Biomaterial Database

Prediction of protein structure from sequence. 1990

M J Sternberg, and M J Zvelebil

Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, U.K.

Methods to predict the three-dimensional structure of a protein from its sequence are reviewed. The approaches to derive information about the local conformation from the local sequence include hydrophobicity plots, secondary structure prediction and the identification of short, functional sequence motifs. The most reliable method of tertiary structure prediction is model building from the experimentally determined coordinates of a protein with an homologous sequence. This approach is illustrated by a prediction of the three-dimensional structure of human cytochrome P450-IA1. If no known homologous structure is available, then the only approach is to suggest models for the tertiary fold of proteins by packing together predicted secondary structures. A three-dimensional model for the dimerisation of the transmembrane alpha-helices of neu, a tyrosine kinase growth factor receptor, is described. In general, structure prediction can suggest approaches for regulating protein activity that may lead to new pharmaceutical therapies for cancer.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D011505	Protein-Tyrosine Kinases	Protein kinases that catalyze the PHOSPHORYLATION of TYROSINE residues in proteins with ATP or other nucleotides as phosphate donors.	Tyrosine Protein Kinase,Tyrosine-Specific Protein Kinase,Protein-Tyrosine Kinase,Tyrosine Kinase,Tyrosine Protein Kinases,Tyrosine-Specific Protein Kinases,Tyrosylprotein Kinase,Kinase, Protein-Tyrosine,Kinase, Tyrosine,Kinase, Tyrosine Protein,Kinase, Tyrosine-Specific Protein,Kinase, Tyrosylprotein,Kinases, Protein-Tyrosine,Kinases, Tyrosine Protein,Kinases, Tyrosine-Specific Protein,Protein Kinase, Tyrosine-Specific,Protein Kinases, Tyrosine,Protein Kinases, Tyrosine-Specific,Protein Tyrosine Kinase,Protein Tyrosine Kinases,Tyrosine Specific Protein Kinase,Tyrosine Specific Protein Kinases
D011518	Proto-Oncogene Proteins	Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.	Cellular Proto-Oncogene Proteins,c-onc Proteins,Proto Oncogene Proteins, Cellular,Proto-Oncogene Products, Cellular,Cellular Proto Oncogene Proteins,Cellular Proto-Oncogene Products,Proto Oncogene Products, Cellular,Proto Oncogene Proteins,Proto-Oncogene Proteins, Cellular,c onc Proteins
D003577	Cytochrome P-450 Enzyme System	A superfamily of hundreds of closely related HEMEPROTEINS found throughout the phylogenetic spectrum, from animals, plants, fungi, to bacteria. They include numerous complex monooxygenases (MIXED FUNCTION OXYGENASES). In animals, these P-450 enzymes serve two major functions: (1) biosynthesis of steroids, fatty acids, and bile acids; (2) metabolism of endogenous and a wide variety of exogenous substrates, such as toxins and drugs (BIOTRANSFORMATION). They are classified, according to their sequence similarities rather than functions, into CYP gene families (>40% homology) and subfamilies (>59% homology). For example, enzymes from the CYP1, CYP2, and CYP3 gene families are responsible for most drug metabolism.	Cytochrome P-450,Cytochrome P-450 Enzyme,Cytochrome P-450-Dependent Monooxygenase,P-450 Enzyme,P450 Enzyme,CYP450 Family,CYP450 Superfamily,Cytochrome P-450 Enzymes,Cytochrome P-450 Families,Cytochrome P-450 Monooxygenase,Cytochrome P-450 Oxygenase,Cytochrome P-450 Superfamily,Cytochrome P450,Cytochrome P450 Superfamily,Cytochrome p450 Families,P-450 Enzymes,P450 Enzymes,Cytochrome P 450,Cytochrome P 450 Dependent Monooxygenase,Cytochrome P 450 Enzyme,Cytochrome P 450 Enzyme System,Cytochrome P 450 Enzymes,Cytochrome P 450 Families,Cytochrome P 450 Monooxygenase,Cytochrome P 450 Oxygenase,Cytochrome P 450 Superfamily,Enzyme, Cytochrome P-450,Enzyme, P-450,Enzyme, P450,Enzymes, Cytochrome P-450,Enzymes, P-450,Enzymes, P450,Monooxygenase, Cytochrome P-450,Monooxygenase, Cytochrome P-450-Dependent,P 450 Enzyme,P 450 Enzymes,P-450 Enzyme, Cytochrome,P-450 Enzymes, Cytochrome,Superfamily, CYP450,Superfamily, Cytochrome P-450,Superfamily, Cytochrome P450
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D013329	Structure-Activity Relationship	The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.	Relationship, Structure-Activity,Relationships, Structure-Activity,Structure Activity Relationship,Structure-Activity Relationships
D018719	Receptor, ErbB-2	A cell surface protein-tyrosine kinase receptor that is overexpressed in a variety of ADENOCARCINOMAS. It has extensive homology to and heterodimerizes with the EGF RECEPTOR, the ERBB-3 RECEPTOR, and the ERBB-4 RECEPTOR. Activation of the erbB-2 receptor occurs through heterodimer formation with a ligand-bound erbB receptor family member.	HER-2 Proto-Oncogene Protein,Proto-Oncogene Protein HER-2,Proto-Oncogene Protein p185(neu),c-erbB-2 Protein,erbB-2 Proto-Oncogene Protein,erbB-2 Receptor Protein-Tyrosine Kinase,neu Proto-Oncogene Protein,Antigens, CD340,CD340 Antigen,Erb-b2 Receptor Tyrosine Kinases,Metastatic Lymph Node Gene 19 Protein,Neu Receptor,Oncogene Protein HER-2,Proto-Oncogene Proteins c-erbB-2,Proto-oncogene Protein Neu,Receptor, Neu,Receptors, erbB-2,Tyrosine Kinase-type Cell Surface Receptor HER2,p185(c-neu),p185erbB2 Protein,CD340 Antigens,Erb b2 Receptor Tyrosine Kinases,ErbB-2 Receptor,HER 2 Proto Oncogene Protein,Oncogene Protein HER 2,Proto Oncogene Protein HER 2,Proto Oncogene Proteins c erbB 2,Proto-Oncogene Protein, HER-2,Proto-Oncogene Protein, erbB-2,Proto-Oncogene Protein, neu,Tyrosine Kinase type Cell Surface Receptor HER2,c erbB 2 Protein,erbB 2 Proto Oncogene Protein,erbB 2 Receptor Protein Tyrosine Kinase,erbB-2 Receptors,neu Proto Oncogene Protein
D066246	ErbB Receptors	A family of structurally related cell-surface receptors that signal through an intrinsic PROTEIN-TYROSINE KINASE. The receptors are activated upon binding of specific ligands which include EPIDERMAL GROWTH FACTORS, and NEUREGULINS.	EGF Receptor,Epidermal Growth Factor Receptor,Epidermal Growth Factor Receptor Family Protein,Epidermal Growth Factor Receptor Protein-Tyrosine Kinase,ErbB Receptor,HER Family Receptor,Receptor, EGF,Receptor, Epidermal Growth Factor,Receptor, TGF-alpha,Receptor, Transforming-Growth Factor alpha,Receptor, Urogastrone,Receptors, Epidermal Growth Factor-Urogastrone,TGF-alpha Receptor,Transforming Growth Factor alpha Receptor,Urogastrone Receptor,c-erbB-1 Protein,erbB-1 Proto-Oncogene Protein,EGF Receptors,Epidermal Growth Factor Receptor Family Proteins,Epidermal Growth Factor Receptor Kinase,HER Family Receptors,Proto-oncogene c-ErbB-1 Protein,Receptor Tyrosine-protein Kinase erbB-1,Receptor, ErbB-1,Receptors, Epidermal Growth Factor,Epidermal Growth Factor Receptor Protein Tyrosine Kinase,ErbB-1 Receptor,Family Receptor, HER,Family Receptors, HER,Proto oncogene c ErbB 1 Protein,Proto-Oncogene Protein, erbB-1,Receptor Tyrosine protein Kinase erbB 1,Receptor, ErbB,Receptor, ErbB 1,Receptor, HER Family,Receptor, TGF alpha,Receptor, Transforming Growth Factor alpha,Receptors, EGF,Receptors, Epidermal Growth Factor Urogastrone,Receptors, ErbB,Receptors, HER Family,c erbB 1 Protein,c-ErbB-1 Protein, Proto-oncogene,erbB 1 Proto Oncogene Protein