylation and ATP‐hydrolysis reactions have key roles signal transduction regulation many proteins, especially enzymes. each cell, proteins with different functions use its derivatives as ligands; adenine, course, is present DNA RNA. We show that binding motif, which differs according to backbone chain direction a loop binds...
The microaerophilic nitrogen-fixing bacterium Azospirillum brasilense formed a sharply defined band in spatial gradient of oxygen. As result aerotaxis, the bacteria were attracted to specific low concentration oxygen (3 5 microM). Bacteria swimming away from aerotactic repelled by higher or lower that they encountered and returned band. This behavior was confirmed using temporal gradients cellular energy level A. brasilense, monitored measuring proton motive force, maximal at 3 microM force...