Polynucleotides Polypeptides

The biopolymer modeling of HyperChem includes Building polynucleotides, polypeptides and polysaccharides, Amino acid sequence (fasta format) editing, Mutations, Overlapping by RMS fit, and Merging structures. To facilitate manipulation of protein structures, there is often a need to display the protein backbone only as follows. 

Select Polynucleotide/Polypeptide/Polysaccharide from the Build menu to open a dialog box. 

Biomacromolecules are considered as single molecules when they are present in a well-defined stoichiometry and when they display little tendency to dissociate spontaneously under physiological conditions. This text deals specifically with covalent bio-macromolecnles in which monomer units are linked together by covalent bonds to form giant biomolecules. They include nucleic acids, proteins and polysaccharides (under this defiifition, biomembranes are excluded). The Web site of the International Union of Bio-chenfistry and Molecular Biology (lUBMB) at http //www.chem.qmw.ac.uk/iubmb/ provides useful information for the nomenclature and conformations of polynucleotides, polypeptides and polysaccharides (Figure 1.1). 

In the following we will briefly describe some selected examples of biohybrid structures and networks consisting of synthetic organic polymers and polynucleotides, polypeptides/proteins, and/or polysaccharides with focus on biomedical applications. In order to provide multifunctional biohybrid materials with the optimal combination of mechanical, biological, and stmctural properties for particular purposes, different design aspects must be considered. 

Organisms produce a number of biological polymers, such as polynucleotides, polypeptides, polysaccharides, polyphosphates, and polyesters. Many scientists have made efforts to elucidate their physiological role and function. The microbial poly(hydroxyalkanoates) (PHAs), a femily of polyesters, are synthesized, and accumulated within the cells of a wide variety of microorganisms [1,2]. Poly(3-hydro butyrate)... 

Theoretical methods for the investigation of interactions between polymer chains are described in Chapter 6. Besides the theoretically clear-cut but, in the case of polymers with larger unit cells, numerically unfeasible, superchain approach, theoretical perturbation methods and the mutually consistent field (MCF) procedure recently developed at Erlangen are reviewed. The first application of the MCF method, which takes into account both the electrostatic part and polarization forces, to polynucleotide-polypeptide interactions (modeling DNA-protein interactions) is presented. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

With the exception of very large systems, e.g., polymer strands (Chapter 18) and polypeptides and polynucleotides (Chapter 16), all calculations have been carried out using ab initio Hartree-Fock theory with the 3-21G basis seF. The perfomance of this technique with regard to the calculation of geometries, relative energies, dipole moments and vibrational frequencies has been extensively documented. ... 

Certain types of molecules, especially polypeptides and polynucleotides, lend themselves to synthesis on solid supports. In such syntheses, the starting material is attached to a small particle (bead) or a surface and the molecule remains attached during the course of the synthetic sequence. Solid phase synthesis also plays a key role in creation of combinatorial libraries, that is, collections of many molecules synthesized by a sequence of reactions in which the subunits are systematically varied to create a range of structures (molecular diversity). 

Isolated polynucleotide clusters from Rhodococcus opacus which encode four polypeptides possessing the activities of a NHase (a and /3 subunits), an auxiliary protein P15K that activates the NHase, and a cobalt transporter protein were expressed in Escherichia coli DSM 14459 cells [34]. Methionine nitrile was added continuously to a suspension of the transformant cells (5.6% w/v of wet cells) in phosphate buffer (50 mM, pH 7.5) at 20 °C, at a rate where the nitrile concentration did not exceed 15 g L 1 while maintaining the pH constant at 7.5. After 320 min, the nitrile was completely converted into amide, corresponding to a final product concentration of 176 gL1.4-Methylthio-a-hydroxybutyramide is readily hydrolyzed with calcium hydroxide, where the calcium salt of 4-methylthio-a-hydroxybutyric acid (MHA) can be directly used as a nutritional supplement in animal feed as an alternative to methionine or MHA. 

Polyamides are converted to polypeptides (as just shown), and nucleotides, because of the dehydrating properties of polyamides, to polynucleotides. This hypothetical model can accept the delivery of HCN polymers from space (e.g., via meteorites) as well as photochemical reactions in a reducing atmosphere. In spite of some convincing experimental evidence, the HCN world favoured by Matthews still awaits further convincing experimental evidence (this is also true for other hypothetical worlds ). 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

The bulk of all carbohydrates in nature exists in the form of polysaccharides. These are very large molecules formed by linking together long chains of monosaccharide units. These chains may be linear, like polypeptides or polynucleotides, or branched. They may contain a single type of monosaccharide unit, similar to polyglycine or polyA for example, or two or more types of monosaccharide, like nucleic acids (four types of nucleotides) or proteins (20 types of amino acids). However, polysaccharides that contain more than two types of monosaccharide are rare in nature. 

Polynucleotide a polymer formed from nucleotide subunits a synon3m for nucleic acid. Polypeptide a synonym for protein. 

Keywords Monte Carlo simulations polypeptides polynucleotides concerted rotations multicanonical ensemble torsional space... 

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