Binding Function (binding + function)

Distribution by Scientific Domains


Selected Abstracts


Perfect coloring and linearly ,-bound P6 -free graphs

JOURNAL OF GRAPH THEORY, Issue 4 2007
S. A. Choudum
Abstract We derive decomposition theorems for P6, K1 + P4 -free graphs, P5, K1 + P4 -free graphs and P5, K1 + C4 -free graphs, and deduce linear ,-binding functions for these classes of graphs (here, Pn (Cn) denotes the path (cycle) on n vertices and K1 + G denotes the graph obtained from G by adding a new vertex and joining it with every vertex of G). Using the same techniques, we also obtain an optimal ,-binding function for P5, C4 -free graphs which is an improvement over that given in [J. L. Fouquet, V. Giakoumakis, F. Maire, and H. Thuillier, 1995, Discrete Math, 146, 33,44.]. © 2006 Wiley Periodicals, Inc. J Graph Theory 54: 293,306, 2007 [source]


The structure and evolution of the murine inhibitor of carbonic anhydrase: A member of the transferrin superfamily

PROTEIN SCIENCE, Issue 9 2010
Brian E. Eckenroth
Abstract The original signature of the transferrin (TF) family of proteins was the ability to bind ferric iron with high affinity in the cleft of each of two homologous lobes. However, in recent years, new family members that do not bind iron have been discovered. One new member is the inhibitor of carbonic anhydrase (ICA), which as its name indicates, binds to and strongly inhibits certain isoforms of carbonic anhydrase. Recently, mouse ICA has been expressed as a recombinant protein in a mammalian cell system. Here, we describe the 2.4 Å structure of mouse ICA from a pseudomerohedral twinned crystal. As predicted, the structure is bilobal, comprised of two ,-, domains per lobe typical of the other family members. As with all but insect TFs, the structure includes the unusual reverse ,-turn in each lobe. The structure is consistent with the fact that introduction of two mutations in the N-lobe of murine ICA (mICA) (W124R and S188Y) allowed it to bind iron with high affinity. Unexpectedly, both lobes of the mICA were found in the closed conformation usually associated with presence of iron in the cleft, and making the structure most similar to diferric pig TF. Two new ICA family members (guinea pig and horse) were identified from genomic sequences and used in evolutionary comparisons. Additionally, a comparison of selection pressure (dN/dS) on functional residues reveals some interesting insights into the evolution of the TF family including that the N-lobe of lactoferrin may be in the process of eliminating its iron binding function. [source]


Disulfide Bond Substitution by Directed Evolution in an Engineered Binding Protein

CHEMBIOCHEM, Issue 8 2009
Antoine Drevelle Dr.
Abstract Breaking ties: The antitumour protein, neocarzinostatin (NCS), is one of the few drug-carrying proteins used in human therapeutics. However, the presence of disulfide bonds limits this protein's potential development for many applications. This study describes a generic directed-evolution approach starting from NCS-3.24 (shown in the figure complexed with two testosterone molecules) to engineer stable disulfide-free NCS variants suitable for a variety of purposes, including intracellular applications. The chromoprotein neocarzinostatin (NCS) has been intensively studied for its antitumour properties. It has recently been redesigned as a potential drug-carrying scaffold. A potential limit of this protein scaffold, especially for intracellular applications, is the presence of disulfide bonds. The objective of this work was to create a disulfide-free NCS-derived scaffold. A generic targeted approach was developed by using directed evolution methods. As a starting point we used a previously engineered NCS variant in which a hapten binding site had been created. A library was then generated in which cysteine Cys88 and Cys93 and neighbouring residues were randomly substituted. Variants that preserved the hapten binding function were selected by phage display and further screened by colony filtration methods. Several sequences with common features emerged from this process. The corresponding proteins were expressed, purified and their biophysical properties characterised. How these selected sequences rescued folding ability and stability of the disulfide-free protein was carefully examined by using calorimetry and the results were interpreted with molecular simulation techniques. [source]


Perfect coloring and linearly ,-bound P6 -free graphs

JOURNAL OF GRAPH THEORY, Issue 4 2007
S. A. Choudum
Abstract We derive decomposition theorems for P6, K1 + P4 -free graphs, P5, K1 + P4 -free graphs and P5, K1 + C4 -free graphs, and deduce linear ,-binding functions for these classes of graphs (here, Pn (Cn) denotes the path (cycle) on n vertices and K1 + G denotes the graph obtained from G by adding a new vertex and joining it with every vertex of G). Using the same techniques, we also obtain an optimal ,-binding function for P5, C4 -free graphs which is an improvement over that given in [J. L. Fouquet, V. Giakoumakis, F. Maire, and H. Thuillier, 1995, Discrete Math, 146, 33,44.]. © 2006 Wiley Periodicals, Inc. J Graph Theory 54: 293,306, 2007 [source]