Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface....

HBx is a hepatitis B virus protein that is required for viral infectivity and replication. Anti-apoptotic Bcl-2 family members are thought to be among the important host targets of HBx. However, the structure and function of HBx are poorly understood and the molecular mechanism of HBx-induced carcinogenesis remains unknown. In this study, we report biochemical and structural characterization of...

Plasmodium falciparum (Pf) employs a crucial PfHRPII catalyzed reaction that converts toxic heme into hemozoin. Understanding heme polymerization mechanism is the first step for rational design of new drugs, targeting this pathway. Heme binding and hemozoin formation have been ascribed to PfHRPII aspartate carboxylate-heme metal ionic interactions. To investigate, if this ionic interaction is i...

Autosomal dominant polycystic kidney disease (ADPKD) affects over 1:1000 of the worldwide population and is caused by mutations in two genes, PKD1 and PKD2. PKD2 encodes a 968-amino acid membrane spanning protein, Polycystin-2 (PC-2), which is a member of the TRP ion channel family. The C-terminal cytoplasmic tail contains an EF-hand motif followed by a short coiled-coil domain. We have determi...

The characteristics of manganese and iron binding to human apotransferrin (apo-tf) have been investigated and compared in this study. Both metal ions were taken up by human apo-tf and formed complexes, with the maximum absorbances observed at 410 and 340 nm for manganese-transferrin (Mn-tf) and 465 nm for iron-transferrin (Fe-tf). Addition of manganese (1.5 µg/ml) to the reaction mixture contai...

RNase H is a prototypical example for two-metal-ion catalysis in enzymes. An activity cleaving the ribonucleic acid (RNA) backbone of DNA/RNA hybrid present not only important drug targets, such as HIV-1 reverse transcriptase, but also many other nucleases, Homo sapiens (Hs) and Escherichia coli (Ec) or, notably, enzymes that are part CRISPR gene editing molecular machinery. Despite its importa...

There is considerable interest in understanding how multiple binding events can be mediated through a single protein interface. Here, a synthetic library approach was developed to generate a novel dual-specific antibody. Using a combinatorial histidine-scanning phage display library, potential metal binding sites were introduced throughout an anti-RNase A antibody interface. Stepwise selection ...

Exposure of a Au(111) surface to ethynylbenzene in solution leads to the formation of a bound monolayer. A chemisorption process occurs to give a stable layer consisting of oxygen-containing hydrocarbon species. Ethynylbenzene itself does not oxidize under the deposition conditions indicating that the gold surface facilitates the oxidation process. Calculations show that ethynylbenzene and its ...

The bacterial heat shock protein Hsp33 is a redox-regulated chaperone activated by oxidative stress. In response to oxidation, four cysteines within a Zn2+ binding C-terminal domain form two disulfide bonds with concomitant release of the metal. This leads to the formation of the biologically active Hsp33 dimer. The crystal structure of the N-terminal domain of the E. coli protein has been repo...

Information about the binding preferences of many transcription factors is known and characterized by a sequence binding motif. However, determining regions of the genome in which a transcription factor binds based on its motif is a challenging problem, particularly in species with large genomes, since there are often many sequences containing matches to the motif but are not bound. Several rul...