1.Origin of pK
Wu X;Lee J;Brooks BR J Phys Chem B. 2017 Apr 20;121(15):3318-3330. doi: 10.1021/acs.jpcb.6b08249. Epub 2016 Oct 18.
Protein internal ionizable groups can exhibit large shifts in pK;a; values. Although the environment and interaction changes have been extensively studied both experimentally and computationally, direct calculation of pK;a; values of these internal ionizable groups in explicit water is challenging due to energy barriers in solvent interaction and in conformational transition. The virtual mixture of multiple states (VMMS) method is a new approach designed to study chemical state equilibrium. This method constructs a virtual mixture of multiple chemical states in order to sample the conformational space of all states simultaneously and to avoid crossing energy barriers related to state transition. By applying VMMS to 25 variants of staphylococcal nuclease with lysine residues at internal positions, we obtained the pK;a; values of these lysine residues and investigated the physics underlining the pK;a; shifts. Our calculation results agree reasonably well with experimental measurements, validating the VMMS method for pK;a; calculation and providing molecular details of the protonation equilibrium for protein internal ionizable groups. Based on our analyses of protein conformation relaxation, lysine side chain flexibility, water penetration, and the microenvironment, we conclude that the hydrophobicity of the microenvironment around the lysine side chain (which affects water penetration differently for different protonation states) plays an important role in the pK;a; shifts.
2.Nitrogen regulator GlnR directly controls transcription of genes encoding lysine deacetylases in Actinobacteria.
Xu Y;You D;Ye BC Microbiology. 2017 Nov;163(11):1702-1710. doi: 10.1099/mic.0.000553. Epub 2017 Oct 23.
N-Lysine acetylation is a dynamic, reversible and regulatory post-translational modification (PTM) in prokaryotes, which integrates and coordinates metabolisms responding to environmental clues. However, the molecular mechanism underlying the signalling pathway from nutrient sensing to protein acetylation remains incompletely understood in micro-organisms. Here we found that global nitrogen regulator GlnR directly controls transcription of genes encoding lysine deacetylases in Actinobacteria. Electrophoretic mobility shift assays and real-time PCR (RT-PCR) in three Actinobacteria species (Saccharopolyspora erythraea, Streptomyces coelicolor and Mycobacterium smegmatis) revealed that GlnR regulator protein is able to interact with the promoter regions of these genes and activate their transcription. Furthermore, it was demonstrated that cellular acetylation status (acetylome) is modulated by extracellular nitrogen availability. Our results present an example of the novel complete signal transduction mechanism of regulating protein deacetylation through a nutrient-sensing pleiotropic regulator in response to nutrient availability.
3.Maleimide-functionalized closo-dodecaborate albumin conjugates (MID-AC): Unique ligation at cysteine and lysine residues enables efficient boron delivery to tumor for neutron capture therapy.
Kikuchi S;Kanoh D;Sato S;Sakurai Y;Suzuki M;Nakamura H J Control Release. 2016 Sep 10;237:160-7. doi: 10.1016/j.jconrel.2016.07.017. Epub 2016 Jul 12.
Maleimide-conjugating closo-dodecaborate sodium form 5c (MID) synthesized by the nucleophilic ring-opening reaction of closo-dodecaborate-1,4-dioxane complex 2 with tetrabutylammonium (TBA) azide was found to conjugate to free SH of cysteine and lysine residues in BSA under physiological conditions, forming highly boronated BSA that showed high and selective accumulation in tumor and significant tumor growth inhibition in colon 26 tumor-bearing mice subjected to thermal neutron irradiation.
