Pattersondemir6709

Cryptochrome proteins are thought to be involved in light-sensitive magnetoreception in migratory birds triggered by flavin adenine dinucleotide (FAD) light absorption. A recent study, however, calls into question the ability of vertebrate cryptochrome proteins to bind FAD, rendering them unlikely to function as magnetoreceptive proteins. In this Letter, we investigate the structural changes occurring in Drosophila melanogaster cryptochrome, upon key amino acid mutations, which reduce FAD binding. Through computational analysis we have now suggested why some mutations do not preclude FAD binding in all vertebrate cryptochrome proteins.Studies of radioactive isotopes at the liquid-solid or gas-solid interface are enabling a detailed mechanistic understanding the effects of radioactive decay on physical, biological, and chemical systems. In recent years, there has been a burgeoning interest in using radioactive isotopes for both imaging and therapeutic purposes by attaching them to the surface of colloidal nanoparticles. By merging the field of nanomedicine with the more mature field of internal radiation therapy, researchers are discovering new ways to diagnose and treat cancer. In this perspective, we discuss state-of-the-art radioactive thin films as applied to both well-defined surfaces and more complex nanoparticles. We highlight the design considerations that are unique to radioactive films, which originate from the damaging and potentially self-destructive emissions produced during radioactive decay and highlight future opportunities in the largely underexplored area between radioisotope chemistry and nanoscience.Phytochromes are photoreceptors that upon light absorption initiate a physiological reaction cascade. Starting point is the photoisomerisation of the tetrapyrrole cofactor in the parent Pr state, followed by thermal relaxation steps culminating in activation of the physiological signal. Here we have employed resonance Raman (RR) spectroscopy to study the chromophore structure in the primary photoproduct Lumi-R, trapped between 130 and 200 K. The investigations covered phytochromes from plants (phyA) and prokaryotes (Cph1, Agp1, CphB, and RpBphP2) including phytochromobilin (PB), phycocyanobilin (PCB), and biliverdin (BV). In PB- and PCB-binding phyA and Cph1, two Lumi-R states (Lumi-R1, Lumi-R2) were identified and discussed in terms of sequential and parallel reaction models. Darolutamide In Lumi-R1 the chromophore structural changes are restricted to the C-D methine bridge isomerization site but extended throughout the chromophore in Lumi-R2. Formation and decay kinetics as well as photochemical activity depend on the specific protein-chromophore interactions and thus account for the different distribution between Lumi-R1 and Lumi-R2 in the photostationary mixtures of the various PB(PCB)-binding phytochromes. For BV-binding bacteriophytochromes only a single Lumi-R(BV) state was found. In this state, which is similar for Agp1, CphB, and RpBphP2, the chromophore structural changes comprise major torsions of the C-D methine bridge but also perturbations at the A-B methine bridge remote from the isomerization site. The different structures of the photoproducts in PB(PCB)-binding phytochromes and BV-binding bacteriophytochromes are attributed to the different disposition of ring D upon isomerization, which leads to distinct protein-chromophore interactions in the Lumi-R states of these two classes of phytochromes.Minimizing the number and duration of design cycles needed to optimize hit or lead compounds into high-quality chemical probes or drug candidates is an ongoing challenge in biomedical research. Small structure modifications to hit or lead compounds can have meaningful impacts on pharmacological profiles due to significant effects on molecular and physicochemical properties and intra- and intermolecular interactions. Rapid pharmacological profiling of an efficiently prepared series of positional analogues stemming from the systematic exchange of methine groups with heteroatoms or other substituents in aromatic or heteroaromatic ring-containing hit or lead compounds is one approach toward minimizing design cycles (e.g., exchange of aromatic or heteroaromatic CH groups with N atoms or CF, CMe, or COH groups). In this Perspective, positional analogue scanning is shown to be an effective strategy for multiparameter optimization in drug design, whereby substantial improvements in a variety of pharmacological parameters can be achieved.Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein \pka calculations on CPUs and GPUs. Here we benchmark the performance of GB-CpHMD for predictions of cysteine \pka's and reactivities using a data set of 24 proteins with both down- and upshifted cysteine pKa's. We found that 10-ns single-pH or 4-ns replica-exchange CpHMD titrations gave root-mean-square errors of 1.2--1.3 and correlation coefficients of 0.8--0.9 with respect to experiment. The accuracy of predicting thiolates or hyperreactive cysteines at physiological pH with single-pH titrations is 86 or 81% with a precision of 100 or 90%, respectively. This performance well surpasses the traditional structure-based methods, particularly, a widely used empirical pKa tool which gives an accuracy less than 50%. We discuss simulation convergence, dependence on starting structures, common determinants of the pKa downshifts and upshifts as well as the origin of the discrepancies from the structure-based calculations. Our work suggests that CpHMD titrations can be performed on a desktop computer equipped with a single GPU card to predict cysteine protonation states for a variety of applications, from understanding biological functions to covalent drug design.