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An alpha helix is a sequence of amino acids in a protein that are twisted into a coil.
Integrins are transmembrane receptors that help cell-cell and cell-extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
An integral, or intrinsic, membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins can be classified as IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane are surrounded by annular lipids, which are defined as lipids that are in direct contact with a membrane protein. Such proteins can only be separated from the membranes by using detergents, nonpolar solvents, or sometimes denaturing agents.
Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane and can either penetrate the membrane (transmembrane) or associate with one or the other side of a membrane. Peripheral membrane proteins are transiently associated with the cell membrane.
A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.
Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein.
A coiled coil is a structural motif in proteins in which 2–7 alpha-helices are coiled together like the strands of a rope. They have been found in roughly 5-10% of proteins and have a variety of functions. They are one of the most widespread motifs found in protein-protein interactions. To aid protein study, several tools have been developed to predict coiled-coils in protein structures. Many coiled coil-type proteins are involved in important biological functions, such as the regulation of gene expression — e.g., transcription factors. Notable examples are the oncoproteins c-Fos and c-Jun, as well as the muscle protein tropomyosin.
The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
The inner mitochondrial membrane (IMM) is the mitochondrial membrane which separates the mitochondrial matrix from the intermembrane space.
Actinin is a microfilament protein. The functional protein is an anti-parallel dimer, which cross-links the thin filaments in adjacent sarcomeres, and therefore coordinates contractions between sarcomeres in the horizontal axis. Alpha-actinin is a part of the spectrin superfamily. This superfamily is made of spectrin, dystrophin, and their homologous and isoforms. In non-muscle cells, it is found by the actin filaments and at the adhesion sites.The lattice like arrangement provides stability to the muscle contractile apparatus. Specifically, it helps bind actin filaments to the cell membrane. There is a binding site at each end of the rod and with bundles of actin filaments.
Mitochondrial carriers are proteins from solute carrier family 25 which transfer molecules across the membranes of the mitochondria. Mitochondrial carriers are also classified in the Transporter Classification Database. The Mitochondrial Carrier (MC) Superfamily has been expanded to include both the original Mitochondrial Carrier (MC) family and the Mitochondrial Inner/Outer Membrane Fusion (MMF) family.
Membranome is the set of biological membranes existing in a specific organism. The term was proposed by British biologist Thomas Cavalier-Smith to discuss epigenetics of biological membranes. The term was also used to define the entire set of membrane proteins in an organism or a combination of membrane proteome and lipidome.
Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer. Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes.
Cell surface receptors are receptors that are embedded in the plasma membrane of cells. They act in cell signaling by receiving extracellular molecules. They are specialized integral membrane proteins that allow communication between the cell and the extracellular space. The extracellular molecules may be hormones, neurotransmitters, cytokines, growth factors, cell adhesion molecules, or nutrients; they react with the receptor to induce changes in the metabolism and activity of a cell. In the process of signal transduction, ligand binding affects a cascading chemical change through the cell membrane.
WALP peptides are a class of synthesized, membrane-spanning α-helices composed of tryptophan (W), alanine (A), and leucine (L) amino acids. They are designed to study properties of proteins in lipid membranes such as orientation, extent of insertion, and hydrophobic mismatch.
Cation diffusion facilitators (CDFs) are transmembrane proteins that provide tolerance of cells to divalent metal ions, such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these divalent metal ions from cells. However, some members of the CDF superfamily are implicated in ion uptake. All members of the CDF family possess six putative transmembrane spanners with strongest conservation in the four N-terminal spanners. The Cation Diffusion Facilitator (CDF) Superfamily includes the following families:
The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location as well as the type of protein secondary structure found in proteins using only backbone chemical shift data The technique was invented by David S. Wishart in 1992 for analyzing 1Hα chemical shifts and then later extended by him in 1994 to incorporate 13C backbone shifts. The original CSI method makes use of the fact that 1Hα chemical shifts of amino acid residues in helices tends to be shifted upfield relative to their random coil values and downfield in beta strands. Similar kinds of upfield and downfield trends are also detectable in backbone 13C chemical shifts.
The peridinin-chlorophyll-protein complex is a soluble molecular complex consisting of the peridinin-chlorophyll a-protein bound to peridinin, chlorophyll, and lipids. The peridinin molecules absorb light in the blue-green wavelengths and transfer energy to the chlorophyll molecules with extremely high efficiency. PCP complexes are found in many photosynthetic dinoflagellates, in which they may be the primary light-harvesting complexes.
A single-pass membrane protein also known as single-spanning protein or bitopic protein is a transmembrane protein that spans the lipid bilayer only once. These proteins may constitute up to 50% of all transmembrane proteins, depending on the organism, and contribute significantly to the network of interactions between different proteins in cells, including interactions via transmembrane alpha helices. They usually include one or several water-soluble domains situated at the different sides of biological membranes, for example in single-pass transmembrane receptors. Some of them are small and serve as regulatory or structure-stabilizing subunits in large multi-protein transmembrane complexes, such as photosystems or the respiratory chain. More than 2300 single-pass membrane proteins were identified in the human genome.
Proton-Translocating NAD(P)+ Transhydrogenase (E.C. 7.1.1.1) is an enzyme in that catalyzes the translocation of hydrons that are connected to the redox reaction NADH + NADP+ + H+outside => NAD+ + NADPH + H+inside
References
- 1 2 Lomize, Andrei L; Lomize, Mikhail A; Krolicki, SR; Pogozheva, Irina D. (2017). "Membranome: a database for proteome-wide analysis of single-pass membrane proteins". Nucleic Acids Res. 45 (D1): D250–D255. doi:10.1093/nar/gkw712. PMC 5210604 . PMID 27510400.
- ↑ Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers, by: Lomize, Andrei L., Hage, Jacob M., Pogozheva, Irina D., Bioinformatics , volume: 34, issue: 6 pages: 1061-1062.
- ↑ TMDOCK: An Energy -Based Method for Modeling alpha-Helical Dimers in Membranes, by Lomize, Andrei L. and Pogozheva, Irina D., J. Mol. Biol., Volume: 429 Issue: 3, pages: 390-398
- ↑ Dimer verification page of Membranome
- ↑ Lomize, A. L.; Schnitzer, K. A.; Todd, S. C.; Cherepanov, S.; Outeiral, C.; Deane, C. M.; Pogozheva, I. D. (2022). "Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models". Protein Science . 31 (5): e4318. doi:10.1002/pro.4318. PMC 9047035 . PMID 35481632.
- ↑ Thermodynamic model of secondary structure for alpha-helical peptides and proteins, by Lomize, AL and Mosberg, HI, Biopolymers, vol 42, issue: 2, pages: 239-269
- ↑ Evolution and adaptation of single-pass transmembrane proteins, by: Pogozheva, Irina D. and Lomize, Andrei L., Biochimica et. Biophysica Acta Biomembranes, Volume: 1860 Issue: 2 Pages: 364-377
- ↑ Membrane proteins structures: A review on computational modeling tools, by Almeida, Jose G.; Preto, Antonio J., Koukos, Panagiotis I., Bonvin, Alexandre M. J. J., Moreira, Irina S. Biochimica et. Biophysica Acta, vol. 1859, issue: 10, pages: 2021-2039
- ↑ NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins, by Lesovoy, D. M., Mineev, K. S., Bragin, P. E., Bocharova, O. V., Bocharov, E. V., Arseniev, A. S., J. Biomol. NMR, vol. 69, issue: 3, pages 165-179
- ↑ Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism, by Mineev, Konstantin S., Goncharuk, Sergey A., Goncharuk, Marina V., Volynsky, Pavel E., Novikova, Ekaterina V., Arseinev, Alexander S., Scientific Reports, vol. 7, article number: 6864