Staphylococcal enterotoxin A is well known as a superantigen and able to be used for cancer immunotherapy. In this study, recombinant Staphylococcal enterotoxin A was genetically conjugated to epidermal growth factor to produce a chimeric protein recombinant Staphylococcal enterotoxin A-epidermal growth factor expressed in Escherichia coli. The recombinant Staphylococcal enterotoxin A-epidermal...

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic reso...

Here, the proposal is investigated that protein tertiary structure prediction methods and threading methods in particular might be applied to the problem of solving a protein structure by X-ray crystallography, thus reducing the need for the more traditional experimental intensity methods of data phasing, such as heavy-metal isomorphous replacement and anomalous scattering methods, and without ...

The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by co...

Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in direction...

Protein unfolding occurs when the balance of forces between the protein's interaction with itself and the protein's interaction with its environment is disrupted. The disruption of this balance of forces may be as simple as a perturbance of the normal water structure around the protein. A decrease in the normal water-water interaction will result in an increase in the relative interaction of wa...

T he article by Liwo et al. in this issue of PNAS (1) on ab initio simulations of the folding pathway of a number of representative small proteins marks a renaissance in efforts to simulate the mechanism of protein folding without prior knowledge of the native structure. While there has been recent progress in predicting the three-dimensional native structure of a protein (2, 3), the most succe...

When a protein's function cannot be experimentally determined, it can often be inferred from sequence similarity. Should this process fail, analysis of the protein structure can provide functional clues or confirm tentative functional assignments inferred from the sequence. Many structure-based approaches exist (e.g. fold similarity, three-dimensional templates), but as no single method can be ...

Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different...