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Other proteins that serve structural functions are motor proteins such as myosin, kinesin, and dynein, which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually. They also generate the forces exerted by contracting muscles [31] :258–64,272 and play essential roles in intracellular transport. Finally, the gold-standard method of cellular localization is immunoelectron microscopy. This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques. The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest. [63] Many proteins are composed of several protein domains, i.e. segments of a protein that fold into distinct structural units. Domains usually also have specific functions, such as enzymatic activities (e.g. kinase) or they serve as binding modules (e.g. the SH3 domain binds to proline-rich sequences in other proteins). Margolin W (January 2000). "Green fluorescent protein as a reporter for macromolecular localization in bacterial cells". Methods. 20 (1): 62–72. doi: 10.1006/meth.1999.0906. PMID 10610805. Hohsaka T, Sisido M (December 2002). "Incorporation of non-natural amino acids into proteins". Current Opinion in Chemical Biology. 6 (6): 809–15. doi: 10.1016/S1367-5931(02)00376-9. PMID 12470735.
Quinary structure: the signatures of protein surface that organize the crowded cellular interior. Quinary structure is dependent on transient, yet essential, macromolecular interactions that occur inside living cells. Mayhew TM, Lucocq JM (August 2008). "Developments in cell biology for quantitative immunoelectron microscopy based on thin sections: a review". Histochemistry and Cell Biology. 130 (2): 299–313. doi: 10.1007/s00418-008-0451-6. PMC 2491712. PMID 18553098. a b c Stoddart, Charlotte (1 March 2022). "Structural biology: How proteins got their close-up". Knowable Magazine. doi: 10.1146/knowable-022822-1 . Retrieved 25 March 2022. Sanger F. (1958), Nobel lecture: The chemistry of insulin (PDF), Nobelprize.org, archived (PDF) from the original on 2013-03-19 , retrieved 2016-02-09 A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).Muirhead H, Perutz MF (August 1963). "Structure of hemoglobin. A three-dimensional fourier synthesis of reduced human hemoglobin at 5.5 Å resolution". Nature. 199 (4894): 633–38. Bibcode: 1963Natur.199..633M. doi: 10.1038/199633a0. PMID 14074546. S2CID 4257461. Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes the EC number system provides a functional classification scheme. Similarly, the gene ontology classifies both genes and proteins by their biological and biochemical function, but also by their intracellular location. Mariotti F, Gardner CD. Dietary protein and amino acids in vegetarian diets—a review. Nutrients. 2019;11(11):2661. doi:10.3390/nu11112661 Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid. [1] Noted examples at the time included albumin from egg whites, blood serum albumin, fibrin, and wheat gluten.
a b c d e f g Murray RF, Harper HW, Granner DK, Mayes PA, Rodwell VW (2006). Harper's Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. ISBN 978-0-07-146197-9. Other possibilities exist, as well. For example, immunohistochemistry usually uses an antibody to one or more proteins of interest that are conjugated to enzymes yielding either luminescent or chromogenic signals that can be compared between samples, allowing for localization information. Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation. [62] While this technique does not prove colocalization of a compartment of known density and the protein of interest, it does increase the likelihood, and is more amenable to large-scale studies. See also: Glycan-protein interactions Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigenMendive-Tapia D, Mangaud E, Firmino T, de la Lande A, Desouter-Lecomte M, Meyer HD, Gatti F (2018). "Multidimensional Quantum Mechanical Modeling of Electron Transfer and Electronic Coherence in Plant Cryptochromes: The Role of Initial Bath Conditions". J. Phys. Chem. B. 122 (1): 126–136. doi: 10.1021/acs.jpcb.7b10412. PMID 29216421. Mulder GJ (1838). "Sur la composition de quelques substances animales". Bulletin des Sciences Physiques et Naturelles en Néerlande: 104. Scalvini B, Sheikhhassani V, Woodard J, Aupič J, Dame RT, Jerala R, Mashaghi A, Topology of Folded Molecular Chains: From Single Biomolecules to Engineered Origami. Trends in Chemistry 2(7), P609-622 (2020) https://www.sciencedirect.com/science/article/pii/S2589597420301118] Ardejani MS, Powers ET, Kelly JW (August 2017). "Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities". Accounts of Chemical Research. 50 (8): 1875–1882. doi: 10.1021/acs.accounts.7b00195. PMC 5584629. PMID 28723063.
Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG ( adenine– uracil– guanine) is the code for methionine. Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. [31] :1002–42 Genes encoded in DNA are first transcribed into pre- messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid. In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. [35] protein, highly complex substance that is present in all living organisms. Proteins are of great nutritional value and are directly involved in the chemical processes essential for life. The importance of proteins was recognized by chemists in the early 19th century, including Swedish chemist Jöns Jacob Berzelius, who in 1838 coined the term protein, a word derived from the Greek prōteios, meaning “holding first place.” Proteins are species-specific; that is, the proteins of one species differ from those of another species. They are also organ-specific; for instance, within a single organism, muscle proteins differ from those of the brain and liver. Copland JA, Sheffield-Moore M, Koldzic-Zivanovic N, Gentry S, Lamprou G, Tzortzatou-Stathopoulou F, Zoumpourlis V, Urban RJ, Vlahopoulos SA (June 2009). "Sex steroid receptors in skeletal differentiation and epithelial neoplasia: is tissue-specific intervention possible?". BioEssays. 31 (6): 629–41. doi: 10.1002/bies.200800138. PMID 19382224. S2CID 205469320. Gutteridge A, Thornton JM (November 2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences. 30 (11): 622–29. doi: 10.1016/j.tibs.2005.09.006. PMID 16214343. Ekman, Diana; Björklund, Åsa K.; Frey-Skött, Johannes; Elofsson, Arne (April 2005). "Multi-domain Proteins in the Three Kingdoms of Life: Orphan Domains and Other Unassigned Regions". Journal of Molecular Biology. 348 (1): 231–243. doi: 10.1016/j.jmb.2005.02.007.a b c Perrett D (August 2007). "From 'protein' to the beginnings of clinical proteomics". Proteomics: Clinical Applications. 1 (8): 720–38. doi: 10.1002/prca.200700525. PMID 21136729. S2CID 32843102. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. [30] :232–34 Structural proteins Fehrenbach KS, Righter AC, Santo RE. A critical examination of the available data sources for estimating meat and protein consumption in the USA. Public Health Nutr. 2016;19(8):1358-1367. doi:10.1017/S1368980015003055 Martin, P D; Malley, D F; Manning, G.; Fuller, L. (Nov 1, 2002). "Determination of soil organic carbon and nitrogen at the field level using near-infrared spectroscopy". Canadian Journal of Soil Science. 82 (4): 413–422. doi: 10.4141/S01-054.
a b Case LP, Daristotle L, Hayek MG, Raasch MF (2010). Canine and Feline Nutrition-E-Book: A Resource for Companion Animal Professionals. Elsevier Health Sciences. As of 2017 [update], the Protein Data Bank has over 126,060 atomic-resolution structures of proteins. [23] Number of proteins encoded in genomes Mostproteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation. [27] :36 Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. [27] :37 Biochemists often refer to four distinct aspects of a protein's structure: [27] :30–34 Kauzmann W (May 1956). "Structural factors in protein denaturation". Journal of Cellular Physiology. 47 (Suppl 1): 113–31. doi: 10.1002/jcp.1030470410. PMID 13332017. Sanger F (1949). "The terminal peptides of insulin". The Biochemical Journal. 45 (5): 563–74. doi: 10.1042/bj0450563. PMC 1275055. PMID 15396627.Sankaranarayanan R, Moras D (2001). "The fidelity of the translation of the genetic code". Acta Biochimica Polonica. 48 (2): 323–35. doi: 10.18388/abp.2001_3918. PMID 11732604. Other methods for elucidating the cellular location of proteins requires the use of known compartmental markers for regions such as the ER, the Golgi, lysosomes or vacuoles, mitochondria, chloroplasts, plasma membrane, etc. With the use of fluorescently tagged versions of these markers or of antibodies to known markers, it becomes much simpler to identify the localization of a protein of interest. For example, indirect immunofluorescence will allow for fluorescence colocalization and demonstration of location. Fluorescent dyes are used to label cellular compartments for a similar purpose. [61] The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis, [66] which allows the separation of many proteins, mass spectrometry, [67] which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow the detection of the relative levels of the various proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein–protein interactions. [68] The total complement of biologically possible such interactions is known as the interactome. [69] A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics. [70] Structure determination Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus. [31] :1002–42
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