High-throughput screening for novel insecticidal proteins revealed evidence that the bacterium exchanges Domain III to enhance its insecticidal activity.

Approximately 3000 (Bt) isolates were screened to discover novel three-domain (3D) Cry proteins active against (corn earworm). From 400 active isolates found during the primary screening, Cry1Ac and Cry2A, which are known to be active against , were removed using multiplex-primer PCR and high-throughput column chromatography. This process reduced the number of active cultures to 48.

Engineering of Cry Proteins to Enhance the Activity against Western Corn Rootworm.

A novel Cry protein, Cry8Hb, active against (Western corn rootworm, WCRW) was discovered. Unexpectedly, the anti-rootworm activity of the Cry8Hb toxin was enhanced significantly by fusing maltose binding protein (MBP) to this Cry toxin. While the exact mechanism of the activity enhancement remains indefinite, it is probable that the enhancement is a result of increased solubility of the MBP-Cry8Hb fusion in the rootworm midgut.

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function.

Structural genomics of minimal organisms and protein fold space.

The initial aim of the Berkeley Structural Genomics Center is to obtain a near-complete structural complement of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter fewer than 700 genes.

Global mapping of the protein structure space and application in structure-based inference of protein function.

We have constructed a map of the "protein structure space" by using the pairwise structural similarity scores calculated for all nonredundant protein structures determined experimentally. As expected, proteins with similar structures clustered together in the map and the overall distribution of structural classes of this map followed closely that of the map of the "protein fold space" we have reported previously. Consequently, proteins sharing similar molecular functions also were found to colocalize in the protein structure space map, pointing toward a previously undescribed scheme for structure-based functional inference for remote homologues based on the proximity in the map of the protein structure space.

A global representation of the protein fold space.

One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the "protein structure universe." Here, we present a 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable.

Fold prediction of helical proteins using torsion angle dynamics and predicted restraints.

We describe a procedure for predicting the tertiary folds of alpha-helical proteins from their primary sequences. The central component of the procedure is a method for predicting interhelical contacts that is based on a helix-packing model. Instead of predicting the individual contacts, our method attempts to identify the entire patch of contacts that involve residues regularly spaced in the sequences.