Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family
The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA du...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Š oltysov á , M. Sieglov á , I. F á bry, M. Brynda, J. Š kerlov á , J. Ř ez á č ov á , P. Tags: SorC/DeoR family protein – DNA complexes transcription repressors Bacillus subtilis deoxyribonucleoside regulator bsDeoR gene regulator bsCggR carbohydrate catabolism research papers Source Type: research
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa
The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063 – PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar a...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Fiorillo, A. Battistoni, A. Ammendola, S. Secli, V. Rinaldo, S. Cutruzzol à , F. Demitri, N. Ilari, A. Tags: PA4063 periplasmic zinc trafficking Pseudomonas aeruginosa ferredoxin-like fold research papers Source Type: research
Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II – transducer complex
Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complem...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Ryzhykau, Y.L. Vlasov, A.V. Orekhov, P.S. Rulev, M.I. Rogachev, A.V. Vlasova, A.D. Kazantsev, A.S. Verteletskiy, D.P. Skoi, V.V. Brennich, M.E. Pernot, P. Murugova, T.N. Gordeliy, V.I. Kuklin, A.I. Tags: membrane proteins two-component systems small-angle scattering ab initio modelling detergent belt oligomerization state sensory rhodopsin II – transducer complex Natronomonas pharaonis research papers Source Type: research
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBU...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Simpkin, A.J. Winn, M.D. Rigden, D.J. Keegan, R.M. Tags: MrBUMP molecular replacement cryo-EM GroEL research papers Source Type: research
Improving sampling of crystallographic disorder in ensemble refinement
Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformat...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Ploscariu, N. Burnley, T. Gros, P. Pearce, N.M. Tags: ensemble refinement structure refinement molecular dynamics disorder modelling research papers Source Type: research
