scholarly journals Structure-Functional Insight Into Transmembrane Helix Dimerization

10.5772/29637 ◽  
2012 ◽  
Author(s):  
Eduard V. ◽  
Konstantin V. ◽  
Pavel E. ◽  
Roman G. ◽  
Alexander S.
Keyword(s):  
Transmembrane Helix ◽  
Insight Into

scholarly journals Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates

2017 ◽  
Vol 28 (15) ◽  
pp. 2076-2090 ◽  
Author(s):  
Christopher J. Guerriero ◽  
Karl-Richard Reutter ◽  
Andrew A. Augustine ◽  
G. Michael Preston ◽  
Kurt F. Weiberth ◽  
...  
Keyword(s):  
Molecular Chaperones ◽  
Transmembrane Helix ◽  
Integral Membrane Proteins ◽  
Membrane Insertion ◽  
Transmembrane Helices ◽  
Vitro Assay ◽  
Dual Pass ◽  
Erad Pathway ◽  
Insight Into

Integral membrane proteins fold inefficiently and are susceptible to turnover via the endoplasmic reticulum–associated degradation (ERAD) pathway. During ERAD, misfolded proteins are recognized by molecular chaperones, polyubiquitinated, and retrotranslocated to the cytoplasm for proteasomal degradation. Although many aspects of this pathway are defined, how transmembrane helices (TMHs) are removed from the membrane and into the cytoplasm before degradation is poorly understood. In this study, we asked whether the hydrophobic character of a TMH acts as an energetic barrier to retrotranslocation. To this end, we designed a dual-pass model ERAD substrate, Chimera A*, which contains the cytoplasmic misfolded domain from a characterized ERAD substrate, Sterile 6* (Ste6p*). We found that the degradation requirements for Chimera A* and Ste6p* are similar, but Chimera A* was retrotranslocated more efficiently than Ste6p* in an in vitro assay in which retrotranslocation can be quantified. We then constructed a series of Chimera A* variants containing synthetic TMHs with a range of ΔG values for membrane insertion. TMH hydrophobicity correlated inversely with retrotranslocation efficiency, and in all cases, retrotranslocation remained Cdc48p dependent. These findings provide insight into the energetic restrictions on the retrotranslocation reaction, as well as a new computational approach to predict retrotranslocation efficiency.

scholarly journals Distinct effects of Q925 mutation on intracellular and extracellular Na+ and K+ binding to the Na+, K+-ATPase

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hang N. Nielsen ◽  
Kerri Spontarelli ◽  
Rikke Holm ◽  
Jens Peter Andersen ◽  
Anja P. Einholm ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Binding Sites ◽  
Functional Role ◽  
Transmembrane Helix ◽  
Binding Properties ◽  
Ion Translocation ◽  
Extracellular Side ◽  
Insight Into

Abstract Three Na+ sites are defined in the Na+-bound crystal structure of Na+, K+-ATPase. Sites I and II overlap with two K+ sites in the K+-bound structure, whereas site III is unique and Na+ specific. A glutamine in transmembrane helix M8 (Q925) appears from the crystal structures to coordinate Na+ at site III, but does not contribute to K+ coordination at sites I and II. Here we address the functional role of Q925 in the various conformational states of Na+, K+-ATPase by examining the mutants Q925A/G/E/N/L/I/Y. We characterized these mutants both enzymatically and electrophysiologically, thereby revealing their Na+ and K+ binding properties. Remarkably, Q925 substitutions had minor effects on Na+ binding from the intracellular side of the membrane – in fact, mutations Q925A and Q925G increased the apparent Na+ affinity – but caused dramatic reductions of the binding of K+ as well as Na+ from the extracellular side of the membrane. These results provide insight into the changes taking place in the Na+-binding sites, when they are transformed from intracellular- to extracellular-facing orientation in relation to the ion translocation process, and demonstrate the interaction between sites III and I and a possible gating function of Q925 in the release of Na+ at the extracellular side.

scholarly journals Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

2021 ◽  
Author(s):  
Koichiro E. Kishi ◽  
Yoon Seok Kim ◽  
Masahiro Fukuda ◽  
Tsukasa Kusakizako ◽  
Elina Thadhani ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Transmembrane Helix ◽  
Action Spectrum ◽  
Light Sensitivity ◽  
Structural Basis ◽  
Ion Pump ◽  
Cryo Electron Microscopy ◽  
Architectural Features ◽  
Computational Analyses ◽  
Insight Into

ChRmine, a recently-discovered bacteriorhodopsin-like cation-conducting channelrhodopsin, exhibits puzzling properties (unusually-large photocurrents, exceptional red-shift in action spectrum, and extreme light-sensitivity) that have opened up new opportunities in optogenetics. ChRmine and its homologs function as light-gated ion channels, but by primary sequence more closely resemble ion pump rhodopsins; the molecular mechanisms for passive channel conduction in this family of proteins, as well as the unusual properties of ChRmine itself, have remained mysterious. Here we present the cryo-electron microscopy structure of ChRmine at 2.0 Å resolution. The structure reveals striking architectural features never seen before in channelrhodopsins including trimeric assembly, a short transmembrane-helix 3 unwound in the middle of the membrane, a prominently-twisting extracellular-loop 1, remarkably-large intracellular cavities and extracellular vestibule, and an unprecedented hydrophilic pore that extends through the center of the trimer, separate from the three individual monomer pores. Electrophysiological, spectroscopic, and computational analyses provide insight into conduction and gating of light-gated channels with these distinct design features, and point the way toward structure-guided creation of novel channelrhodopsins for optogenetic applications in biology.

scholarly journals Crystal structure of heme A synthase from Bacillus subtilis

2018 ◽  
Vol 115 (47) ◽  
pp. 11953-11957 ◽  
Author(s):  
Satomi Niwa ◽  
Kazuki Takeda ◽  
Masayuki Kosugi ◽  
Erika Tsutsumi ◽  
Tatsushi Mogi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Transmembrane Helix ◽  
Integral Membrane Protein ◽  
Heme Binding ◽  
Terminal Oxidases ◽  
Domain Structures ◽  
Heme A Synthase ◽  
Insight Into ◽  
Heme Molecule

Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-containing integral membrane protein, and its structure and reaction mechanisms have remained unknown. Thus, little is known about HAS despite of its importance. Here we report the crystal structure of HAS from Bacillus subtilis at 2.2-Å resolution. The N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant. Many water molecules are found in the transmembrane region and around the substrate-binding site, and some of them interact with the main chain of transmembrane helix. Comparison of these two domain structures enables us to construct a substrate-heme binding state structure. This structure implies that a completely conserved glutamate, Glu57 in B. subtilis, is the catalytic residue for the formylation reaction. These results provide valuable suggestions of the substrate-heme binding mechanism. Our results present significant insight into the heme A biosynthesis.

Kinetic modeling of Nav1.7 provides insight into erythromelalgia-associated F1449V mutation

2011 ◽  
Vol 105 (4) ◽  
pp. 1546-1557 ◽  
Author(s):  
Meron Gurkiewicz ◽  
Alon Korngreen ◽  
Stephen G. Waxman ◽  
Angelika Lampert
Keyword(s):  
Markov Model ◽  
Transmembrane Helix ◽  
Pain Syndrome ◽  
Human Embryonic Kidney Cells ◽  
Whole Cell Patch Clamp ◽  
Activation Gate ◽  
Equivalent State ◽  
Single Transition ◽  
Domain Iii ◽  
Insight Into

Gain-of-function mutations of the voltage-gated sodium channel (VGSC) Nav1.7 have been linked to human pain disorders. The mutation F1449V, located at the intracellular end of transmembrane helix S6 of domain III, induces the inherited pain syndrome erythromelalgia. A kinetic model of wild-type (WT) and F1449V Nav1.7 may provide a basis for predicting putative intraprotein interactions. We semiautomatically constrained a Markov model using stochastic search algorithms and whole cell patch-clamp recordings from human embryonic kidney cells transfected with Nav1.7 and its F1449V mutation. The best models obtained simulated known differences in action potential thresholds and firing patterns in spinal sensory neurons expressing WT and F1449V. The most suitable Markov model consisted of three closed, one open, and two inactivated states. The model predicted that the F1449V mutation shifts occupancy of the closed states closer to the open state, making it easier for the channel pore to open. It also predicted that F1449V's second inactivated state is more than four times more likely to be occupied than the equivalent state in WT at hyperpolarized potentials, although the mutation still lowered the firing threshold of action potentials. The differences between WT and F1449V were not limited to a single transition. Thus a point mutation in position F1449, while phenotypically most probably affecting the activation gate, may also modify channel functions mediated by structures in more distant areas of the channel protein.

scholarly journals Structures of dimeric human NPC1L1 provide insight into mechanisms for cholesterol absorption

2021 ◽  
Vol 7 (34) ◽  
pp. eabh3997
Author(s):  
Tao Long ◽  
Yang Liu ◽  
Yu Qin ◽  
Russell A. DeBose-Boyd ◽  
Xiaochun Li
Keyword(s):  
Low Density Lipoprotein ◽  
Transmembrane Helix ◽  
Dietary Cholesterol ◽  
Density Lipoprotein ◽  
Cholesterol Absorption ◽  
Oligomeric State ◽  
Cryo Electron Microscopy ◽  
Niemann Pick ◽  
Circulating Levels ◽  
Insight Into

Polytopic Niemann-Pick C1-like 1 (NPC1L1) plays a major role in intestinal absorption of biliary cholesterol, vitamin E (VE), and vitamin K (VK). The drug ezetimibe inhibits NPC1L1-mediated absorption of cholesterol, lowering of circulating levels of low-density lipoprotein cholesterol. Here, we report cryo–electron microscopy structures of human NPC1L1 (hNPC1L1) bound to either cholesterol or a lipid resembling VE. These findings, together with functional assays, reveal that the same intramolecular channel in hNPC1L1 mediates transport of VE and cholesterol. hNPC1L1 exists primarily as a homodimer; dimerization is mediated by aromatic residues within a region of transmembrane helix 2 that exhibits a horizonal orientation in the membrane. Mutation of tryptophan-347 lies in this region disrupts dimerization and the resultant monomeric NPC1L1 exhibits reduced efficiency of cholesterol uptake. These findings identify the oligomeric state of hNPC1L1 as a target for therapies that inhibit uptake of dietary cholesterol and reduce the incidence of cardiovascular disease.

scholarly journals Structure-Functional Insight into Transmembrane Helix Dimerization by Protein Engineering, Molecular Modeling and Heteronuclear NMR Spectroscopy

2012 ◽  
Vol 102 (3) ◽  
pp. 470a ◽  
Author(s):  
Eduard Bocharov ◽  
Pavel Volynsky ◽  
Konstantin Mineev ◽  
Dmitry Lesovoy ◽  
Kirill Nadezhdin ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Nmr Spectroscopy ◽  
Protein Engineering ◽  
Heteronuclear Nmr ◽  
Transmembrane Helix ◽  
Heteronuclear Nmr Spectroscopy ◽  
Insight Into

scholarly journals Pharmacokinetic modeling reveals parameters that govern tumor targeting and delivery by a pH-Low Insertion Peptide (pHLIP)

2020 ◽  
Vol 118 (1) ◽  
pp. e2016605118
Author(s):  
Alexander A. Svoronos ◽  
Donald M. Engelman
Keyword(s):  
Normal Tissue ◽  
Tumor Targeting ◽  
Pharmacokinetic Model ◽  
Transmembrane Helix ◽  
Membrane Insertion ◽  
Targeted Imaging ◽  
Wild Type ◽  
Helix Formation ◽  
Insertion Process ◽  
Insight Into

A pH-Low Insertion Peptide (pHLIP) is a pH-sensitive peptide that undergoes membrane insertion, resulting in transmembrane helix formation, on exposure to acidity at a tumor cell surface. As a result, pHLIPs preferentially accumulate within tumors and can be used for tumor-targeted imaging and drug delivery. Here we explore the determinants of pHLIP insertion, targeting, and delivery through a computational modeling approach. We generate a simple mathematical model to describe the transmembrane insertion process and then integrate it into a pharmacokinetic model, which predicts the tumor vs. normal tissue biodistribution of the most studied pHLIP, “wild-type pHLIP,” over time after a single intravenous injection. From these models, we gain insight into the various mechanisms behind pHLIP tumor targeting and delivery, as well as the various biological parameters that influence it. Furthermore, we analyze how changing the properties of pHLIP can influence the efficacy of tumor targeting and delivery, and we predict the properties for optimal pHLIP phenotypes that have superior tumor targeting and delivery capabilities compared with wild-type pHLIP.

Calibration problems in hydrogen luminosities

1966 ◽  
Vol 24 ◽  
pp. 322-330
Author(s):  
A. Beer
Keyword(s):  
Galactic Structure ◽  
B Stars ◽  
Insight Into

The investigations which I should like to summarize in this paper concern recent photo-electric luminosity determinations of O and B stars. Their final aim has been the derivation of new stellar distances, and some insight into certain patterns of galactic structure.

Stochasting modeling of planetary ring systems

1984 ◽  
Vol 75 ◽  
pp. 461-469 ◽  
Author(s):  
Robert W. Hart
Keyword(s):  
Maximum Entropy ◽  
Ring System ◽  
The Sun ◽  
Ultimate State ◽  
Interparticle Interactions ◽  
Ring Systems ◽  
First Order ◽  
Planetary Ring ◽  
Insight Into

ABSTRACTThis paper models maximum entropy configurations of idealized gravitational ring systems. Such configurations are of interest because systems generally evolve toward an ultimate state of maximum randomness. For simplicity, attention is confined to ultimate states for which interparticle interactions are no longer of first order importance. The planets, in their orbits about the sun, are one example of such a ring system. The extent to which the present approximation yields insight into ring systems such as Saturn's is explored briefly.

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