• While simple molecules can be described by these types of conformations, more complex molecules require the use of the Klyne-Prelog system to describe the different conformers. (wikipedia.org)
  • Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. (cnr.it)
  • M. Yevdokimov, "Magnetic properties of copper as a constituent of nanobridges formed between spatially fixed deoxyribonucleic acid molecules", JETP Letters, Vol. 81, 2005, pp. 327-329. (scirp.org)
  • Isolated nucleic acid molecules encoding the peptides are also disclosed. (justia.com)
  • RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. (aip.org)
  • many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
  • Bronsted's acids (proton acids) are neutral molecules or ions, which are able to donate proton (proton donors). (ppt-online.org)
  • Definition of the bioactive conformation of biologically active analogs derived from synthetic molecules, or from natural compounds whose pharmacological characteristics are well known. (biu.ac.il)
  • Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. (biorxiv.org)
  • Bio-polymers include peptides and proteins, polysaccharides (carbohydrates), nucleic acids. (ppt-online.org)
  • The four families of organic compounds with important biological functionsâ carbohydrates, lipids, proteins, and nucleic acidsâ are covered here. (compnetsys.com)
  • Monomers and Polymers of Carbs, Lipids, Proteins and Nucleic Acids. (compnetsys.com)
  • They are therefore also called polymers Carbohydrates, lipids, proteins, and nucleic acids are all examples of polymers which is why polymers are a key component of human composition. (compnetsys.com)
  • PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). (lookformedical.com)
  • This is in contrast with the exponential complexity of the amino acid-level configuration space of proteins. (biomedcentral.com)
  • The number of degrees of freedom needed for the description, comparison and classification of the macroscopic, biologically-relevant features of proteins is necessarily much smaller than that associated with the collection of amino acids. (biomedcentral.com)
  • A disadvantage of the rmsd -based measures is that it assumes a strict one-to-one correspondence between at least the C alpha (C α ) atom coordinates of the compared proteins, i.e., it requires an alignment at the amino acid level of detail. (biomedcentral.com)
  • Here, we present a 3D-printable kit for the construction of DNA and peptide nucleic acid (PNA). (allenpress.com)
  • We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence. (cnr.it)
  • Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. (cnr.it)
  • in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. (cnr.it)
  • We show here that the cementoin domain adopts an α-helical conformation both by circular dichroism and nuclear magnetic resonance analyses in the presence of membrane mimetics, a characteristic shared with a large number of linear polycationic antimicrobial peptides. (biomedcentral.com)
  • This group includes lipids, which are not high molecular combinations by themselves but in the organism they are usually bonded to other biopolymers. (ppt-online.org)
  • A lipids is made out of a carbon backbone and fatty acid tails. (compnetsys.com)
  • For example, the formation of lipid domains in a copolymer-rich membrane was described with lipids of high T m such as hydro-genated soy phosphatidylcholine (HSPC) [15] or DPPC (1,2-dipal- Lipids are the polymers of fatty acids that contain a long, non-polar hydrocarbon chain with a small polar region containing oxygen. (compnetsys.com)
  • While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. (wikipedia.org)
  • A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
  • The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. (bvsalud.org)
  • Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. (researchgate.net)
  • Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences Between Available Variants of the AMBER RNA Force Fields. (upol.cz)
  • Stability and mechanism of threose nucleic acid toward acid-mediated degradation. (uci.edu)
  • Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
  • Only minor changes in the positions of amino acid residues present in the vicinity of the mutated Trp56 were observed in case of this mutation. (org.pk)
  • As more research labs and classrooms dive into the field of structural nucleic acid nanotechnology, students and researchers need access to interactive, dynamic, handheld models. (allenpress.com)
  • Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. (biorxiv.org)
  • Further investigations for the non-testosterone-based platinum agent reveal the occurrence of insignificant change of DNA conformation due to the absence of testosterone ligand in such agent. (biomedcentral.com)
  • Finally, to our knowledge, the presented structure-search machinery is the only one to permit arbitrary combinations of amino-acid-type constraints, secondary structure constraints, distance constraints, and sequence separation constraints. (biomedcentral.com)
  • 1995. Significance of bound water to local chain conformations in protein crystals . (ibpc.fr)
  • Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. (upol.cz)
  • Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. (wikipedia.org)
  • The study of the energetics between different conformations is referred to as conformational analysis. (wikipedia.org)
  • More specific examples of conformational isomerism are detailed elsewhere: Ring conformation Cyclohexane conformations, including with chair and boat conformations among others. (wikipedia.org)
  • Nucleotide bases as CH-Acids. (org.ua)
  • Protein conformation is critically linked to function and often controlled by interactions with regulatory factors. (cipsm.de)
  • Shorter Is Better: The α-(l)-Threofuranosyl Nucleic Acid Modification Improves Stability, Potency, Safety, and Ago2 Binding and Mitigates Off-Target Effects of Small Interfering RNAs. (uci.edu)
  • NMR spectroscopy or X-ray crystallography, but important width measurements at a single resonance frequency (or questions remain concerning the energetics, stability, and magnetic field strength), making it difficult to separate dynamics of this structurally diverse nucleic acid class. (lu.se)
  • Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the "standard" B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. (hindawi.com)
  • Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. (allenpress.com)
  • Here we propose such a parameterization and study its relationship to the standard Euclidian description based on amino acid representative coordinates. (biomedcentral.com)
  • Dynamic and flexible nucleic acid models can provide current and future scientists with physical intuition for the structure of DNA and the ways that DNA and its synthetic mimics can be used to build self-assembling structures and advanced nanomachines. (allenpress.com)
  • Guanine quadruplexes are nucleic acid structures built ions in slow exchange with bulk ions. (lu.se)
  • During her M.S., she focused on the development of fluorescent amino acids and peptide synthesis. (rsc.org)
  • Here we report the selection of camelid-derived single-domain antibodies (nanobodies) that modulate the conformation and spectral properties of the green fluorescent protein (GFP). (cipsm.de)
  • The energy parameters are also different for the two nucleic acids. (wikipedia.org)
  • H. Tokumitsu, J. Hiratsuka, Y. Sakurai, T. Kobayashi, H. Ichikawa, Y. Fukumori, "Gadolinium neutron-capture therapy using novel gadopentetic acid-chitosan complex nanoparticles: in vivo growth suppression of experimental melanoma solid tumor", Cancer Letters, Vol. 150, pp. 177-182. (scirp.org)
  • For experimental methods, see Nucleic acid structure determination . (wikipedia.org)
  • The tautomerism of the nucleic acid bases revisited: from non-interacting to interacting bases. (org.ua)
  • The local changes that occur in the surface accessibilities of amino acids in response to the incorporation of mutated residues are presented in Table. (org.pk)
  • The order of amino acids as they occur in a polypeptide chain. (lookformedical.com)
  • Nucleic Acids Research. (umassmed.edu)
  • H. Tokumitsu, H. Ichikawa, Y. Fukumori, "Chitosan-gadopentetic acid complex nanoparticles for gadolinium neutron-capture therapy of cancer: preparation of novel emulsion-droplet coalescence technique and characterization", Pharmaceutical Research, Vol. 16, 1999, pp. 1830-1835. (scirp.org)
  • Structure of the human clamp loader reveals an autoinhibited conformation of a substrate-bound AAA+ switch. (umassmed.edu)
  • This article is about the computational prediction of nucleic acid structure. (wikipedia.org)
  • Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
  • Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. (bvsalud.org)
  • The structure of the fatty acids determines whether or not the fat is considered saturated or unsaturated. (compnetsys.com)
  • How do the elastic constants of nucleic acids change under mechanical stress? (salvatoreassenza.com)
  • New article on the force-dependent elastic constants of nucleic acids out in Nanoscale! (salvatoreassenza.com)
  • The present investigations provide useful information of DNA conformation affected by a testosterone-based platinum complex at the atomic level. (biomedcentral.com)
  • Side chain accessibilities (å2) of amino acids in the vicinity of Phe56 and the corresponding mutated residues in wild type and mutated human gB-crystallin models respectively. (org.pk)
  • Therefore, for some purposes, the description of the configuration based on amino acid coordinates is over-detailed. (biomedcentral.com)
  • This will be achieved mainly by means of our coarse-grained model MADna , which provides an accurate sequence-dependent description of the elasticity and conformation of double-stranded DNA based on a recent extensive dataset of all-atom simulations. (salvatoreassenza.com)
  • The three eclipsed conformations, in which the dihedral angles are zero, are transition states (energy maxima) connecting two equivalent energy minima, the staggered conformers. (wikipedia.org)
  • The three eclipsed conformations with dihedral angles of 0°, 120°, and 240° are transition states between conformers. (wikipedia.org)
  • Stereo-isomery is divided into conformation and configuration. (ppt-online.org)
  • Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid. (uci.edu)
  • In this work, we present a method that generates plausible physics-based protein motions and conformations. (biorxiv.org)
  • A common feature ascribed to AMP is their ability to interact with the negatively charged bacterial membranes and polyanionic cell surface (lipopolysaccharide (LPS) of Gram-negative and lipoteichoic acid of Gram-positive bacteria). (biomedcentral.com)