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polypeptides

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Overview of polypeptide structure. Presented here are the basic structures of an amino acid and an example of a polypeptide, with the amide bond (CONH) indicated by the arrow. Note that the peptide amide bond has partial p bond character, and adopts a planar structure. Examples of primary sequence (6-residue polypeptide presented in 3- and 1-letter amino acid code formats), secondary structure (37-residue alpha-helix), and tertiary structure (65-residues orthogonally arranged beta-hairpin structure) are given. Although not shown, quaternary structure is defined as the assemblage of individual protein subunits which are stabilized as a complex by non-covalent bonds between subunits.
Published: 03 January 2003
Figure 5. Overview of polypeptide structure. Presented here are the basic structures of an amino acid and an example of a polypeptide, with the amide bond (CONH) indicated by the arrow. Note that the peptide amide bond has partial p bond character, and adopts a planar structure. Examples
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Schematic to show how the three polypeptide chains of the collagen macromolecule are wound in a coiled-coil helix. (a) Each polypeptide chain is composed of glycine, proline and hydroxyproline aminoacid residues (black spheres). The distance between adjacent residues is 3.1 Å. Each of the polypeptide chain is wound around its own long axis (“minor helix” axis) as a left-handed helix in a three-fold screw fashion, resulting in a primary repeat distance of 9.3 Å. Each chain is located at the vertex of an equilateral triangle and they are parallel; (b, c) The individual “minor helix” axes of the three chains are now coiled about the central axis (“major helix” axis) in a long right-handed helix; (d) This slightly distorts the distance between adjacent residues to 2.86 Å, yielding a repeat distance of the major helix axis to 28.6 Å, but gives rise to a very highly repetitive structure, sufficiently ordered to generate a wide angle X-ray diffraction pattern. [Reprinted with permission from Glimcher (1960). Copyright AAAS.]
Published: 01 January 2006
Figure 4. Schematic to show how the three polypeptide chains of the collagen macromolecule are wound in a coiled-coil helix. (a) Each polypeptide chain is composed of glycine, proline and hydroxyproline aminoacid residues (black spheres). The distance between adjacent residues is 3.1 Å. Each
Journal Article
Published: 03 January 2003
Reviews in Mineralogy and Geochemistry (2003) 54 (1): 31–56.
...Figure 5. Overview of polypeptide structure. Presented here are the basic structures of an amino acid and an example of a polypeptide, with the amide bond (CONH) indicated by the arrow. Note that the peptide amide bond has partial p bond character, and adopts a planar structure. Examples...
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FTIR spectroscopy of clay bubbles in biofilms, showing not only Si–O and Al–O bands due to clay minerals, but also various kinds of organic bands, such as fatty acids, nucleic acids and polypeptides. * Possible assignments after Filip and Hermann, (2001).
Published: 01 June 2005
Figure 7. FTIR spectroscopy of clay bubbles in biofilms, showing not only Si–O and Al–O bands due to clay minerals, but also various kinds of organic bands, such as fatty acids, nucleic acids and polypeptides. * Possible assignments after Filip and Hermann, (2001) .
Journal Article
Journal: PALAIOS
Published: 30 April 2021
PALAIOS (2021) 36 (4): 155–164.
... gram of bone. MALDI-TOF analysis of the extracted protein demonstrated the presence of approximately 5 kD molecules in one fossil sample, consistent with the presence of highly fragmented polypeptides. An LC-MS/MS analysis of the fragmentation pattern of the tryptic digest of extracted protein...
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Overview of protein translation. The scheme for building the polypeptide chain using the codons provided by mRNA starts with the assembly of the small and large ribosomal subunits at the mRNA AUG initiation codon to form the ribosomal complex. This assembly takes place at the AUG initiation codon of the mRNA, and requires the aminoacyl tRNA-Met and proteins called initiation factors to allow ribosomal assembly to proceed. Next, with the help of elongation factor proteins, the aminoacyl tRNA which has an anticodon that matches the next mRNA codon enters the “A” site of the ribosome. The peptidyl transferase enzyme will catalyze the formation of a peptide bond between Met and the new amino acid, leading to the release of the tRNA that was originally linked to Met. The new Met-AA-tRNA complex is translocated to the “P” site, leaving the “A” site vacant for the next incoming tRNA-AA aminoacyl whose anticodon matches the next mRNA codon. The ribosomal complex proceeds in a 5′ to 3′ direction along the mRNA, synthesizing the nascent peptide chain from the N-terminal to the C-terminal end, using the repetitive process just described. The arrival of the ribosome at the stop codon, combined with the action of releasing factor proteins, leads to the disassembly of the ribosomal complex, the last tRNA, and the release of the polypeptide chain.
Published: 03 January 2003
Figure 4. Overview of protein translation. The scheme for building the polypeptide chain using the codons provided by mRNA starts with the assembly of the small and large ribosomal subunits at the mRNA AUG initiation codon to form the ribosomal complex. This assembly takes place at the AUG
Journal Article
Published: 01 August 2014
European Journal of Mineralogy (2014) 26 (4): 523–535.
... observed in experiments using synthetic polypeptides or SOM from corals. In the presence of SOMs and diffusing magnesium ions, the analyses of the precipitates suggested that crystallization proceeded through transient amorphous calcium carbonate phases. These favoured the crystallization of aragonite...
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Series: Clay Minerals Society Workshop Lectures
Published: 01 January 2007
DOI: 10.1346/CMS-WLS-15.8
EISBN: 9781881208358
... Abstract The use of biopolymers in the preparation of clay mineral-based nanocomposites paves the way for development of an emerging class of bio-nanohybrid systems consisting of unique structural and/or functional properties. Natural polymers such as polysaccharides, polypeptides and proteins...
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Journal Article
Published: 01 July 2004
American Mineralogist (2004) 89 (7): 1048–1055.
... with lower pI. In contrast, calcite (pH pzc = 9.5) adsorbs a variety of amino acids with a range of pI. Calcite thus represents a more plausible template than quartz for prebiotic selection and organization of homochiral polypeptides. * E-mail: [email protected] 29 01 2004 16 09 2003...
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Series: AAPG Memoir
Published: 01 January 1974
DOI: 10.1306/M20377C25
EISBN: 9781629812151
... suggests that minerals in sediments can act as catalysts, in a manner similar to the function of enzymes in cellular systems. Minerals also are capable of synthesizing polypeptides, polysaccharides, or lipids from basic monomers; in brief, like certain macromolecules, minerals function as templates...
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Chemical synthesis of biomacromolecules. This scheme has a general application to the syntheses of polypeptides, carbohydrates, and oligonucleotides and has been used recently to generate defined-length polymers and other organic molecules. The protecting groups at both ends of the monomer differ in terms of the reagents required for their removal; this insures that only one specific end become deprotected at any given step in the scheme.
Published: 03 January 2003
Figure 12. Chemical synthesis of biomacromolecules. This scheme has a general application to the syntheses of polypeptides, carbohydrates, and oligonucleotides and has been used recently to generate defined-length polymers and other organic molecules. The protecting groups at both ends
Journal Article
Journal: Elements
Published: 01 April 2009
Elements (2009) 5 (2): 111–116.
... mechanical resistance, to mimic the exceptional features of natural biohybrid materials. Natural polymers such as polysaccharides, polypeptides, and proteins intimately mixed within clay mineral assemblies have key advantages. These nontoxic, biodegradable, and biocompatible materials may lead to so-called...
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Journal Article
Published: 01 April 2010
Clays and Clay Minerals (2010) 58 (2): 272–279.
..., and various molecular-sized proteins including polypeptides and enzymes into the surrounding environments. Among these organic molecules, organic acids and polysaccharides are commonly present in soil and various sediments at sufficient concentrations to impact mineral weathering ( Barker et al ., 1997...
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Journal Article
Published: 01 January 2013
Reviews in Mineralogy and Geochemistry (2013) 75 (1): 607–648.
... by covalent peptide bonds into the polypeptide chain. However, their most surprising characteristic is the fact that each polypeptide chain folds into a unique three-dimensional structure that is defined by the amino acid sequence. This feature makes proteins stand out among all macromolecules, biological...
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Journal Article
Published: 01 August 2021
Clays and Clay Minerals (2021) 69 (4): 434–442.
... that the Candida antarctica lipase B (CALB) immobilized on poly (glycidyl methacrylate-co-methylacrylate)/feather polypeptide (P(GMA-coMA)/FP) nanofibrous membranes that contain reactive epoxy groups and biocompatible FP preserved ~38% of the catalytic activity after treatment at 70°C for 3 h (Liu et al., 2018a...
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(a) Schematic of the proposed 3D organization of the collagen molecules in a collagen fibril of bone and other fibrous connective tissues, based on studies of rat tail tendon. Collagen fibrils illustrating the “hole zone” and the formation of channels across the diameter of a collagen fibril. Intermolecular spaces are called “pores.” (b) Schematic of proposed steric arrangement of the Ca–Pi nanocrystals of bone in the early stages of mineralization. A few nanocrystals have also been deposited in the “pores.” (c) Schematic of the later stages of calcification with continued deposition of bone nanocrystals into the intermolecular pore spaces between collagen molecules. (d) Schematic depiction of the Hodge and Petruska (1963) channel model, and the location of mineral deposition in channels during early and late mineralization, and in the intermolecular (pore) spaces in the later stages of mineralization. Collagen molecules are shown as spheres numbered 1, 2, 3, 4; the three polypeptide chains constituting each molecule are shown only in molecule 1 as empty and filled “small spots” [Figs. a–c reproduced from Glimcher (1960). Copyright AAAS. Fig. d used with permission of Taylor and Francis from Katz et al. (1989).].
Published: 01 January 2006
in the later stages of mineralization. Collagen molecules are shown as spheres numbered 1, 2, 3, 4; the three polypeptide chains constituting each molecule are shown only in molecule 1 as empty and filled “small spots” [Figs. a–c reproduced from Glimcher (1960) . Copyright AAAS. Fig. d used with permission
Journal Article
Published: 01 July 2000
Geological Magazine (2000) 137 (4): 471–472.
... the polypeptides (the precursors of the proteins) are ‘read off’ the DNA strand, she shows how it is seriously misleading to regard the relevant segment of DNA as simply a template that can be divorced from the overall developmental context in which it finds itself. Equally upsetting to the atomistic view...
Journal Article
Published: 01 May 2001
Journal of Sedimentary Research (2001) 71 (3): 430–435.
..., such as glycoproteins, glycine, and polypeptides (i.e., polyaspartates) favors the precipitation of vaterite ( Kitano and Hood 1965 ). These last organic compounds are especially important for the precipitation of the oriented fibers of vaterite ( Falini et al. 1998 ; Gower and Tirrell 1998 ). The presence...
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Journal Article
Published: 03 January 2003
Reviews in Mineralogy and Geochemistry (2003) 54 (1): 291–327.
... domuncula ( Krasko et al. 2000 ) have 70% identical and 79% similar (identical plus physico-chemically related amino acids) with the T. aurantia silicatein polypeptide. In contrast to a cathepsin isolated from the sponge G. cydonium ( Krasko et al. 1997 ) the silicatein sequences have two potential...
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Journal Article
Published: 01 July 2005
American Mineralogist (2005) 90 (7): 1213–1217.
...-mediated biomineralization strategy outlined above, we performed bio-inspired model experiments for CaCO 3 precipitation, which were observed directly at the nanometer scale with an atomic force microscope (AFM). We used the polypeptide polyaspartate (pAsp), polyanionic chain molecules of amino acid...
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