Proteins are the major actors in all cellular processes, from the generation of energy to the division of the cell. Knowing their structure is relevant for studying their function, their evolution and potentially for the design of drugs. Although our knowledge of protein sequences has grown consid...
In seeking an explanation for this phenomenon, it is observed that the privileged structure represents a generic substructure that matches commonly recurring conserved structural motifs in the target proteins, which may otherwise be quite diverse in sequence and function. Using sequence-handling tools, ...
This represents the first structure of a Rab protein bound to GDP. Sec4 in both states grossly resembles other G proteins bound to GDP and GppNHp. In Sec4-GppNHp, structural features common to active Rab proteins are observed. In Sec4-GDP, the switch I region is highly disordered and ...
where \(x\) represents the real-time position of atoms or residues, \(t\) represents time and \(\widetilde{x}\) represents the mean position over a period of time \({T}\). In addition to the experimental cryo-EM maps, RMSF-net incorporates fitted PDB models, which represent the mean...
Cell wall biosynthesis represents a valid target for antibacterial action but only a limited number of chemical structure classes selectively interact with... FW A,NH A,SG B,... - 《International Journal of Medical Microbiology》 被引量: 0发表: 2019年 Synthesis and Medicinal Chemistry of Muray...
The NMR spectrum of a two-domain protein (VcLysM1+2), in which VcLysM1 and VcLysM2 are linked in tandem through a flexible linker, suggested that the individual domains of VcLysM1+2 independently fold and do not interact with each other. ITC analysis of chitin-oligomer binding revealed ...
We propose a new method to train deep learning protein structure prediction models using molecular dynamics force fields to work toward these goals. Our custom PyTorch loss function, OpenMM-Loss, represents the potential energy of a predicted structure. OpenMM-Loss can be applied to any all-atom ...
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characteri...
This study represents a major expansion of the utility of coevolution by applying it to predict PPIs on a proteome-wide scale in E. coli and M. tuberculosis. Article CAS PubMed PubMed Central Google Scholar Stiffler, M. A. et al. Protein structure from experimental evolution. Cell Syst....
Allosteric control of protein function is defined as a change in one site–the allosteric site–that influences another site by exploiting the protein's flexibility (6). An allosteric disulfide bond thus represents the “allosteric site,” and the conformational change triggered by cleavage of the ...