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Lukasz Jaroszewski

Publications and source records attributed to Lukasz Jaroszewski.

At least 37 records · Page 2Linked to original sources
PubMed2005

FFAS03: a server for profile--profile sequence alignments.

The FFAS03 server provides a web interface to the third generation of the profile-profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org.

Algorithms↗
PubMed2005

The structure of the neurotoxin-associated protein HA33/A from Clostridium botulinum suggests a reoccurring beta-trefoil fold in the progenitor toxin complex.

The hemagglutinating protein HA33 from Clostridium botulinum is associated with the large botulinum neurotoxin secreted complexes and is critical in toxin protection, internalization, and possibly activation. We report the crystal structure of serotype A HA33 (HA33/A) at 1.5 A resolution that contains a unique domain organization and a carbohydrate recognition site. In addition, sequence alignments of the other toxin complex components, including the neurotoxin BoNT/A, hemagglutinating protein HA17/A, and non-toxic non-hemagglutinating protein NTNHA/A, suggests that most of the toxin complex consists of a reoccurring beta-trefoil fold.

Amino Acid Sequence↗
PubMed2004

Crystal structure of the actin binding domain of the cyclase-associated protein.

Cyclase-associated protein (CAP or Srv2p) is a modular actin monomer binding protein that directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localization and the establishment of cell polarity. The crystal structure of the C-terminal dimerization and actin monomer binding domain (C-CAP) reveals a highly unusual dimer, composed of monomers possessing six coils of right-handed beta-helix flanked by antiparallel beta-strands. Domain swapping, involving the last two strands of each monomer, results in the formation of an extended dimer with an extensive interface. This structural and biochemical characterization provides new insights into the organization and potential mechanistic properties of the multiprotein assemblies that integrate dynamic actin processes into the overall physiology of the cell. An unanticipated finding is that the unique tertiary structure of the C-CAP monomer provides a structural model for a wide range of molecules, including RP2 and cofactor C, proteins involved in X-linked retinitis pigmentosa and tubulin maturation, respectively, as well as several uncharacterized proteins that exhibit very diverse domain organizations. Thus, the unusual right-handed beta-helical fold present in C-CAP appears to support a wide range of biological functions.

Actins↗