Showing papers in "Journal of Molecular Biology in 2004"

TL;DR: Improvements of the currently most popular method for prediction of classically secreted proteins, SignalP, which consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated.

TL;DR: Phobius, a combined transmembrane protein topology and signal peptide predictor based on a hidden Markov model, noted a drastic reduction of false classifications compared to TMHMM/SignalP, suggesting that Phobius is well suited for whole-genome annotation of signal peptides and trans Membrane regions.

TL;DR: An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment and represents a statistically significant improvement on the methods evaluated on the same targets at CASP.

TL;DR: Phylogenetic analysis of bacterial HDAC relatives suggests that all three HDAC classes precede the evolution of histone proteins and raises the possibility that the primary activity of some "histone deacetylase" enzymes is directed against non-histone substrates.

TL;DR: A new high-resolution structure is reported for bovine rhodopsin, the visual pigment in rod photoreceptor cells, and a theoretical study of the chromophore geometry has been carried out using combined quantum mechanics/force field molecular dynamics.

TL;DR: The complex history of the mir17 microRNA family appears to be closely linked to the early evolution of the vertebrate lineage.

TL;DR: Integrases of the serine family have been shown to work efficiently in mammalian cells, mediating efficient integration at introduced att sites or native sequences that have partial identity to att sites, which has applications in areas such as gene therapy, construction of transgenic organisms, and manipulation of cell lines.

TL;DR: It is proposed that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preference represent flexible linkers between them, which implies that Iups draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner.

TL;DR: A residue propensity score and a hydrophobic interaction score are developed to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and indexes are derived to evaluate the atomic packing, which is found to be less compact at non-specific than at specific interfaces.

TL;DR: This work transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges, and found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values.

TL;DR: The ability to predict the location of protein-protein interfaces has far reaching implications both towards the understanding of specificity and kinetics of binding, as well as in assisting in the analysis of the proteome.

TL;DR: Comparing the structures and locations of the 50S ribosomal proteins from H.marismortui and D.radiodurans revealed striking examples of molecular mimicry, illustrating that identical RNA structures can be stabilized by unrelated proteins.

TL;DR: The STAND class belongs to the additional strand, catalytic E division of P-loop NTPases together with the AAA+ ATPases, RecA/helicase-related ATPase, ABC-ATPases, and VirD4/PilT-like ATPases.

TL;DR: It is demonstrated that high-affinity human antibodies can be generated from libraries with completely synthetic CDRs displayed on a single scaffold.

TL;DR: This is the first case where a glycoform modification is shown to improve glycoprotein affinity for the receptors without carbohydrate-binding capacity, suggesting a novel glyco-engineering strategy to improve ligand-receptor binding.

TL;DR: An algorithm called the ICM-flexible receptor docking algorithm (IFREDA) is presented to account for protein flexibility in virtual screening and was used in eight protein kinase complexes and was able to find the correct ligand conformation and discriminate the correct conformations from the "misdocked" conformations solely on the basis of energy calculation.

TL;DR: Stability of amyloid fibrils, rather than being driven exclusively by the formation of H-bonded beta-sheet, is achieved, as in globular proteins, through a balance of stabilizing and destabilizing forces.

TL;DR: The analysis of the beta aggregation propensity of all-alpha, all-beta and mixed alpha/beta globular proteins as well as membrane-associated proteins is fairly similar, illustrating firstly that globular structures possess an appreciable amount of structural frustration and secondly that beta-aggregation is not determined by hydrophobicity and beta-sheet propensity alone.

TL;DR: The structure of human alpha-GAL brings Fabry disease into the realm of molecular diseases, where insights into the structural basis of the disease phenotypes might help guide the clinical treatment of patients.

TL;DR: The results suggest that two different molecular mechanisms of peptide-membrane assemblies are involved in Abeta's pathophysiology with the finely balanced type of Abeta-lipid interactions against release of Abetas from neuronal membranes being overcompensated by an AbETA- Membrane assembly which causes toxic beta-structured aggregates in AD.

TL;DR: In this paper, the authors use kinetic studies in conjunction with assessments of lipid binding and electron microscopy to investigate the interactions of IAPP with phospholipid bilayers and the morphological effects of membranes on IAPP fibers.

TL;DR: 3DCoffee, a novel method for combining protein sequences and structures in order to generate high-quality multiple sequence alignments, is developed and it is found that combining TCoffee with the threading program Fugue makes it possible to improve the accuracy of the HOMSTRAD dataset.

TL;DR: The conformation space of a 20 residue antiparallel beta-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways.

TL;DR: The patterns of hypermutation in antibodies and retroviruses owe much to the intrinsic sequence preferences of the AID/APOBEC family of DNA deaminases: analogous biases might also contribute to the spectra of cancer-associated mutation.

TL;DR: The results indicate that the formation of protein aggregates can be rationalised to a considerable extent in terms of simple physico-chemical parameters that describe the properties of polypeptide chains and their environment.

TL;DR: The results support the view that synthetic heavy chain diversity alone may be sufficient for the generation of high-affinity antibodies from phage-displayed libraries; thus, it may be possible to dispense with the light chain altogether, as is the case in natural camelid immunoglobulins.

TL;DR: Solid state NMR measurements suggest that the supramolecular organization of β-sheets in amyloid fibrils is determined by a sensitive balance of multiple side-chain–side-chain interactions.

TL;DR: A class of hybrid methods that combine evolutionary and entropic information from multiple sequence alignments are introduced that show the hybrids' greater robustness with respect to the input choice of sequences, as well as improved sensitivity and specificity of prediction.

TL;DR: A fungal big-Pi predictor has been developed for the assessment of query sequence concordance with fungi-specific recognition signal requirements, and recognizes that the human PLAP C terminus is not a target for the fungal transamidase complex.

TL;DR: Protein docking simulations and analysis of the interaction energy landscapes are applied to identify protein-protein interaction sites to guide the design of mutations on the surfaces of proteins, provide geometrical details of a possible interaction, and help to annotate protein surfaces in structural proteomics.