A method is described for the selective isolation of peptides derived from the carboxyi-terminus of proteins. The method is of general applicability since it is independent of the primary structure of the protein in this region. The principle behind the isolation procedure is as follows: when an enzymic digestion is performed on a protein in which all free carboxyl groups have been modified by ...

The dead-end elimination theorem has proved to be a powerful method to reduce the theoretically accessible conformational space when modeling protein side chains by using a rotameric representation of possible conformations. In this work, theoretical details about variants to the original criterion are discussed. We also provide information on how the equations can be algorithmically implemente...

The sequences of different proteins evolve at different rates. The relative evolutionary rate (ER) of a single protein also changes over evolutionary time. The cause of this ER fluctuation remains uncertain, and study of this phenomenon may shed light on protein evolution more broadly. We have characterized ER fluctuation in mammals and Drosophila. We found little correlation between the amount...

Here we describe how the systematic redesign of a protein's hydrophobic core alters its structure and stability. We have repacked the hydrophobic core of the four-helix-bundle protein, Rop, with altered packing patterns and various side chain shapes and sizes. Several designs reproduce the structure and native-like properties of the wild-type, while increasing the thermal stability. Other desig...

Although the increasing number of available 3D proteins structures has made a wide variety of computational protein structure research possible, yet the success is still hindered by the high 3D computational complexity. Based on 3D information, several 1D protein structural alphabets have been developed, which can not only describe the global folding structure of a protein as a 1D sequence, but...

Two-dimensional protein crystallization on lipid monolayers at a quiescent air/water interface is now a well-established process, but it only operates under a very restricted set of conditions and on a very slow time scale. We have recently been able to significantly extend the conditions under which the proteins will crystallize as well as speed up the process by subjecting the interface to a ...

In this study we present two methods to predict the local quality of a protein model: ProQres and ProQprof. ProQres is based on structural features that can be calculated from a model, while ProQprof uses alignment information and can only be used if the model is created from an alignment. In addition, we also propose a simple approach based on local consensus, Pcons-local. We show that all the...