scholarly journals Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity

2017 ◽  
Author(s):  
Yongchan Lee ◽  
Tomohiro Nishizawa ◽  
Mizuki Takemoto ◽  
Kaoru Kumazaki ◽  
Keitaro Yamashita ◽  
...  
Keyword(s):  
Inorganic Phosphate ◽  
Structural Information ◽  
Chloroplast Envelope ◽  
Triose Phosphate ◽  
Phosphate Translocator ◽  
Drug Metabolite ◽  
Tightly Coupled ◽  
Group A ◽  
Dynamics Simulations ◽  
Metabolite Transporter

AbstractThe triose-phosphate/phosphate translocator (TPT) catalyzes the strict 1:1 exchange of triose phosphate, 3-phosphoglycerate and inorganic phosphate across the chloroplast envelope, and plays crucial roles in photosynthesis. Despite rigorous studies for more than 40 years, the molecular mechanism of TPT is poorly understood due to the lack of structural information. Here we report crystal structures of TPT bound to two different substrates, 3-phosphoglycerate and inorganic phosphate, in occluded conformations. The structures reveal that TPT adopts a 10-transmembrane drug/metabolite transporter fold. Both substrates are bound within the same central pocket, where conserved lysine, arginine, and tyrosine residues recognize the shared phosphate group. A structural comparison with the outward-open conformation of the bacterial drug/metabolite transporter suggests a rocking-type motion of helix bundles, and molecular dynamics simulations support a model in which this helix rocking is tightly coupled to the substrate binding, to ensure strict 1:1 exchange. These results reveal the unique mechanism of sugar phosphate/phosphate exchange by TPT.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals Free energy landscape for the entire transport cycle of triose-phosphate/phosphate translocator

2017 ◽  
Author(s):  
Mizuki Takemoto ◽  
Yongchan Lee ◽  
Ryuichiro Ishitani ◽  
Osamu Nureki
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Conformational Transition ◽  
Substrate Binding ◽  
Energy Landscape ◽  
Umbrella Sampling ◽  
Free Energy Landscape ◽  
Coupling Mechanism ◽  
Triose Phosphate ◽  
Phosphate Translocator

AbstractSecondary active transporters translocate their substrates using the electrochemical potentials of other chemicals, undergoing large-scale conformational changes. Despite extensive structural studies, the atomic details of the transport mechanism still remain elusive. Here we performed a series of all-atom molecular dynamics simulations of the triose-phosphate/phosphate translocator (TPT), which exports organic phosphates in the chloroplast stroma in strict counter exchange with inorganic phosphate (Pi). Biased sampling methods, including string method and umbrella sampling, successfully reproduced the conformational changes between the inward– and outward-facing states, along with the substrate binding. The free energy landscape of this entire TPT transition pathway demonstrated the alternating access and substrate translocation mechanisms, which revealed Pi is relayed by positively charged residues along the transition pathway. Furthermore, the conserved Glu207 functions as a “molecular switch”, linking the local substrate binding and the global conformational transition. Our results provide atomic-detailed insights into the energy coupling mechanism of antiporter.

scholarly journals Automated and optimally FRET-assisted structural modeling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mykola Dimura ◽  
Thomas-Otavio Peulen ◽  
Hugo Sanabria ◽  
Dmitro Rodnin ◽  
Katherina Hemmen ◽  
...  
Keyword(s):  
Open Source Software ◽  
Structural Information ◽  
Structural Modeling ◽  
Automated Design ◽  
Design Tool ◽  
Coarse Grained ◽  
Complex Dynamic ◽  
X Ray ◽  
Link Type ◽  
Dynamics Simulations

Abstract FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET experiments, they need to be combined with computer simulations. We introduce a program suite with (i) an automated design tool for FRET experiments, which determines how many and which FRET pairs should be used to minimize the uncertainty and maximize the accuracy of an integrative structure, (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (iii) a quantitative quality estimate for judging the accuracy of FRET-derived structures as opposed to precision. We benchmark our tools against simulated and experimental data of proteins with multiple conformational states and demonstrate an accuracy of ~3 Å RMSDCα against X-ray structures for sets of 15 to 23 FRET pairs. Free and open-source software for the introduced workflow is available at https://github.com/Fluorescence-Tools. A web server for FRET-assisted structural modeling of proteins is available at http://nmsim.de.

scholarly journals Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis

2019 ◽  
Vol 218 (8) ◽  
pp. 2638-2658 ◽  
Author(s):  
Junya Zhang ◽  
Shan Wu ◽  
Susan K. Boehlein ◽  
Donald R. McCarty ◽  
Gaoyuan Song ◽  
...  
Keyword(s):  
Inorganic Phosphate ◽  
Phosphate Uptake ◽  
Soluble Sugars ◽  
Chloroplast Envelope ◽  
Envelope Membrane ◽  
Double Membrane ◽  
Plastid Envelope ◽  
Membrane Envelope ◽  
Bacterial Outer Membrane ◽  
Outer Membrane Biogenesis

Chloroplasts are of prokaryotic origin with a double-membrane envelope separating plastid metabolism from the cytosol. Envelope membrane proteins integrate chloroplasts with the cell, but envelope biogenesis mechanisms remain elusive. We show that maize defective kernel5 (dek5) is critical for envelope biogenesis. Amyloplasts and chloroplasts are larger and reduced in number in dek5 with multiple ultrastructural defects. The DEK5 protein is homologous to rice SSG4, Arabidopsis thaliana EMB2410/TIC236, and Escherichia coli tamB. TamB functions in bacterial outer membrane biogenesis. DEK5 is localized to the envelope with a topology analogous to TamB. Increased levels of soluble sugars in dek5 developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Proteomics and antibody-based analyses show dek5 reduces levels of Toc75 and chloroplast envelope transporters. Moreover, dek5 chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable transport of metabolites and proteins.

scholarly journals The increase of oxygen consumption after a flash of light is tightly coupled to sodium pumping in the lateral ocellus of barnacle.

1990 ◽  
Vol 96 (1) ◽  
pp. 83-108 ◽  
Author(s):  
H Widmer ◽  
S Poitry ◽  
M Tsacopoulos
Keyword(s):  
Oxygen Consumption ◽  
Inorganic Phosphate ◽  
Photoreceptor Cells ◽  
Adenosine Diphosphate ◽  
Bathing Solution ◽  
Intracellular Injection ◽  
Metabolic Products ◽  
Lateral Ocellus ◽  
Tightly Coupled ◽  
Intense Light

In the lateral ocellus of the barnacle, we have tested the hypothesis that the transient increase of oxygen consumption (delta QO2) induced by light results from an increase in the rate of Na+ pumping. With a Na(+)-sensitive microelectrode, we measured the intracellular concentration of Na+ (Nai) in the photoreceptor cells. Nai was 17.6 +/- 1.2 mM (SE; n = 18) in darkness and it increased transiently by 10-20 mM after an 80-ms flash of intense light. The increase of Nai recovered in about the same time as the delta QO2, and the Na+/O2 ratio was 19.2 +/- 3.8 (SE; n = 6). Removing Na+ from the bath caused the delta QO2 to decrease by 79 +/- 3% (SE; n = 5). Exposure to 25 microM ouabain inhibited Na+ pumping and abolished the delta QO2. Removal of K+ from the bathing solution inhibited Na+ pumping in darkness, but mostly shortened the duration of the delta QO2; with a K(+)-sensitive microelectrode, we measured pericellular [K+] and found that it increased after the flash for about the same time as the delta QO2. Increasing Na+ pumping in darkness by reintroducing K+ in the bath or by injecting Na+ into one of the photoreceptor cells induced a delta QO2. Finally, intracellular injection of adenosine diphosphate and inorganic phosphate (ADP + Pi), the metabolic products of ATP splitting by the Na+ pump, also induced a delta QO2 in darkness. We conclude that all the results obtained are consistent with the formulated hypothesis.

Molecular cloning and expression analysis of the rice triose phosphate/phosphate translocator gene

Plant Science ◽  
2002 ◽  
Vol 162 (5) ◽  
pp. 785-790 ◽  
Author(s):  
Qingmei Wang ◽  
Jia Chen ◽  
Xuechen Wang ◽  
Jinyue Sun ◽  
Wei Sha
Keyword(s):  
Molecular Cloning ◽  
Expression Analysis ◽  
Cloning And Expression ◽  
Triose Phosphate ◽  
Phosphate Translocator

Lattice-Fringe Fingerprinting: Structural identification of nanocrystals by HRTEM

2007 ◽  
Vol 1026 ◽  
Author(s):  
Moeck Peter ◽  
Ruben Bjorge
Keyword(s):  
Structural Information ◽  
Reciprocal Lattice ◽  
Chemical Information ◽  
Fourier Synthesis ◽  
Transmission Electron ◽  
Structure Factors ◽  
Lattice Geometry ◽  
Group A ◽  
Experimental Side ◽  
Novel Method

AbstractA novel method for the structurally identification of a nanocrystal from a single high resolution (HR) transmission electron microscopy (TEM) micrograph is described. Components of this method are demonstrated on both experimental and simulated HRTEM images. On the experimental side, the structural information that can be extracted from a HRTEM image is the projected reciprocal lattice geometry, the plane symmetry group, a few structure factor amplitudes and phases, and an outline of the projected atomic structure to the limited resolution of the HRTEM (via a Fourier synthesis of the structure factors). Searching for this information in a comprehensive database and matching it with high figures of merit to that of candidate structures should allow for highly discriminatory identifications of nanocrystals, even without additional chemical information as obtainable in analytical TEMs.

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