The discovery of novel noncoding RNAs in 50 bacterial genomes.

Structured noncoding RNAs (ncRNAs) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. Few ncRNA classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. We previously developed a computational pipeline that enables the near-comprehensive identification of structured ncRNAs expressed from individual bacterial genomes.

A conserved uORF in the mRNA of species regulates operon expression.

Computational methods can be used to identify putative structured noncoding RNAs (ncRNAs) in bacteria, which can then be validated using various biochemical and genetic approaches. In a search for ncRNAs in , we observed a conserved region called the -II motif located upstream of the gene that is also present in other members of this genus. This gene codes for an enzyme involved in the production of branched-chain amino acids (BCAAs).

On the evolution of protein-adenine binding.

Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction.

ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.

Patterns observed by examining the evolutionary relationships among proteins of common origin can reveal the structural and functional importance of specific residue positions. In particular, amino acids that are highly conserved (i.e.

Navigating Among Known Structures in Protein Space.

Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints.

Structural and Dynamics Characterization of the MerR Family Metalloregulator CueR in its Repression and Activation States.

CueR (Cu export regulator) is a metalloregulator protein that "senses" Cu(I) ions with very high affinity, thereby stimulating DNA binding and the transcription activation of two other metalloregulator proteins. The crystal structures of CueR when unbound or bound to DNA and a metal ion are very similar to each other, and the role of CueR and Cu(I) in initiating the transcription has not been fully understood yet. Using double electron-electron resonance (DEER) measurements and structure modeling, we investigate the conformational changes that CueR undergoes upon binding Cu(I) and DNA in solution.

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure.

Protein function involves conformational changes, but often, for a given protein, only some of these conformations are known. The missing conformations could be predicted using the wealth of data in the PDB. Most PDB proteins have multiple structures, and proteins sharing one similar conformation often share others as well.