27 research outputs found
VENN, a tool for titrating sequence conservation onto protein structures
Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/
Ga+, In+ and Tl+ Impurities in Alkali Halide Crystals: Distortion Trends
A computational study of the doping of alkali halide crystals (AX: A = Na, K;
X = Cl, Br) by ns2 cations (Ga+, In+ and Tl+) is presented. Active clusters of
increasing size (from 33 to 177 ions) are considered in order to deal with the
large scale distortions induced by the substitutional impurities. Those
clusters are embedded in accurate quantum environments representing the
surrounding crystalline lattice. The convergence of the distortion results with
the size of the active cluster is analyced for some selected impurity systems.
The most important conclusion from this study is that distortions along the
(100) and (110) crystallographic directions are not independent. Once a
reliable cluster model is found, distortion trends as a function of impurity,
alkali cation and halide anion are identified and discussed. These trends may
be useful when analycing other cation impurities in similar host lattices.Comment: LaTeX file. 7 pages and 2 pictures. Accepted for publication in J.
Chem. Phy
Lattice Distortions Around a Tl+ Impurity in NaI:Tl+ and CsI:Tl+ Scintillators. An Ab Initio Study Involving Large Active Clusters
Ab initio Perturbed Ion cluster-in-the-lattice calculations of the impurity
centers NaI:Tl+ and CsI:Tl+ are pressented. We study several active clusters of
increasing complexity and show that the lattice relaxation around the Tl+
impurity implies the concerted movement of several shells of neighbors. The
results also reveal the importance of considering a set of ions that can
respond to the geometrical displacements of the inner shells by adapting
selfconsistently their wave functions. Comparison with other calculations
involving comparatively small active clusters serves to assert the significance
of our conclusions. Contact with experiment is made by calculating absorption
energies. These are in excellent agreement with the experimental data for the
most realistic active clusters considered.Comment: 7 pages plus 6 postscript figures, LaTeX. Submmited to Phys, Rev.
Minimotif miner 2nd release: a database and web system for motif search
Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries. We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions. The web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis. A sample analysis of prion shows how MnM 2 can be used. Weblink: http://mnm.engr.uconn.edu, weblink for version 1 is http://sms.engr.uconn.edu
Ab Initio Calculation of the Lattice Distortions induced by Substitutional Ag- and Cu- Impurities in Alkali Halide Crystals
An ab initio study of the doping of alkali halide crystals (AX: A = Li, Na,
K, Rb; X = F, Cl, Br, I) by ns2 anions (Ag- and Cu-) is presented. Large active
clusters with 179 ions embedded in the surrounding crystalline lattice are
considered in order to describe properly the lattice relaxation induced by the
introduction of substitutional impurities. In all the cases considered, the
lattice distortions imply the concerted movement of several shells of
neighbors. The shell displacements are smaller for the smaller anion Cu-, as
expected. The study of the family of rock-salt alkali halides (excepting CsF)
allows us to extract trends that might be useful at a predictive level in the
study of other impurity systems. Those trends are presented and discussed in
terms of simple geometric arguments.Comment: LaTeX file. 8 pages, 3 EPS pictures. New version contains
calculations of the energy of formation of the defects with model clusters of
different size
Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function. © 2012 Sargeant et al
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300 000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease