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Streptococcus
Published in Dongyou Liu, Laboratory Models for Foodborne Infections, 2017
Multilocus sequence typing (MLST) targeting seven core housekeeping genes (glucose kinase, gki; glutamine transporter protein, gtr; glutamate racemase, murI; DNA mismatch repair protein, mutS; transketolase, recP; xanthine phosphoribosyl transferase, xpt; and acetyl coenzyme A acetyltransferase, yqiL) offers another valuable approach for determination of S. pyogenes strains, with clones of S. pyogenes being defined by their sequence type (ST) (http://pubmlst.org/spyogenes/). Interestingly, while most emm pattern A–C strains correspond to same clone (ST) or clonal complex, emm patterns D and E strains correlate with distant ST [4].
The prediction of protein–ligand unbinding for modern drug discovery
Published in Expert Opinion on Drug Discovery, 2022
Qianqian Zhang, Nannan Zhao, Xiaoxiao Meng, Fansen Yu, Xiaojun Yao, Huanxiang Liu
In SMD simulation, Jarzynski’s equality can be applied to predict the relative binding free energy and rank ligands accurately. In addition, the rupture force of the pulling of ligands from the pocket in SMD simulation can also be used to characterize the binding affinity of ligands. For example, in a previous study [134], the SMD method was utilized to estimate the binding affinity of ligands on FKBP, trypsin and cyclin-dependent kinase 2 (CDK2) in accordance with the calculated binding free energies by using the second-order cumulant expansion of Jarzynski’s equality. Mai et al. [135] ranked the binding affinity of 32 ligands for the glycoprotein neuraminidase from swine influenza virus on the basis of the rupture force of the pulling of the ligands out of the binding pocket in the SMD simulation. They also demonstrated that compared with the MM–PBSA method, SMD can achieve the same accuracy but is more efficient. The self-adaptive SMD developed by Gu et al. can find the optimal dissociation path of the ligand and obtain a lower rupture force and energy barrier than conventional SMD and may thus identify active ligands [136] with increased accuracy. When combined with molecular docking or VS, SMD can enable the comparison of the binding affinity of candidate compounds with targets [137] and distinguish active and inactive enzyme inhibitors [138,139]. The SMD-based docking method is highly promising. This method has been conducted to screen the potential inhibitors of the cancer target lysine specific demethylase 1 from natural products [140]. A hybrid ensemble docking and SMD scheme was applied, and 17 validated ligands of glutamate racemase were screened out by ranking the binding affinity of the ligands [141].
Regulatory mechanisms of exopolysaccharide synthesis and biofilm formation in Streptococcus mutans
Published in Journal of Oral Microbiology, 2023
Ting Zheng, Meiling Jing, Tao Gong, Jiangchuan Yan, Xiaowan Wang, Mai Xu, Xuedong Zhou, Jumei Zeng, Yuqing Li
Recombinase A (RecA) is related to the SOS-response in S. mutans. The RecA-deficient mutant strain possesses a lower acid tolerance and produces a biofilm with a lower density than the wild type [107]. Glutamate racemase (MurI) is an essential enzyme for the biosynthesis of peptidoglycan. murI deficiency in S. mutans weakens the ability to form the biofilm and virulence factors. The expression of comE, comD, gtfB and gtfC, genes related to biofilm formation are down-regulated 8-, 43-, 85- and 298-fold, as revealed by qRT-PCR [108].