A5068406248- Protein Structure and Dynamics
- Lipid Membrane Structure and Behavior
- RNA and protein synthesis mechanisms
- Neuroscience and Neuropharmacology Research
- Amino Acid Enzymes and Metabolism
- Ion channel regulation and function
- Receptor Mechanisms and Signaling
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Molecular Sensors and Ion Detection
- Bacterial Genetics and Biotechnology
- DNA and Nucleic Acid Chemistry
- Neurotransmitter Receptor Influence on Behavior
- Mass Spectrometry Techniques and Applications
- Drug Transport and Resistance Mechanisms
- Analytical Chemistry and Chromatography
- Ion Transport and Channel Regulation
- Nanopore and Nanochannel Transport Studies
- Spectroscopy and Quantum Chemical Studies
- Electron Spin Resonance Studies
- Parathyroid Disorders and Treatments
- Advanced NMR Techniques and Applications
- Genomics and Phylogenetic Studies
- Magnesium in Health and Disease
- Ion Channels and Receptors
National Institute of Neurological Disorders and Stroke
2015-2024
National Institutes of Health
2015-2024
Max Planck Institute of Biophysics
2008-2016
Max Planck Society
2009-2015
Howard Hughes Medical Institute
2004-2008
Columbia University
2004-2007
MRC Mitochondrial Biology Unit
2003
Wellcome Trust
2003
Royal Society
2003
Johns Hopkins Medicine
2003
Long-distance RNA transport enables local protein synthesis at metabolically-active sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for in which granules "hitchhike" on moving lysosomes. In vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), granule-associated phosphoinositide-binding protein,...
Crystal structures of LeuT, a bacterial homologue mammalian neurotransmitter transporters, show molecule bound substrate that is essentially exposed to the extracellular space but occluded from cytoplasm. Thus, there must exist an alternate conformation for LeuT in which accessible cytoplasm and corresponding mechanism switches accessibility one side membrane other. Here, we identify cytoplasmic pathway serotonin transporter (SERT) (a member same family as LeuT). We also propose model...
The recent determination of the crystal structure leucine transporter from Aquifex aeolicus (aaLeuT) has provided significant insights into function neurotransmitter:sodium symporters. Transport by aaLeuT is Cl(-) independent, whereas many symporters higher organisms depend on ions. However, only ion identified in interacts with nonconserved residues extracellular loops, and thus relevance this binding site unclear. Here, we use calculations pK(A)s homology modeling to predict location a...
Glutamate transporters regulate synaptic concentrations of this neurotransmitter by coupling its flux to that sodium and other cations. Available crystal structures an archeal homologue these transporters, GltPh, resemble extracellular-facing state, in which the bound substrate is occluded only a small helical hairpin segment called HP2. However, pathway cytoplasmic side membrane not clearly apparent. We previously modeled alternate state transporter from neurotransmitter:sodium symporter...
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest MFS fold facilitates transport through rearrangement their two six-helix bundles around a central ligand binding site; how this is achieved, however, poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we...
Molecular dynamics simulations allow a direct study of the structure and membrane proteins lipids. We describe behavior aromatic residues lipid properties in POPE POPC bilayer models with Escherichia coli OmpF trimer, single alamethicin Influenza M2 helices, 4-helix bundles, two 6-helix channel models. The total simulation time is over 24 ns, systems containing solvent, protein, between 104 318 Various types adjustment lipids occur, depending on size protein degree hydrophobic mismatch...
We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling backbone conformations, side chain addition, use statistical potential to select subset these and, finally, an energy minimization ranking with all-atom force field. find that Direct Tweak algorithm used previously developed LOOPY program is successful generating ensemble on average are closer native conformation than those generated by other...
X-ray crystal structures have revealed that numerous secondary transporter proteins originally categorized into different sequence families share similar structures, namely, the LeuT fold. The core of this fold consists two units five transmembrane helices, whose conformations been proposed to exchange form alternate states required for transport. That these are related implies LeuT-like transporters evolved from gene-duplication and fusion events. Thus, origins structural repeat may be...
Serotonin transporter (SERT) is the main target for widely used antidepressant agents. Several of these drugs, including imipramine, citalopram, sertraline, and fluoxetine (Prozac), bound more avidly to SERT in presence Cl − . In contrast, did not enhance cocaine or paroxetine binding. A binding site recently identified SERT, shown be important dependent transport, was also critical dependence affinity. Mutation residues contributing this eliminated -mediated affinity increase imipramine...
Significance Most studies of neurotransmitter:sodium symporter (NSS) function and dynamics have been carried out in detergent even though the activity these integral membrane proteins is heavily modulated by surrounding lipids. Here, we reconstituted prokaryotic homolog LeuT into nanodiscs subjected preparation to hydrogen–deuterium exchange mass spectrometry reveal a global view hallmarks transporter two disparate conformations. The data were interpreted with aid molecular simulations,...
Sodium-coupled substrate transport plays a central role in many biological processes. However, despite knowledge of the structures several sodium-coupled transporters, location sodium-binding site(s) often remains unclear. Several these have five transmembrane-helix inverted-topology repeat, LeuT-like (FIRL) fold, whose pseudosymmetry has been proposed to facilitate alternating-access mechanism required for transport. Here, we provide biophysical, biochemical, and computational evidence two...
We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The makes available two operational modes AlignMe: (i) sequence to alignment, taking sequences in fasta format as input, combining information about each from multiple sources and producing (PW mode); (ii) alignments create family-averaged hydropathy profile (HP mode). For PW mode, four different optimized parameter sets are provided, suited pairs with specific similarity level. These...
The recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties this important family ion proteins. To facilitate mechanistic investigations, we constructed structure-based alignment transmembrane domains 120 structures. Comparison determined in absence or presence activating stimuli reveals similar constrictions central permeation pathway near intracellular end S6 helices, pointing to conserved cytoplasmic gate and...