Rafael G. da Silva's research while affiliated with University of St Andrews and other places

... For A. baumannii ATPPRT, unique among other reported ATPPRTs due to its reaction proceeding via a rapid equilibrium random mechanism 30 , steady-state and pre-steady-state kinetics studies point to chemistry as the rate-limiting step for nonactivated HisG S (henceforth referred to as AbHisG S ). Allosteric activation by HisZ (AbHisZ) disproportionately enhances the chemical step, making product release rate-limiting for the hetero-octameric holoenzyme (henceforth referred to as AbATPPRT) 46 . With AbHisG S , the lack of a burst of product formation suggested no step after chemistry is rate-limiting for the reaction. ...

... [2] Hence, HsDNPH1 is a promising target for inhibition to potentiate PARPi action and to counter resistance to PARPi therapy resulting from 5hmdUMP depletion. [2] To help elucidate its catalytic mechanism and aid inhibitor design, HsDNPH1 structures have been solved in unliganded form and bound to the slow-reacting substrate 2'-deoxyuridine 5'-monophosphate (dUMP), [4] and in complex with an inhibitor. [5] HsDNPH1's specificity constant k cat /K M is 1,940-fold higher for 5hmdUMP than for dUMP at 37°C. ...

... This suggests that the landscape design, which includes soil and plant materials, creates microhabitats that support diverse microbial communities with both pathogenic and resistant strains. Phosphoribosyl-AMP cyclohydrolase, detected in MIRAI7, is crucial for nucleotide biosynthesis and microbial proliferation, indicating that soil microbes are well-equipped for growth and survival in these enriched environments [65] . ...

... chemistry 23 . Curiously, this approach has not yet been reported for enzymes modulated by allosteric effectors, even though protein motions at various timescales in these systems are proposed to mediate communication between allosteric effector binding and the active-site response 2,3,24,25 . ...

... 68 Moreover, the TrmK-encoding gene is expressed almost constitutively in cell models of infection, 71 during acute and chronic osteomyelitis, 72 and in the highly infectious and multidrug-resistant USA300 strain of S. aureus during infection. 73 In silico screening of compounds has identified a cryptic binding pocket in the vicinity of the SAMbinding site, 34 and SAM-adenine bisubstrate analogues have been proposed to serve as scaffolds to target TrmK, 74 laying foundations for future structure-based drug discovery. The challenge lies in specifically targeting TrmK, whose catalytic domain structure is shared by all class I MTases. ...

... ATPPRT activity is also dependent on KCl. [29][30][31][32][33] ATPPRT is the focus of protein engineering efforts to optimize histidine biocatalytic production 34 , and a promising target for novel antibiotic discovery against some pathogenic bacteria, including Acinetobacter baumannii and Mycobacterium tuberculosis 30,35,36 . Unlike hexameric long-form ATPPRTs, where one polypeptide chain harbours the catalytic and regulatory domains 37 , hetero-octameric short-form ATPPRTs constitute a more complex allosteric system made up of catalytic (HisG S ) and regulatory (HisZ) proteins where two dimers of HisG S flank a tetramer of HisZ 27,29,[38][39][40][41] . ...

... The most common functional unit of the SDRs appears to be the homotetramer, but homodimers are also found in the superfamily, and even a functional monomer. 21−24 In the case of PaHBDH, 20,25 it was found that the tetramer is present in solution and the crystal structure also showed the classical tetrameric arrangement with P-and Q-axis contacts 22,24 between monomers. Moreover, kinetic measurements showed that with 3-oxovalerate as the substrate, the chemistry involving concerted hydride and proton transfer is rate-limiting in the temperature range of 283−318 K. 19 Quantum mechanics/molecular mechanics (QM/MM) calculations on the 3-oxovalerate reaction further gave a detailed description of the reaction path and a good representation of the energetics. ...

... One promising candidate is AB680, a highly potent and selective CD73 inhibitor with improved metabolic stability [97]. In preclinical experiments it restores the adenosine-mediated inhibition of anti-tumour immune responses [102,103]. It is also the first small-molecule CD73 inhibitor tested in ongoing clinical trials. ...

... HisZ also contains the histidine binding site and allosterically inhibits ATPPRT catalysis in the presence of histidine, playing a dual regulatory role 40,43 . Owing to their architectural versatility alongside their biomedical and biotechnological importance, ATPPRTs have been model systems to interrogate allostery, dynamics, and catalysis 2,8,30,32,38,40,44,45 . ...

... This analysis allows the determina7on of the thermodynamic proper7es of the system, namely the enthalpy of ac7va7on ΔΗ ‡ and the entropy of ac7va7on ΔS ‡ . Eyring plots follow the ln(kcat/T) as a func7on of temperature, which usually corresponds to a straight line 35 . The slope of this line is propor7onal to the enthalpy of ac7va7on ΔΗ ‡ , and the intercept is related . ...