The roles of a light-dependent protochlorophyllide oxidoreductase (LPOR), and ATP-dependent dark operative protochlorophyllide oxidoreductase (DPOR) in chlorophyll biosynthesis

Chlorophyll is a green photosynthetic pigment, and photosynthesis drives the global carbon cycle. The reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate stage of biosynthesis of chlorophyll (Chl) is catalyzed by light-independent protochlorophyllide reducatse (DPOR), and the light-dependent protochlorophyllide oxidoreductase (LPOR). The search was done to all manuscript sections according to terms chlorophyll, a light-dependent protochlorophyllide oxidoreductase, ATP-dependent dark operative protochlorophyllide oxidoreductase, chlorophyll, photosynthesis and chlorophyllide. Within the framework of photosynthesis and chlorophyll, this review article was aimed to provide an overview of the functional studies in chlorophyll biosynthesis, protein crystal structure, disclosure of action mechanisms, and possible future available direction of LPOR and DPOR in the biosynthesis of chlorophyll.

INSILICO METHOD FOR PREDICTION OF MAXIMUM BINDING AFFINITY AND LIGAND – PROTEIN INTERACTION STUDIES ON ALZHEIMER’S DISEASE

The aim of this study is to perform the molecular docking, identifying the drug likeness, ADME properties of drugs, Ligand-Protein interactions using different softwares. Due to the excess activity of Acetylcholinesterase, plaque formation and tau protein aggregation in the brain is the main cause for the Alzheimer’s disease. The interaction of Donepezil, Rivastigmine and Chlorzoxazone against AChE protein crystal structure (4EY5, 4EY6, 4EY7) using molecular docking were analyzed. Docking results of Rivastigmine and Chlorzoxazone were compared with Donepezil (widely used drug for Alzheimer’s disease) to identify the binding affinity. To verify whether Chlorzoxazone could act similarly as effective drug of Donepezil and also finding in which protein structure, ligands could bind effectively were employed using BIOVIA Discovery Studio software. Among those ligands interaction with all protein structure, 4EY7 on Rivastigmine (-7.1 kcal/mol) exhibits maximum binding affinity. The interactions of three ligands were compared with one another, in that Hydrogen bond formation of Chlorzoxazone and Donepezil with 4EY6 and 4EY7 interacting the similar aminoacids residues (4EY6-ARG165; 4EY7-ASP74) were studied using insilico studies .

Efficiency of Homology Modeling assisted Molecular Docking in G-protein coupled receptors

Background: Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery. Objective: The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane bound proteins with complex constitution and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures however majority of the GPCR structures remain unsolved. In this context HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs. Methods: The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in absence of GPCR crystal structures (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor sub type selectivity and receptor behaviour in comparison with GPCR crystal structures . Results: The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases HM proteins were found to outscore crystal structures also. Conclusion: The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at molecular level. Thus HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.

Protein crystal structure determination with the crystallophore, a nucleating and phasing agent

Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

Protein crystal structure from non-oriented, single-axis sparse X-ray data

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.

Protein-complex structure completion usingIPCAS(Iterative Protein Crystal structure Automatic Solution)

Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite,IPCAS(Iterative Protein Crystal structure Automatic Solution). TheIPCASiteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to useIPCASto build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case,IPCASwas able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.