Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters (original) (raw)
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Structures and Models of Transporter Proteins
Journal of Pharmacology and Experimental Therapeutics, 2004
Transporter proteins in biological membranes may be divided into channels and carriers. Channels function as selective pores that open in response to a chemical or electrophysiological stimulus, allowing movement of a solute down an electrochemical gradient. Active carrier proteins use an energy producing process to translocate a substrate against a concentration gradient. Secondary active transporters use the movement of a solute down a concentration gradient to drive the translocation of another substrate across a membrane. ATP-binding cassette (ABC) transporters couple hydrolysis of adenosine triphosphate (ATP) to the translocation of various substrates across cell membranes. High-resolution three-dimensional structures have now been reported from X-ray crystallographic studies of six different transporters, including two ATP-binding cassette (ABC) transporters. These structures have explained the results
The channel in transporters is formed by residues that are rare in transmembrane helices
In Silico Biology, 2003
Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Even less is known about the 3D structure of transporters. Nevertheless, the published experimental data demonstrate that channel-forming residues determine the substrate specificity of secondary transporters and analysis of these residues would provide better understanding of the transport mechanism. We developed a simple computational method for identification of channel-forming residues in transporter sequences. It is based on the analysis of amino acids frequencies in bacterial secondary transporters. We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure.
Journal of Biological Chemistry, 2012
The transport mechanism of organic cation transporter OCT1 is not understood. Results: Voltage-dependent movements of transmembrane ␣-helices in OCT1 were identified that were blocked by mutations of glycine in the substrate binding domain of ␣-helix 11. Conclusion: A hinge domain pivotal for transport-related structural changes has been identified. Significance: The hinge domain allows substrate occlusion during translocation.
Membrane Transporters: Structure, Function and Targets for Drug Design
Topics in Medicinal Chemistry, 2008
Current therapeutic drugs act on four main types of molecular targets: enzymes, receptors, ion channels and transporters, among which a major part (60-70%) are membrane proteins. This review discusses the molecular structures and potential impact of membrane transporter proteins on new drug discovery. The three-dimensional (3D) molecular structure of a protein contains information about the active site and possible ligand binding, and about evolutionary relationships within the protein family. Transporters have a recognition site for a particular substrate, which may be used as a target for drugs inhibiting the transporter or acting as a false substrate. Three groups of transporters have particular interest as drug targets: the major facilitator superfamily, which includes almost 4000 different proteins transporting sugars, polyols, drugs, neurotransmitters, metabolites, amino acids, peptides, organic and inorganic anions and many other substrates; the ATP-binding cassette superfamily, which plays an important role in multidrug resistance in cancer chemotherapy; and the neurotransmitter:sodium symporter family, which includes the molecular targets for some of the most widely used psychotropic drugs. Recent technical advances have increased the number of known 3D structures of membrane transporters, and demonstrated that they form a divergent group of proteins with large conformational flexibility which facilitates transport of the substrate.
Structural domains involved in substrate selectivity in two neutral amino acid transporters
American journal of physiology. Cell physiology, 2004
The ability of the two highly homologous Na(+)/Cl(-)-dependent neutral amino acid transporters KAAT1 and CAATCH1, cloned from the midgut epithelium of the larva Manduca sexta, to transport different amino acids depends on the cotransported ion, on pH, and on the membrane voltage. Different organic substrates give rise to transport-associated currents with their own characteristics, which are notably distinct between the two proteins. Differences in amplitude, kinetics, and voltage dependence of the transport-associated currents have been observed, as well as different substrate selectivity patterns measured by radioactive amino acid uptake assays. These diversities represent useful tools to investigate the structural determinants involved in the substrate selectivity. To identify these regions, we built four chimeric proteins between the two transporters. These proteins, heterologously expressed in Xenopus laevis oocytes, were analyzed by two-electrode voltage clamp and uptake measu...
The major facilitator superfamily, discovered in the late 1980s, is currently composed of thousands of characterized integral membrane transporters. These transport systems of the superfamily have an extremely diverse array of substrates and organismal origins, but share similarities in their molecular evolution, modes of energization (passive and secondary active), mechanisms of transport (uniport, symport and antiport), and overall two-and three-dimensional protein structures. Extensive collections of transporter protein sequences have been deposited in sequence databases since the first sequences were reported from gene cloning studies, and these early studies of a relatively few number of transporter sequences have revealed several conserved sequence motifs that have been studied at the structure-function level. This review article summarizes the evidence produced to assign the functional roles for these conserved amino acid residues and sequence motifs of the major facilitator superfamily. The implications of these functional roles are considered, with emphasis placed on their usefulness in biomedical science and medicine.
Roles of membrane transporters: connecting the dots from sequence to phenotype
Annals of Botany, 2019
• Background Plant membrane transporters are involved in diverse cellular processes underpinning plant physiology, such as nutrient acquisition, hormone movement, resource allocation, exclusion or sequestration of various solutes from cells and tissues, and environmental and developmental signalling. A comprehensive characterization of transporter function is therefore key to understanding and improving plant performance. • Scope and Conclusions In this review, we focus on the complexities involved in characterizing transporter function and the impact that this has on current genomic annotations. Specific examples are provided that demonstrate why sequence homology alone cannot be relied upon to annotate and classify transporter function, and to show how even single amino acid residue variations can influence transporter activity and specificity. Misleading nomenclature of transporters is often a source of confusion in transporter characterization, especially for people new to or outside the field. Here, to aid researchers dealing with interpretation of large data sets that include transporter proteins, we provide examples of transporters that have been assigned names that misrepresent their cellular functions. Finally, we discuss the challenges in connecting transporter function at the molecular level with physiological data, and propose a solution through the creation of new databases. Further fundamental in-depth research on specific transport (and other) proteins is still required; without it, significant deficiencies in large-scale data sets and systems biology approaches will persist. Reliable characterization of transporter function requires integration of data at multiple levels, from amino acid residue sequence annotation to more in-depth biochemical, structural and physiological studies.