Decision letter: Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

The recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters toward the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

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Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

10.1101/2020.05.14.096792 ◽

2020 ◽

Cited By ~ 1

Author(s):

Katherine E. Huffer ◽

Antoniya A. Aleksandrova ◽

Andrés Jara-Oseguera ◽

Lucy R. Forrest ◽

Kenton J. Swartz

Keyword(s):

Transmembrane Domain ◽

Ion Selectivity ◽

Structural Data ◽

Trp Channel ◽

Structural Basis ◽

Global Alignment ◽

Functional Studies ◽

Domain Structures ◽

Mechanistic Basis ◽

Channel Structures

AbstractThe recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters towards the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

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The Pivotal Roles of the Epithelial Membrane Protein Family in Cancer Invasiveness and Metastasis

Cancers ◽

10.3390/cancers11111620 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1620 ◽

Cited By ~ 3

Author(s):

Ahmat Amin ◽

Shimizu ◽

Ogita

Keyword(s):

Cell Migration ◽

Cancer Progression ◽

Cancer Biology ◽

Transmembrane Domain ◽

Small Gtpase ◽

Migration And Invasion ◽

Amino Acid Residues ◽

Peripheral Myelin Protein 22 ◽

Domain Structures ◽

Cancer Invasiveness

The members of the family of epithelial membrane proteins (EMPs), EMP1, EMP2, and EMP3, possess four putative transmembrane domain structures and are composed of approximately 160 amino acid residues. EMPs are encoded by the growth arrest-specific 3 (GAS3)/peripheral myelin protein 22 kDa (PMP22) gene family. The GAS3/PMP22 family members play roles in cell migration, growth, and differentiation. Evidence indicates an association of these molecules with cancer progression and metastasis. Each EMP has pro- and anti-metastatic functions that are likely involved in the complex mechanisms of cancer progression. We have recently demonstrated that the upregulation of EMP1 expression facilitates cancer cell migration and invasion through the activation of a small GTPase, Rac1. The inoculation of prostate cancer cells overexpressing EMP1 into nude mice leads to metastasis to the lymph nodes and lungs, indicating that EMP1 contributes to metastasis. Pro-metastatic properties of EMP2 and EMP3 have also been proposed. Thus, targeting EMPs may provide new insights into their clinical utility. Here, we highlight the important aspects of EMPs in cancer biology, particularly invasiveness and metastasis, and describe recent therapeutic approaches.

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7 × 7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors

Journal of Structural Biology ◽

10.1016/j.jsb.2017.02.005 ◽

2017 ◽

Vol 199 (2) ◽

pp. 87-101 ◽

Cited By ~ 2

Author(s):

Ting Wang ◽

Yang Wang ◽

Leihan Tang ◽

Yong Duan ◽

Haiguang Liu

Keyword(s):

G Protein ◽

Transmembrane Domain ◽

Quantitative Comparison ◽

G Protein Coupled Receptors ◽

New Method ◽

Domain Structures ◽

G Protein Coupled

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Assessment of the transmembrane domain structures in GPCR Dock 2013 models

Journal of Structural Biology ◽

10.1016/j.jsb.2017.11.007 ◽

2018 ◽

Vol 201 (3) ◽

pp. 210-220 ◽

Cited By ~ 1

Author(s):

Ting Wang ◽

Haiguang Liu ◽

Yong Duan

Keyword(s):

Transmembrane Domain ◽

Domain Structures

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A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

10.1101/209213 ◽

2017 ◽

Author(s):

Julia Koehler Leman ◽

Richard Bonneau

Keyword(s):

Membrane Proteins ◽

Biological Function ◽

Transmembrane Domain ◽

Search Space ◽

Full Length ◽

Conformational Search ◽

Membrane Domains ◽

Native Structure ◽

Domain Structures ◽

Fragment Insertion

AbstractMembrane proteins composed of soluble and membrane domains are often studied one domain at a time. However, to understand the biological function of entire protein systems and their interactions with each other and drugs, knowledge of full-length structures or models is required. Although few computational methods exist that could potentially be used to model full-length constructs of membrane proteins, none of these methods are perfectly suited for the problem at hand. Existing methods either require an interface or knowledge of the relative orientations of the domains, are not designed for domain assembly, and none of them are developed for membrane proteins. Here we describe the first domain assembly protocol specifically designed for membrane proteins that assembles intra- and extracellular soluble domains and the transmembrane domain into models of the full-length membrane protein. Our protocol does not require an interface between the domains and samples possible domain orientations based on backbone dihedrals in the flexible linker regions, created via fragment insertion, while keeping the transmembrane domain fixed in the membrane. Our method, mp_domain_assembly, implemented in RosettaMP samples domain orientations close to the native structure and is best used in conjunction with experimental data to reduce the conformational search space.

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Nucleation of Disorder in Fe3Al Alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100061574 ◽

1967 ◽

Vol 25 ◽

pp. 312-313

Author(s):

P. R. Swann ◽

W. R. Duff ◽

R. M. Fisher

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Annealing Temperature ◽

Antiphase Domain ◽

Effect Of Temperature ◽

Domain Structures ◽

Transmission Electron ◽

Domain Boundaries ◽

Higher Temperature ◽

The One

Recently we have investigated the phase equilibria and antiphase domain structures of Fe-Al alloys containing from 18 to 50 at.% Al by transmission electron microscopy and Mössbauer techniques. This study has revealed that none of the published phase diagrams are correct, although the one proposed by Rimlinger agrees most closely with our results to be published separately. In this paper observations by transmission electron microscopy relating to the nucleation of disorder in Fe-24% Al will be described. Figure 1 shows the structure after heating this alloy to 776.6°C and quenching. The white areas are B2 micro-domains corresponding to regions of disorder which form at the annealing temperature and re-order during the quench. By examining specimens heated in a temperature gradient of 2°C/cm it is possible to determine the effect of temperature on the disordering reaction very precisely. It was found that disorder begins at existing antiphase domain boundaries but that at a slightly higher temperature (1°C) it also occurs by homogeneous nucleation within the domains. A small (∼ .01°C) further increase in temperature caused these micro-domains to completely fill the specimen.

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Temperature Dependence of Magnetic Domains and Wall Structures

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010009573x ◽

1972 ◽

Vol 30 ◽

pp. 496-497

Author(s):

Sonoko Tsukahara ◽

Tadami Taoka ◽

Hisao Nishizawa

Keyword(s):

Temperature Dependence ◽

Domain Walls ◽

Magnetic Domain ◽

Iron Film ◽

Objective Lens ◽

Lorentz Microscopy ◽

Domain Structures ◽

Wall Structures ◽

Crystal Films ◽

Metallurgical Structure

The high voltage Lorentz microscopy was successfully used to observe changes with temperature; of domain structures and metallurgical structures in an iron film set on the hot stage combined with a goniometer. The microscope used was the JEM-1000 EM which was operated with the objective lens current cut off to eliminate the magnetic field in the specimen position. Single crystal films with an (001) plane were prepared by the epitaxial growth of evaporated iron on a cleaved (001) plane of a rocksalt substrate. They had a uniform thickness from 1000 to 7000 Å.The figure shows the temperature dependence of magnetic domain structure with its corresponding deflection pattern and metallurgical structure observed in a 4500 Å iron film. In general, with increase of temperature, the straight domain walls decrease in their width (at 400°C), curve in an iregular shape (600°C) and then vanish (790°C). The ripple structures with cross-tie walls are observed below the Curie temperature.

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Tubulin structure at intermediate resolution

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140634 ◽

1995 ◽

Vol 53 ◽

pp. 852-853

Author(s):

K. H. Downing ◽

S. G. Wolf ◽

E. Nogales

Keyword(s):

High Resolution ◽

Structural Data ◽

Therapeutic Drug ◽

Zinc Ions ◽

Two Dimensional ◽

X Ray Diffraction ◽

X Ray ◽

Negative Stain ◽

Functional Mechanisms ◽

Tubulin Structure

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.

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