Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase.

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.

Role of multi-parametric magnetic resonance imaging fusion biopsy in active surveillance of prostate cancer: a systematic review.

Background: Our goal is to review current literature regarding the role of multi-parametric magnetic resonance imaging (mpMRI) in the active surveillance (AS) of prostate cancer (PCa) and identify trends in rate of reclassification of risk category, performance of fusion biopsy (FB) versus systematic biopsy (SB), and progression-free survival. Methods: We performed a comprehensive literature search in PubMed and identified 121 articles. A narrative summary was performed. Results: Thirty-two articles were chosen to be featured in this review. SB and FB are complementary in detecting higher-grade disease in follow-up. While FB was more likely than SB to detect clinically significant disease, FB missed 6.4-11% of clinically significant disease. Imaging factors that predicted upgrading include number of lesions on magnetic resonance imaging (MRI), lesion density, and MRI suspicion level. Conclusion: Incorporating mpMRI FB in conjunction with SB should be part of contemporary AS protocols. mpMRI should additionally be used routinely for follow-up; however, mpMRI is not currently sensitive enough in detecting disease progression to replace biopsy in the surveillance protocol.