scholarly journals Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2441
Author(s):  
Kevin Clark ◽  
Natalia B. Pigni ◽  
Kithmini Wijesiri ◽  
José A. Gascón
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Quantum Mechanical ◽  
Electronic Coupling ◽  
Spectral Features ◽  
Coupling Interaction ◽  
Functional Roles ◽  
Terminal Domain ◽  
Orange Carotenoid Protein ◽  
Insight Into

The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions.

scholarly journals Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase

2020 ◽  
Vol 76 (10) ◽  
pp. 488-494
Author(s):  
Rahul Singh ◽  
Sonali Deshmukh ◽  
Ashwani Kumar ◽  
Venuka Durani Goyal ◽  
Ravindra D. Makde
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Xanthomonas Campestris ◽  
Protein Quality ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
Homologous Proteins ◽  
Terminal Domain ◽  
Α Helix ◽  
Terminal Domains

LonA peptidase is a major component of the protein quality-control mechanism in both prokaryotes and the organelles of eukaryotes. Proteins homologous to the N-terminal domain of LonA peptidase, but lacking its other domains, are conserved in several phyla of prokaryotes, including the Xanthomonadales order. However, the function of these homologous proteins (LonNTD-like proteins) is not known. Here, the crystal structure of the LonNTD-like protein from Xanthomonas campestris (XCC3289; UniProt Q8P5P7) is reported at 2.8 Å resolution. The structure was solved by molecular replacement and contains one polypeptide in the asymmetric unit. The structure was refined to an R free of 29%. The structure of XCC3289 consists of two domains joined by a long loop. The N-terminal domain (residues 1–112) consists of an α-helix surrounded by β-sheets, whereas the C-terminal domain (residues 123–193) is an α-helical bundle. The fold and spatial orientation of the two domains closely resembles those of the N-terminal domains of the LonA peptidases from Escherichia coli and Mycobacterium avium. The structure is also similar to that of cereblon, a substrate-recognizing component of the E3 ubiquitin ligase complex. The N-terminal domains of both LonA and cereblon are known to be involved in specific protein–protein interactions. This structural analysis suggests that XCC3289 and other LonNTD-like proteins might also be capable of such protein–protein interactions.

scholarly journals Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Core Nuclear Egress Complex Provides Insight into a Unique Assembly Scaffold for Virus-Host Protein Interactions

2015 ◽  
Vol 290 (46) ◽  
pp. 27452-27458 ◽  
Author(s):  
Sascha A. Walzer ◽  
Claudia Egerer-Sieber ◽  
Heinrich Sticht ◽  
Madhumati Sevvana ◽  
Katharina Hohl ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Human Cytomegalovirus ◽  
Protein Interactions ◽  
Host Protein ◽  
Nuclear Egress ◽  
Insight Into

scholarly journals Crystal structure of the glutamate receptor GluA1 N-terminal domain

2011 ◽  
Vol 438 (2) ◽  
pp. 255-263 ◽  
Author(s):  
Guorui Yao ◽  
Yinong Zong ◽  
Shenyan Gu ◽  
Jie Zhou ◽  
Huaxi Xu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Ampa Receptors ◽  
Neurological Diseases ◽  
Protein Protein Interactions ◽  
Terminal Domain ◽  
The Central Nervous System ◽  
In Trans ◽  
Excitatory Neurotransmission ◽  
Active Channels

The AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid) subfamily of iGluRs (ionotropic glutamate receptors) is essential for fast excitatory neurotransmission in the central nervous system. The malfunction of AMPARs (AMPA receptors) has been implicated in many neurological diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. The active channels of AMPARs and other iGluR subfamilies are tetramers formed exclusively by assembly of subunits within the same subfamily. It has been proposed that the assembly process is controlled mainly by the extracellular ATD (N-terminal domain) of iGluR. In addition, ATD has also been implicated in synaptogenesis, iGluR trafficking and trans-synaptic signalling, through unknown mechanisms. We report in the present study a 2.5 Å (1 Å=0.1 nm) resolution crystal structure of the ATD of GluA1. Comparative analyses of the structure of GluA1-ATD and other subunits sheds light on our understanding of how ATD drives subfamily-specific assembly of AMPARs. In addition, analysis of the crystal lattice of GluA1-ATD suggests a novel mechanism by which the ATD might participate in inter-tetramer AMPAR clustering, as well as in trans-synaptic protein–protein interactions.

Structure and Function of NzeB, a Versatile C–C and C–N Bond Forming Diketopiperazine Dimerase

2020 ◽  
Author(s):  
Vikram V. Shende ◽  
Yogan Khatri ◽  
Sean A. Newmister ◽  
Jacob N. Sanders ◽  
Petra Lindovska ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cytochrome P450 ◽  
Active Site ◽  
Structure And Function ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Bond Forming ◽  
And Function ◽  
Insight Into

This report details the discovery and characterization of a versatile bacterial cytochrome P450, NzeB, which catalyzes the dimerization of diketopiperazines via enzymatic C–H functionalization. This includes the first high-resolution crystal structure of a diketopiperazine dimerase, which along with active site via mutagenesis and quantum mechanical calculations, provides insight into the selectivity and mechanism of these enzymes.

scholarly journals Structure and Function of NzeB, a Versatile C–C and C–N Bond Forming Diketopiperazine Dimerase

2020 ◽  
Author(s):  
Vikram V. Shende ◽  
Yogan Khatri ◽  
Sean A. Newmister ◽  
Jacob N. Sanders ◽  
Petra Lindovska ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cytochrome P450 ◽  
Active Site ◽  
Structure And Function ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Bond Forming ◽  
And Function ◽  
Insight Into

This report details the discovery and characterization of a versatile bacterial cytochrome P450, NzeB, which catalyzes the dimerization of diketopiperazines via enzymatic C–H functionalization. This includes the first high-resolution crystal structure of a diketopiperazine dimerase, which along with active site via mutagenesis and quantum mechanical calculations, provides insight into the selectivity and mechanism of these enzymes.

scholarly journals Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis

2016 ◽  
Vol 113 (7) ◽  
pp. 1802-1807 ◽  
Author(s):  
Akimasa Miyanaga ◽  
Shohei Iwasawa ◽  
Yuji Shinohara ◽  
Fumitaka Kudo ◽  
Tadashi Eguchi
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Acyl Carrier Protein ◽  
Complex Structure ◽  
Binding Pocket ◽  
Carrier Protein ◽  
Protein Protein Interactions ◽  
Substrate Binding Pocket ◽  
Insight Into

Acyltransferases (ATs) are key determinants of building block specificity in polyketide biosynthesis. Despite the importance of protein–protein interactions between AT and acyl carrier protein (ACP) during the acyltransfer reaction, the mechanism of ACP recognition by AT is not understood in detail. Herein, we report the crystal structure of AT VinK, which transfers a dipeptide group between two ACPs, VinL and VinP1LdACP, in vicenistatin biosynthesis. The isolated VinK structure showed a unique substrate-binding pocket for the dipeptide group linked to ACP. To gain greater insight into the mechanism of ACP recognition, we attempted to crystallize the VinK–ACP complexes. Because transient enzyme–ACP complexes are difficult to crystallize, we developed a covalent cross-linking strategy using a bifunctional maleimide reagent to trap the VinK–ACP complexes, allowing the determination of the crystal structure of the VinK–VinL complex. In the complex structure, Arg-153, Met-206, and Arg-299 of VinK interact with the negatively charged helix II region of VinL. The VinK–VinL complex structure allows, to our knowledge, the first visualization of the interaction between AT and ACP and provides detailed mechanistic insights into ACP recognition by AT.

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

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