• The biological polymers that have been most widely analyzed in structural and practical terms are proteins and nucleic acids (DNA and RNA) [2-5]. (opioid-receptors.com)
  • In addition, it can react with proteins and nucleic acids, causing biological damage to cells and carbonyl stress. (frontiersin.org)
  • active site - A region in proteins and nucleic acids (that participate in chemical reactions), where reacting molecules (substrates) bind and make specific contacts necessary for chemical catalysis. (rcsb.org)
  • The answer, of course, is proteins and nucleic acids. (sciencing.com)
  • Proteins and nucleic acids are critical components of the nervous system. (iterainfo.com)
  • Stability of protein and nucleic acid structures. (pathfinderacademy.in)
  • It is now well established that the information needed to determine the three-dimensional structure of a protein is entirely contained in its linear amino acid sequence. (opioid-receptors.com)
  • The protein folding problem was first introduced in 1968 and referred to the challenge to predict the 3D structure of a protein based solely on its sequence of amino acids. (febs.org)
  • The AlphaFold method is not designed to predict structures for complexes of protein with other proteins, nucleic acids or small molecule ligands. (febs.org)
  • AlphaFold models do not include any non-protein components such as cofactors, metals, ligands including drug-like molecules, ions, carbohydrates and other post-translational modifications. (febs.org)
  • Each structure in the database represents a possible conformation of the protein of interest. (febs.org)
  • basic concepts of sequence alignment: local and global alignments, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results Multiple sequence alignments (MSA): the need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc. (entrance.net.in)
  • 3-10 helix - A type of protein secondary structural element that is more tightly coiled than the alpha helix (3 amino acids per turn with 10 atoms in the ring completed by each intra-helical hydrogen bond). (rcsb.org)
  • alignment - A comparison of two or more gene or protein sequences in order to determine their degree of similarity in amino acid or bases, respectively. (rcsb.org)
  • allosteric protein - A protein that changes among two or more structural conformations upon binding to a small molecule called an effector. (rcsb.org)
  • nucleic acid and protein . (sciencing.com)
  • Surprisingly, the nucleic acid portion contributes to most of the structure of the ribosome while the proteins fill in gaps and amp up protein synthesis, which would occur much more slowly without them. (sciencing.com)
  • Knowledge of the three-dimensional structures of the carbo-hydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. (iucr.org)
  • The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. (iucr.org)
  • Glycosylation is classified by the way the carbohydrate chain is linked to the protein. (iucr.org)
  • Low-frequency resonances of biomacromolecules are generated by THz wave radiation, which affects protein spatial conformation and DNA. (iterainfo.com)
  • Nucleic acid having higher density finds place as 'core', medium denser protein in intermediate and least dense fat in the periphery. (webmedcentral.com)
  • Various interior dynamics including self organization of macromolecules, protein conformation, movement of human thoracic diaphragm, formation of logarithmic spiral in nature were discussed in the light of potential energy of self gravity and kinetic energy of metabolic energy. (webmedcentral.com)
  • There are 20 different types of amino acids that can be combined to form a protein. (atlasbars.com)
  • The specific sequence of amino acids in a protein determines how it will fold, and this folding determines the protein's final shape. (atlasbars.com)
  • The primary structure of a protein is the linear chain of amino acids, while the secondary structure is the folding of the primary structure into a helix or sheet. (atlasbars.com)
  • The structure of the fatty acids determines whether or not the fat is considered saturated or unsaturated. (compnetsys.com)
  • Fatty acids can be saturated or unsaturated. (compnetsys.com)
  • Fatty acids are lipid monomers that consist of a hydrocarbon chain with a carboxyl group attached at the end. (compnetsys.com)
  • The monomers that make up a lipid are glycerol and fatty acids. (compnetsys.com)
  • Vaughn and Gardner (1993) showed that four reactive carbonyl species (RCSs) generated by the oxidation of polyunsaturated fatty acids (PUFA) in soybean, including (E)-2-Hexenal, (E)-2-nonenal, (E)-4-Hydroxy-2-nonenal and (Z)-3-nonenal could stress the coexisting fungi. (frontiersin.org)
  • It is worth noting that the antibacterial mechanism of fatty acids was studied. (frontiersin.org)
  • Unsaturated fatty acids can be cis or trans isomers. (ivy-way.com)
  • Triglycerides are formed by condensation from three fatty acids and one glycerol. (ivy-way.com)
  • 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)
  • Bronsted's acids (proton acids) are neutral molecules or ions, which are able to donate proton (proton donors). (ppt-online.org)
  • The definition of the em spatial conformation /em of either a microscopic or a macroscopic em anatomical structure /em (sub-cellular entity, cell, cells, organ, apparatus, organism), and the definition of a switch or em changes /em in its em shape /em , are still unresolved problems, much debated by contemporary morphologists [7-12]. (opioid-receptors.com)
  • The ribosome uses this mRNA as a template to build long chains of amino acids, supplied to the ribosome by another nucleic acid called transfer RNA (tRNA). (sciencing.com)
  • Proteins are made up of long chains of amino acids that are connected by peptide bonds. (atlasbars.com)
  • These long chains of amino acids fold and twist into complex three-dimensional shapes that determine their function. (atlasbars.com)
  • Current research in my lab focuses on the study of the diverse functional roles of structural disorder and its modulation in carbohydrates (glycans), proteins and glycoproteins with implications on molecular recognition . (maynoothuniversity.ie)
  • NA removes sialic acids from glycans, which enables virus particles to be released from the cell surface after assembly and from decoy receptors (e.g., in mucus). (cdc.gov)
  • AlphaFold is an Artificial Intelligence (AI) system developed by DeepMind that predicts a protein's three-dimensional (3D) structure from its amino-acid sequence. (embl.org)
  • These bioelements can be classified into primary, secondary and tertiary elements or trace elements according to the conformation of the biomolecules. (exampleslab.com)
  • By following specific rules for drawing these projections, one can depict complex carbohydrates such as glucose and fructose in a way that conveys their structural information. (khanacademy.org)
  • These structures define the structural rearrangements that occur from the outward-open to inward-open conformations, and provide insight into the mechanism of neurotransmitter transport and ibogaine inhibition. (rcsb.org)
  • The amino acid residues important in these kringle/ligand binding interactions have been proposed by structural determinations, and their relative importance quantified by site-directed mutagenesis experimentation. (embl.de)
  • During her M.S., she focused on the development of fluorescent amino acids and peptide synthesis. (rsc.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)
  • It was subsequently realised that proteins (or domains) with similar amino-acid sequences have similar overall 3D structures, and that the degree of this similarity (measured by the root-mean-square distance, or RMSD, between corresponding atoms in the two models) is correlated with the degree of sequence similarity. (embl.org)
  • As a result, AlphaFold is able to produce accurate structure predictions even for amino-acid sequences that it has never encountered before. (embl.org)
  • The heavy chain of HPlm consists of five repeating triple-disulfide-linked peptide regions, c. 80 amino acid residues in length, termed kringles (K), that are responsible for interactions of HPlg and HPlm with substrates, inhibitors and regulators of HPlg activation. (embl.de)
  • Knowing that ribosomes synthesize proteins from nucleic acid templates, you can probably guess the two types of molecule from which a ribosome is made. (sciencing.com)
  • This makes sense because the ribosome's job in the cell is to use a nucleic acid template called messenger RNA (mRNA) to build new proteins. (sciencing.com)
  • Ribosomes receive bits of this blueprint via specialized nucleic acids called messenger RNA (mRNA) . (sciencing.com)
  • Once complete, the chain folds in a specific way, called a conformation . (sciencing.com)
  • Here we report cryo-electron microscopy structures of SERT-ibogaine complexes captured in outward-open, occluded and inward-open conformations. (rcsb.org)
  • This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. (iucr.org)
  • Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site . (wn.com)
  • Kringle domains [ ( PUBMED:3131537 ) ( PUBMED:3891096 ) ( PUBMED:1879523 ) ] are characterised by a triple loop, 3-disulphide bridge structure, whose conformation is defined by a number of hydrogen bonds and small pieces of anti-parallel beta-sheet. (embl.de)
  • These Multiple Choice Questions (MCQs) should be practiced to improve the Nucleic Acid Structure skills required for various interviews (campus interview, walk-in interview, company interview), placement, entrance exam and other competitive examinations. (dapzoi.com)
  • Therefore, carbohydrate chains are usually displayed as a tree-like two-dimensional graph. (iucr.org)
  • Isolation and purification of nucleic acids. (nipaers.com)
  • They can also interact with nucleic acids, like DNA and RNA, regulating gene expression. (atlasbars.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)
  • For example, the backbone carbon atom linked to the carbonyl group in an alpha amino acid, to which the side chain is attached. (rcsb.org)
  • It is characterized by hydrogen bonds between the carbonyl group (-C=O) of one amino acid and the amino (N-H) group of the amino acid 4 residues below it along the helix. (rcsb.org)
  • The resulting HPlm contains a heavy chain of 561 amino acid residues, originating from the N-terminus of HPlg, doubly disulfide-linked to a light chain of 230 amino acid residues. (embl.de)
  • amino acid - A building block of proteins is an alpha amino acid which contains a basic amino group, an acidic carboxyl group, and a hydrogen or organic side chain attached to the central carbon atom. (rcsb.org)
  • The normal form is easily digested by proteinase K and much of the conformation is α-helix. (sanfoundry.com)
  • alanine (Ala, A) - Alpha amino acid with a non-polar side chain. (rcsb.org)
  • Alanine is an amino acid that is used to make proteins. (iterainfo.com)
  • More specific examples of conformational isomerism are detailed elsewhere: Ring conformation Cyclohexane conformations, including with chair and boat conformations among others. (wikipedia.org)
  • Carbohydrates differ from proteins in two important features. (iucr.org)
  • Glycine is an amino acid with a number of important functions in the body. (iterainfo.com)