scholarly journals Structure of the sodium-dependent phosphate transporter reveals insights into human solute carrier SLC20

2020 ◽  
Vol 6 (32) ◽  
pp. eabb4024
Author(s):  
Jia-Yin Tsai ◽  
Chen-Hsi Chu ◽  
Min-Guan Lin ◽  
Ying-Hsuan Chou ◽  
Ruei-Yi Hong ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Essential Element ◽  
Phosphate Transport ◽  
Phosphate Transporter ◽  
Dimensional Structure ◽  
Phosphate Binding ◽  
Structure Based Drug Design ◽  
Nucleotide Biosynthesis ◽  
Sodium Dependent

Inorganic phosphate (Pi) is a fundamental and essential element for nucleotide biosynthesis, energy supply, and cellular signaling in living organisms. Human phosphate transporter (hPiT) dysfunction causes numerous diseases, but the molecular mechanism underlying transporters remains elusive. We report the structure of the sodium-dependent phosphate transporter from Thermotoga maritima (TmPiT) in complex with sodium and phosphate (TmPiT-Na/Pi) at 2.3-angstrom resolution. We reveal that one phosphate and two sodium ions (Pi-2Na) are located at the core of TmPiT and that the third sodium ion (Nafore) is located near the inner membrane boundary. We propose an elevator-like mechanism for sodium and phosphate transport by TmPiT, with the TmPiT-Na/Pi complex adopting an inward occluded conformation. We found that disease-related hPiT variants carry mutations in the corresponding sodium- and phosphate-binding residues identified in TmPiT. Our three-dimensional structure of TmPiT provides a framework for understanding PiT dysfunction and for future structure-based drug design.

scholarly journals Online biophysical predictions for SARS-CoV-2 proteins

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luciano Kagami ◽  
Joel Roca-Martínez ◽  
Jose Gavaldá-García ◽  
Pathmanaban Ramasamy ◽  
K. Anton Feenstra ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Static Structure ◽  
Homologous Proteins ◽  
Structure Based Drug Design ◽  
Protein Protein Interaction ◽  
Link Type ◽  
Dynamics Simulations ◽  
Β Sheet

Abstract Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. Main We present a website (https://bio2byte.be/sars2/) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. Conclusion The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

scholarly journals Identification of the Mg2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY

1999 ◽  
Vol 339 (2) ◽  
pp. 223-226 ◽  
Author(s):  
Ivo S. RIDDER ◽  
Bauke W. DIJKSTRA
Keyword(s):  
Binding Site ◽  
Response Regulator ◽  
Three Dimensional ◽  
Structural Similarity ◽  
Dimensional Structure ◽  
Phosphate Binding ◽  
Haloacid Dehalogenase ◽  
Regulator Protein ◽  
P Type ◽  
Response Regulator Protein

The large HAD (haloacid dehalogenase) superfamily of hydrolases comprises P-type ATPases, phosphatases, epoxide hydrolases and l-2-haloacid dehalogenases. A comparison of the three-dimensional structure of l-2-haloacid dehalogenase with that of the response regulator protein CheY allowed the assignment of a conserved pair of aspartate residues as the Mg2+-binding site in the P-type ATPase and phosphatase members of the superfamily. From the resulting model of the active site, a conserved serine/threonine residue is suggested to be involved in phosphate binding, and a mechanism comprising a phosphoaspartate intermediate is postulated.

scholarly journals Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches

2011 ◽  
Vol 9 (66) ◽  
pp. 20-33 ◽  
Author(s):  
Pierre Tuffery ◽  
Philippe Derreumaux
Keyword(s):  
Binding Affinity ◽  
Protein Interactions ◽  
Large Scale ◽  
De Novo ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structure Based Drug Design ◽  
Body Protein ◽  
Technical Problems ◽  
Multi Body

The recognition process between a protein and a partner represents a significant theoretical challenge. In silico structure-based drug design carried out with nothing more than the three-dimensional structure of the protein has led to the introduction of many compounds into clinical trials and numerous drug approvals. Central to guiding the discovery process is to recognize active among non-active compounds. While large-scale computer simulations of compounds taken from a library (virtual screening) or designed de novo are highly desirable in the post-genomic area, many technical problems remain to be adequately addressed. This article presents an overview and discusses the limits of current computational methods for predicting the correct binding pose and accurate binding affinity. It also presents the performances of the most popular algorithms for exploring binary and multi-body protein interactions.

scholarly journals Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Genomic Region ◽  
Dimensional Structure ◽  
Structure Based Drug Design ◽  
Stem Loop ◽  
Rna Molecules ◽  
Conformational Ensembles ◽  
Dynamics Simulations

The 5' untranslated region (UTR) of SARS-CoV-2 genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structure is not known yet. Here, we predict structure and dynamics of five RNA stem-loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrengements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterisation of these systems, and provide putative three-dimensional models for structure-based drug design studies.

scholarly journals Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose

2006 ◽  
Vol 395 (3) ◽  
pp. 457-462 ◽  
Author(s):  
François Alberto ◽  
Emmanuelle Jordi ◽  
Bernard Henrissat ◽  
Mirjam Czjzek
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Catalytic Efficiency ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Acid Base ◽  
Hydrolase Family ◽  
Binding Subsites

Thermotoga maritima invertase (β-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases β-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves β-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed β-propeller catalytic domain linked to a β-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule α-D-galactopyranosyl-(1,6)-α-D-glucopyranosyl-β-D-fructofuranoside (raffinose) at 1.87 Å (1 Å=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.

scholarly journals Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways

2007 ◽  
Vol 190 (5) ◽  
pp. 1773-1782 ◽  
Author(s):  
Chen Yang ◽  
Dmitry A. Rodionov ◽  
Irina A. Rodionova ◽  
Xiaoqing Li ◽  
Andrei L. Osterman
Keyword(s):  
Metabolic Pathways ◽  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Degradation Pathway ◽  
Dimensional Structure ◽  
Active Site Residues ◽  
Hydroxypyruvate Reductase ◽  
In Vitro Reconstitution

ABSTRACT Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the GarK (GK-I) family. The recently reported three-dimensional structure of GK-II from Thermotoga maritima (TM1585; PDB code 2b8n) revealed a new fold distinct from other known kinase families. Here, we verified the enzymatic activity of TM1585, assessed its kinetic characteristics, and used directed mutagenesis to confirm the essential role of the two active-site residues Lys-47 and Arg-325. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria and, in particular, in T. maritima. Comparative analyses of ∼400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of T. maritima, a three-step serine degradation pathway was inferred based on the tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively), that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution.

scholarly journals Evidence of an intestinal phosphate transporter alternative to type IIb sodium-dependent phosphate transporter in rats with chronic kidney disease

2020 ◽  
Vol 36 (1) ◽  
pp. 68-75
Author(s):  
Yasuhiro Ichida ◽  
Shuichi Ohtomo ◽  
Tessai Yamamoto ◽  
Naoaki Murao ◽  
Yoshinori Tsuboi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Mrna Expression ◽  
Messenger Rna ◽  
Phosphate Uptake ◽  
Maximum Velocity ◽  
Phosphate Transport ◽  
Phosphate Transporter ◽  
Sodium Dependent

Abstract Background Phosphate is absorbed in the small intestine via passive flow and active transport.NaPi-IIb, a type II sodium-dependent phosphate transporter, is considered to mediate active phosphate transport in rodents. To study the regulation of intestinal phosphate transport in chronic kidney disease (CKD), we analyzed the expression levels of NaPi-IIb, pituitary-specific transcription factor 1 (PiT-1) and PiT-2 and the kinetics of intestinal phosphate transport using two CKD models. Methods CKD was induced in rats via adenine orThy1 antibody injection. Phosphate uptake by intestinal brush border membrane vesicles (BBMV) and the messenger RNA (mRNA) expression of NaPi-IIb, PiT-1 and PiT-2 were analyzed. The protein expression level of NaPi-IIb was measured by mass spectrometry (e.g. liquid chromatography tandem mass spectrometry). Results In normal rats, phosphate uptake into BBMV consisted of a single saturable component and its Michaelis constant (Km) was comparable to that of NaPi-IIb. The maximum velocity (Vmax) correlated with mRNA and protein levels of NaPi-IIb. In the CKD models, intestinal phosphate uptake consisted of two saturable components. The Vmax of the higher-affinity transport, which is thought to be responsible for NaPi-IIb, significantly decreased and the decrease correlated with reduced NaPi-IIb expression. The Km of the lower-affinity transport was comparable to that of PiT-1 and -2. PiT-1 mRNA expression was much higher than that of PiT-2, suggesting that PiT-1 was mostly responsible for phosphate transport. Conclusions This study suggests that the contribution of NaPi-IIb to intestinal phosphate absorption dramatically decreases in rats with CKD and that a low-affinity alternative to NaPi-IIb, in particular PiT-1, is upregulated in a compensatory manner in CKD.

Topology Scanning and Putative Three-Dimensional Structure of the Extracellular Binding Domains of the Apical Sodium-Dependent Bile Acid Transporter (SLC10A2)†

Biochemistry ◽  
2004 ◽  
Vol 43 (36) ◽  
pp. 11380-11392 ◽  
Author(s):  
Eric Y. Zhang ◽  
Mitch A. Phelps ◽  
Antara Banerjee ◽  
Chandra M. Khantwal ◽  
Cheng Chang ◽  
...  
Keyword(s):  
Bile Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Binding Domains ◽  
Sodium Dependent ◽  
Bile Acid Transporter ◽  
Acid Transporter

scholarly journals Stimulation of ribosomal frameshifting by antisense LNA

2010 ◽  
Vol 38 (22) ◽  
pp. 8277-8283 ◽  
Author(s):  
Chien-Hung Yu ◽  
Mathieu H. M. Noteborn ◽  
René C. L. Olsthoorn
Keyword(s):  
Rna Stability ◽  
Three Dimensional ◽  
Fixed Ratio ◽  
Essential Element ◽  
Dimensional Structure ◽  
Ribosomal Frameshifting ◽  
Dna Oligonucleotides ◽  
Ribosomal Tunnel ◽  
Slippery Sequence

Abstract Programmed ribosomal frameshifting is a translational recoding mechanism commonly used by RNA viruses to express two or more proteins from a single mRNA at a fixed ratio. An essential element in this process is the presence of an RNA secondary structure, such as a pseudoknot or a hairpin, located downstream of the slippery sequence. Here, we have tested the efficiency of RNA oligonucleotides annealing downstream of the slippery sequence to induce frameshifting in vitro. Maximal frameshifting was observed with oligonucleotides of 12–18 nt. Antisense oligonucleotides bearing locked nucleid acid (LNA) modifications also proved to be efficient frameshift-stimulators in contrast to DNA oligonucleotides. The number, sequence and location of LNA bases in an otherwise DNA oligonucleotide have to be carefully manipulated to obtain optimal levels of frameshifting. Our data favor a model in which RNA stability at the entrance of the ribosomal tunnel is the major determinant of stimulating slippage rather than a specific three-dimensional structure of the stimulating RNA element.

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