scholarly journals Inward-facing conformation of a multidrug resistance MATE family transporter

2019 ◽  
Vol 116 (25) ◽  
pp. 12275-12284 ◽  
Author(s):  
Sandra Zakrzewska ◽  
Ahmad Reza Mehdipour ◽  
Viveka Nand Malviya ◽  
Tsuyoshi Nonaka ◽  
Juergen Koepke ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Structural Information ◽  
Pyrococcus Furiosus ◽  
Conformational Flexibility ◽  
Transmembrane Helices ◽  
Body Movements ◽  
Detailed Mechanism ◽  
Toxic Metabolites ◽  
Alternating Access ◽  
Mate Transporter

Multidrug and toxic compound extrusion (MATE) transporters mediate excretion of xenobiotics and toxic metabolites, thereby conferring multidrug resistance in bacterial pathogens and cancer cells. Structural information on the alternate conformational states and knowledge of the detailed mechanism of MATE transport are of great importance for drug development. However, the structures of MATE transporters are only known in V-shaped outward-facing conformations. Here, we present the crystal structure of a MATE transporter from Pyrococcus furiosus (PfMATE) in the long-sought-after inward-facing state, which was obtained after crystallization in the presence of native lipids. Transition from the outward-facing state to the inward-facing state involves rigid body movements of transmembrane helices (TMs) 2–6 and 8–12 to form an inverted V, facilitated by a loose binding of TM1 and TM7 to their respective bundles and their conformational flexibility. The inward-facing structure of PfMATE in combination with the outward-facing one supports an alternating access mechanism for the MATE family transporters.

scholarly journals Crystal Structure of a ligand-bound LacY–Nanobody Complex

2018 ◽  
Vol 115 (35) ◽  
pp. 8769-8774 ◽  
Author(s):  
Hemant Kumar ◽  
Janet S. Finer-Moore ◽  
Xiaoxu Jiang ◽  
Irina Smirnova ◽  
Vladimir Kasho ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Lactose Permease ◽  
Transmembrane Helices ◽  
Helical Bundle ◽  
Flexible Loop ◽  
Sugar Binding ◽  
Open Conformation ◽  
Substrate Analog ◽  
Multiple Conformations ◽  
Alternating Access

The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane transport protein, catalyzes galactoside/H+ symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar-binding. Camelid nanobodies were made against a double-mutant Gly46 → Trp/Gly262 → Trp (LacYWW) that produces an outward-open conformation, as opposed to the cytoplasmic open-state crystal structure of WT LacY. Nanobody 9047 (Nb9047) stabilizes WT LacY in a periplasmic-open conformation. Here, we describe the X-ray crystal structure of a complex between LacYWW, the high-affinity substrate analog 4-nitrophenyl-α-d-galactoside (NPG), and Nb9047 at 3-Å resolution. The present crystal structure demonstrates that Nb9047 binds to the periplasmic face of LacY, primarily to the C-terminal six-helical bundle, while a flexible loop of the Nb forms a bridge between the N- and C-terminal halves of LacY across the periplasmic vestibule. The bound Nb partially covers the vestibule, yet does not affect the on-rates or off-rates for the substrate binding to LacYWW, which implicates dynamic flexibility of the Nb–LacYWW complex. Nb9047-binding neither changes the overall structure of LacYWW with bound NPG, nor the positions of side chains comprising the galactoside-binding site. The current NPG-bound structure exhibits a more occluded periplasmic vestibule than seen in a previous structure of a (different Nb) apo-LacYWW/Nb9039 complex that we argue is caused by sugar-binding, with major differences located at the periplasmic ends of transmembrane helices in the N-terminal half of LacY.

Polymorphism of monotropic forms: relationships between thermochemical and structural characteristics

2020 ◽  
Vol 76 (1) ◽  
pp. 65-75 ◽  
Author(s):  
German Perlovich ◽  
Artem Surov
Keyword(s):  
Molecular Descriptors ◽  
Structural Information ◽  
Structural Characteristics ◽  
Conformational Flexibility ◽  
Similarity Coefficients ◽  
Tanimoto Similarity ◽  
Group I ◽  
Bivariate Statistical Analysis ◽  
Polymorphic Forms ◽  
Group Ii

In this work, a database containing thermochemical and structural information about 208 monotropic polymorphic forms has been created and analyzed. Most of the identified compounds (77 cases) have been found to have two polymorphs, 14 compounds have three forms and there are only three examples of systems with four polymorphs. The analysis of density distribution within the database has revealed that only 62 out of 114 metastable polymorphs (referred to as group I) obey the `density rule' proposed by Burger and Ramberger [(1979), Mikrochim. Acta, 72, 259–271], while the remaining 45% of the monotropic systems (group II) violate the rule. A number of physicochemical, structural and molecular descriptors have been used to find and highlight the differences between group I and group II of the polymorphs. Group II is characterized (on average) by higher values of descriptors, which are responsible for conformational flexibility of molecules. An algorithm has been proposed for carrying out bivariate statistical analysis. It implies partitioning the database into structurally related clusters based on Tanimoto similarity coefficients and subsequent analysis of each cluster in terms of the number of hydrogen bonds per molecule.

scholarly journals Multidrug resistance-associated ABC transporters – too much of one thing, good for nothing

2012 ◽  
Vol 3 (4) ◽  
pp. 319-331 ◽  
Author(s):  
Jirina Prochazkova ◽  
Martina Lanova ◽  
Jiri Pachernik
Keyword(s):  
Multidrug Resistance ◽  
Cancer Cells ◽  
Abc Transporters ◽  
Family Members ◽  
Atp Binding ◽  
Detailed Mechanism ◽  
P Glycoprotein ◽  
The Future ◽  
Good For

AbstractOverexpression of ATP-binding cassette (ABC) transporters in cancer cells results in multidrug resistance (MDR) which leads to unsuccessful chemotherapy. The most important MDR-associated members of ABC superfamily are ABC B1/P-glycoprotein/MDR1, ABC C1/multidrug resistance associated protein 1 (MRP1), and ABC G2/BCRP. This study is not only focused on function, substrates, and localization of these popular proteins but also on other ABC C family members such as ABC C2–6/MRP2-6 and ABC C7/CFTR. Current research is mainly oriented on the cancer-promoting role of these proteins, but important lessons could also be learned from the physiological roles of these proteins or from polymorphisms affecting their function. Thorough knowledge of structure and detailed mechanism of efflux can aid in the discovery of new chemotherapy targets in the future. Although the best way on how to deal with MDR would be to prevent its development, we describe some new promising strategies on how to conquer both inherited and induced MDRs.

scholarly journals A chemiosmotic mechanism of symport

2015 ◽  
Vol 112 (5) ◽  
pp. 1259-1264 ◽  
Author(s):  
H. Ronald Kaback
Keyword(s):  
Driving Forces ◽  
Lactose Permease ◽  
Transmembrane Helices ◽  
Electrochemical Gradient ◽  
Induced Fit ◽  
X Ray ◽  
Membrane Transport Proteins ◽  
Limiting Step ◽  
Experimental Findings ◽  
Alternating Access

Lactose permease (LacY), a paradigm for the largest family of membrane transport proteins, catalyzes the coupled translocation of a galactoside and an H+ across the Escherichia coli membrane (galactoside/H+ symport). Initial X-ray structures reveal N- and C-terminal domains, each with six largely irregular transmembrane helices surrounding an aqueous cavity open to the cytoplasm. Recently, a structure with a narrow periplasmic opening and an occluded galactoside was obtained, confirming many observations and indicating that sugar binding involves induced fit. LacY catalyzes symport by an alternating access mechanism. Experimental findings garnered over 45 y indicate the following: (i) The limiting step for lactose/H+ symport in the absence of the H+ electrochemical gradient (∆µ̃H+) is deprotonation, whereas in the presence of ∆µ̃H+, the limiting step is opening of apo LacY on the other side of the membrane; (ii) LacY must be protonated to bind galactoside (the pK for binding is ∼10.5); (iii) galactoside binding and dissociation, not ∆µ̃H+, are the driving forces for alternating access; (iv) galactoside binding involves induced fit, causing transition to an occluded intermediate that undergoes alternating access; (v) galactoside dissociates, releasing the energy of binding; and (vi) Arg302 comes into proximity with protonated Glu325, causing deprotonation. Accumulation of galactoside against a concentration gradient does not involve a change in Kd for sugar on either side of the membrane, but the pKa (the affinity for H+) decreases markedly. Thus, transport is driven chemiosmotically but, contrary to expectation, ∆µ̃H+ acts kinetically to control the rate of the process.

scholarly journals Crystal structures of bacterial Small Multidrug Resistance transporter EmrE in complex with structurally diverse substrates

2022 ◽  
Author(s):  
Ali A Kermani ◽  
Olive E. Burata ◽  
B Ben Koff ◽  
Akiko Koide ◽  
Shohei Koide ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Binding Site ◽  
Quaternary Ammonium ◽  
Structural Information ◽  
Structural Description ◽  
Small Multidrug Resistance ◽  
Novel Approach ◽  
Backbone Structure ◽  
Multidrug Resistance Transporter ◽  
Ammonium Compounds

Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of the Escherichia coli transporter, EmrE, has been studied extensively, but a lack of high-resolution structural information has impeded a structural description of its molecular mechanism. Here we apply a novel approach, multipurpose crystallization chaperones, to solve several structures of EmrE, including a 2.9 Å structure at low pH without substrate. We report five additional structures in complex with structurally diverse transported substrates, including quaternary phosphonium, quaternary ammonium, and planar polyaromatic compounds. These structures show that binding site tryptophan and glutamate residues adopt different rotamers to conform to disparate structures without requiring major rearrangements of the backbone structure. Structural and functional comparison to Gdx-Clo, an SMR protein that transports a much narrower spectrum of substrates, suggests that in EmrE, a relatively sparse hydrogen bond network among binding site residues permits increased sidechain flexibility.

scholarly journals 4096 Refined structure of human ferroportin using restraints from mass spectrometry

2020 ◽  
Vol 4 (s1) ◽  
pp. 101-102
Author(s):  
Christian S. Parry ◽  
Andrey Ivanov ◽  
Guelaguetza Vazquez-meves ◽  
Fatemah A. Alhakami ◽  
Jessika Agyepong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Model ◽  
Structural Information ◽  
Comparative Modeling ◽  
Mass Spectrometry Data ◽  
Peptide Transporter ◽  
Transmembrane Helices ◽  
Intracellular Loop ◽  
Water Solvent ◽  
Dynamics Simulations

OBJECTIVES/GOALS: Mammals require iron for hemoglobin, respiration, immunity and as cofactor in enzymes. But free iron is toxic from the production of reactive oxygen species. Ferroportin is the sole exporter of cellular iron and it crucially determines cellular and systemic iron levels. Labile iron must be tightly regulated. This requires structural understanding. METHODS/STUDY POPULATION: We built structure of human ferroportin (FPN1) using the ab ignition prediction approaches of Rosetta/Robetta and by comparative modeling with distance restraints in MODELLER. Templates selected were from solute carrier protein families of distantly related orthologs and homologs including a proton coupled peptide transporter (PDB ID: 4IKV) and the bacterial iron transporter in outward-open and inward-open states, (PDB ID: 5AYM, 5AYO). Each model was validated by experimental mass spectrometry data. The energy minimized structural model was inserted into a lipid bilayer, placed in a rectangular simulation box, covered with TIP3P water solvent balanced with counterions and conditioned. Finally, we carried out 350 nanoseconds molecular dynamics simulations. RESULTS/ANTICIPATED RESULTS: Our first model of FPN1 (571aa), using Rosetta/Robetta ab initio approach, resembles the structure of the proton-dependent transporter, POT and consists of 12 transmembrane helices. The membrane spanning helices veer away from the orientation in the structure of 4IKV. The alternate model using MODELLER and the method of satisfaction of constraints, returned one template, the structure of Bdellovibrio bacteriovorus iron (Fe2+) transporter homolog (5AYN, 440aa) with sequence identity of 19%. Aligning FPN1 on the template sequence incorporating structural information revealed better conservation (29%). This model also comprises 12 transmembrane helices in two bundles separated by a large intracellular loop. The iron binding site predicted in both models match the structures of distant bacterial homologs. DISCUSSION/SIGNIFICANCE OF IMPACT: We are using these experimentally verified structures and functional data to answer questions about the mechanism of ferroportin iron transport, structural dynamics and the significance of mutations in ferroportin seen in different populations, especially the Q248H mutation found in Africans and black Americans with moderate to high prevalence.

Alpha-periodicity analysis of small multidrug resistance (SMR) efflux transporters

1998 ◽  
Vol 76 (5) ◽  
pp. 791-797 ◽  
Author(s):  
Robert A Edwards ◽  
Raymond J Turner
Keyword(s):  
Amino Acids ◽  
Multidrug Resistance ◽  
Transmembrane Helix ◽  
Power Spectra ◽  
Substitution Matrix ◽  
Transmembrane Helices ◽  
Homologous Proteins ◽  
Small Multidrug Resistance ◽  
Amino Acid Properties ◽  
Periodicity Analysis

Proteins in the small multidrug resistance (SMR) family of transport proteins are about 110 amino acids in length and are predicted to have four transmembrane helices. This family is divided into a two groups, one of which we have referred to as small multidrug pumps (Smp) and confer resistance to a wide variety of quaternary ammonium compounds through a proton-drug efflux antiport mechanism. Members of the second group within this family have, as yet, not had their substrate profile characterized and are referred to as Sug proteins. Alpha-periodicity analysis was conducted on a set of six homologous proteins of the SMR family consisting of three established Smp and three Sug proteins. Several amino acid properties were used in the analysis including hydropathy, variability, and a substitution matrix for lipid exposed amino acids. The scanning window was varied between 8 and 14 residues and the alpha-periodicity was calculated from the peaks in the Fourier transform power spectra in the region between 3.0 and 4.3 residues/turn. This analysis adds to the hydropathy analysis to give a more confident prediction of which residues are within the lipid bilayer for each of the four transmembrane helices. Information was also obtained that allowed for the identification of zones within each transmembrane helix that face the interior of the helical bundle on one side and are lipid exposed on the other face.Key words: modeling, SMR, QAC, multidrug resistance, transporter, hydrophopathy, periodicity, amphipathicity.

scholarly journals Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter

2020 ◽  
Vol 117 (9) ◽  
pp. 4732-4740 ◽  
Author(s):  
Kevin L. Jagessar ◽  
Derek P. Claxton ◽  
Richard A. Stein ◽  
Hassane S. Mchaourab
Keyword(s):  
Pyrococcus Furiosus ◽  
Mechanistic Model ◽  
Site Directed Mutagenesis ◽  
Spin Labels ◽  
Structural Determinants ◽  
Cytotoxic Compounds ◽  
Binding Cavity ◽  
Double Electron Electron Resonance ◽  
Two Sides ◽  
Alternating Access

Multidrug and toxic compound extrusion (MATE) transporters are ubiquitous ion-coupled antiporters that extrude structurally and chemically dissimilar cytotoxic compounds and have been implicated in conferring multidrug resistance. Here, we integrate double electron–electron resonance (DEER) with functional assays and site-directed mutagenesis of conserved residues to illuminate principles of ligand-dependent alternating access of PfMATE, a proton-coupled MATE from the hyperthermophilic archaeonPyrococcus furiosus. Pairs of spin labels monitoring the two sides of the transporter reconstituted into nanodiscs reveal large-amplitude movement of helices that alter the orientation of a putative substrate binding cavity. We found that acidic pH favors formation of an inward-facing (IF) conformation, whereas elevated pH (>7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. The lipid-dependent PfMATE isomerization between OF and IF conformation is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access.

NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies

2017 ◽  
Vol 15 (03) ◽  
pp. 1750009 ◽  
Author(s):  
Bruno Grisci ◽  
Márcio Dorn
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Structural Information ◽  
Protein Structures ◽  
Three Dimensional ◽  
Conformational Flexibility ◽  
Amino Acid Sequences ◽  
Conformational Search ◽  
Back Propagation Algorithm

The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT–FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally. The proposed method manipulates structural information from the Protein Data Bank (PDB) and predicts the conformational flexibility (FLEX) of residues of a target amino acid sequence. This information may be used in three-dimensional structure prediction approaches as a way to reduce the conformational search space. The proposed method was tested with 24 different amino acid sequences. Evolving neural networks were compared against a traditional error back-propagation algorithm; results show that the proposed method is a powerful way to extract and represent structural information from protein molecules that are determined experimentally.

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