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T Blundell

Publications and source records attributed to T Blundell.

At least 19 recordsLinked to original sources
PubMed1998

Phosducin induces a structural change in transducin beta gamma.

BACKGROUND: Phosducin binds tightly to the beta gamma subunits (Gt beta gamma) of the heterotrimeric G protein transducin, preventing Gt beta gamma reassociation with Gt alpha-GDP and thereby inhibiting the G-protein cycle. Phosducin-like proteins appear to be widely distributed and may play important roles in regulating many heterotrimeric G-protein signaling pathways. RESULTS: The 2.8 A crystal structure of a complex of bovine retinal phosducin with Gt beta gamma shows how the two domains of phosducin cover one side and the top of the seven-bladed beta propeller of Gt beta gamma. The binding of phosducin induces a distinct structural change in the beta propeller of Gt beta gamma, such that a small cavity opens up between blades 6 and 7. Electron density in this cavity has been assigned to the farnesyl moiety of the gamma subunit. CONCLUSIONS: beta gamma subunits of heterotrimeric G proteins can exist in two distinct conformations. In the R (relaxed) state, corresponding to the structure of the free beta gamma or the structure of beta gamma in the alpha beta gamma heterotrimer, the hydrophobic farnesyl moiety of the gamma subunit is exposed, thereby mediating membrane association. In the T (tense) state, as observed in the phosducin-Gt beta gamma structure, the farnesyl moiety of the gamma subunit is effectively buried in the cavity formed between blades 6 and 7 of the beta subunit. Binding of phosducin to Gt beta gamma induces the formation of this cavity, resulting in a switch from the R to the T conformation. This sequesters beta gamma from the membrane to the cytosol and turns off the signal-transduction cascade. Regulation of this membrane association/dissociation switch of Gt beta gamma by phosducin may be a general mechanism for attenuation of G protein coupled signal transduction cascades.

Amino Acid Sequence↗
PubMed1997

Domain structure of hepatocyte growth factor/scatter factor (HGF/SF).

The modular structure of hepatocyte growth factor/scatter factor (HGF/SF) has facilitated structure-function analysis. Domain deletion experiments have established that the N-domain, kringle 1 and kringle 2 are essential for HGF/SF activity on target cells and that, conversely, truncated variants containing the N-domain and kringle 1 (NK1) or kringles 1 and 2 (NK2) exhibit partial agonistic or antagonistic activity depending on target cells and the presence of full length HGF/SF. The 3D structures of the six domains of HGF/SF have been modelled on the structure of homologues, offering interesting insights into putative mechanisms of domain interactions, receptor binding and activation. The predictions offered by such models are currently assessed by protein engineering techniques and will ultimately be measured against experimental structures.

Gene Deletion↗
PubMed1995

Exploring the binding preferences/specificity in the active site of human cathepsin E.

Aspartic proteinases are produced in the human body by a variety of cells. Some of these proteins, examples of which are pepsin, gastricsin, and renin, are secreted and exert their effects in the extracellular spaces. Cathepsin D and cathepsin E on the other hand are intracellular enzymes. The least characterized of the human aspartic proteinases is cathepsin E. Presented here are results of studies designed to characterize the binding specificities in the active site of human cathepsin E with comparison to other mechanistically similar enzymes. A peptide series based on Lys-Pro-Ala-Lys-Phe*Nph-Arg-Leu was generated to elucidate the specificity in the individual binding pockets with systematic substitutions in the P5-P2, and P2'-P3' based on charge, hydrophobicity, and hydrogen bonding. Also, to explore the S2 binding preferences, a second series of peptides based on Lys-Pro-Ile-Glu-Phe*Nph-Arg-Leu was generated with systematic replacements in the P2 position. Kinetic parameters were determined for both sets of peptides. The results were correlated to a rule-based structural model of human cathepsin E, constructed on the known three-dimensional structures of several highly homologous aspartic proteinases; porcine pepsin, bovine chymosin, yeast proteinase A, human cathepsin D, and mouse and human renin. Important specificity-determining interactions were found in the S3 (Glu-13) and S2 (Thr-222, Gln-287, Leu-289, Ile-300) subsites.

Amino Acid Sequence↗
PubMed1994

Crystal structure of the pleckstrin homology domain from dynamin.

The pleckstrin homology (PH) domain is a conserved module present in many signal transducing and cytoskeletal proteins. Here we report the 2.8 A crystal structure of the PH domain from dynamin. This domain consists of seven beta-strands forming two roughly orthogonal antiparallel beta-sheets terminating with an amphipathic alpha-helix. The structure also reveals a non-covalent dimeric association of the PH domain and a hydrophobic pocket surrounded by a charged rim. The dynamin PH domain structure is discussed in relation to its potential role in mediating interactions between proteins.

Amino Acid Sequence↗
PubMed1992

Structural biology and diabetes mellitus: molecular pathogenesis and rational drug design.

Emerging concepts in the aetiology and pathogenesis of Type 1 (insulin-dependent) diabetes mellitus may offer new opportunities for treatment and cure. Here we describe recent advances in structural molecular biology and molecular design relevant to rational drug discovery. Such approaches focus on the three-dimensional structures of macromolecules and their interactions. In the coming decade such techniques may be applied to a wide variety of diabetes-related targets.

Amino Acid Sequence↗
PubMed1989

X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes.

Knowledge of the tertiary structure of the proteinase from human immunodeficiency virus HIV-1 is important to the design of inhibitors that might possess antiviral activity and thus be useful in the treatment of AIDS. The conserved Asp-Thr/Ser-Gly sequence in retroviral proteinases suggests that they exist as dimers similar to the ancestor proposed for the pepsins. Although this has been confirmed by X-ray analyses of Rous sarcoma virus and HIV-1 proteinases, these structures have overall folds that are similar to each other only where they are also similar to the pepsins. We now report a further X-ray analysis of a recombinant HIV-1 proteinase at 2.7 A resolution. The polypeptide chain adopts a fold in which the N- and C-terminal strands are organized together in a four-stranded beta-sheet. A helix precedes the single C-terminal strand, as in the Rous sarcoma virus proteinase and also in a synthetic HIV-1 proteinase, in which the cysteines have been replaced by alpha-aminobuytric acid. The structure reported here provides an explanation for the amino acid invariance amongst retroviral proteinases, but differs from that reported earlier in some residues that are candidates for substrate interactions at P3, and in the mode of intramolecular cleavage during processing of the polyprotein.

Crystallography↗
PubMed1989

Structure-function relationships of growth factors and their receptors.

The primary amino acid sequences of several receptor tyrosine kinases have recently made it possible to deduce similarities in the molecular organization of these large multidomain proteins. This has allowed a classification of these receptors into three groups (see Waterfield this Issue and for review in Ref.1). Class I includes the EGF receptor and the neu proto-oncogene, Class II includes the insulin and insulin-like growth factor 1 (IGF-1) receptors, and Class III the platelet derived growth factor (PDGF) and the colony stimulating factor 1 (CSF-1) receptors. The conformation of the ligands for the Classes I and II receptors have been defined using X-ray diffraction, 2-D nuclear magnetic resonance (NMR) and knowledge based modelling procedures. It seems that the ligands are more diverse in sequence than the receptor tyrosine kinases so they cannot be classified as rigorously. However, certain features are common to all growth factors (so far defined) which form compact, globular structures and this allows a discussion of possible interactions between the ligand and receptor; but in the absence of a molecular structure for any of the receptors, we can only review biochemical evidence and deductions from predictive and modelling studies. Various models for the signal transduction process are discussed in the light of current work on receptor interactions.

Growth Substances↗
PubMed1988

Protein chemical characterization of Mucor pusillus aspartic proteinase. Amino acid sequence homology with the other aspartic proteinases, disulfide bond arrangement and site of carbohydrate attachment.

The amino acid sequence of Mucor pusillus aspartic proteinase was determined by analysis of fragments obtained from cleavage of the enzyme by CNBr and limited tryptic digestion. The proteinase is a single polypeptide chain protein containing 361 amino acid residues, cross-linked by two disulfide bonds. A sugar moiety composed of two GlcNAc residues and four neutral sugar residues is asparagine-linked to the chain. The sequence of M. pusillus proteinase is highly homologous with the M. miehei proteinase (83% identity). The homology with other aspartic proteinases is low (22-24%) and indicates that the Mucor proteinases diverged at an early evolutionary phase. The most conservative regions of the molecule are those involved in catalysis and forming the binding cleft and the core region of the molecule.

Amino Acid Sequence↗
PubMed1988

18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design.

A systematic technique for protein modelling that is applicable to the design of drugs, peptide vaccines and novel proteins is described. Our approach is knowledge-based, depending on the structures of homologous or analogous proteins and more generally on a relational data base of protein three-dimensional structures. The procedure simultaneously aligns the known tertiary structures, selects fragments from the structurally conserved regions on the basis of sequence homology, aligns these with the 'average structure' or 'framework', builds on the loops selected from homologous proteins or a wider database, substitutes sidechains and energy minimises the resultant model. Applications to modelling an homologous structure, tissue plasminogen activator on the basis of another serine proteinase, and to modelling an analogous protein, HIV viral proteinase on the basis of aspartic proteinases, are described. The converse problem of ab initio design is also addressed: this involves the selection of an amino acid sequence to give a particular tertiary structure, in this case a symmetrical domain of two Greek-key motifs.

Base Sequence↗
PubMed1987

On the tertiary structure of the extracellular domains of the epidermal growth factor and insulin receptors.

Alignment of the sequences, the identification of conserved residue patterns and secondary structure predictions indicate that the extra-cellular regions of the human and Drosophila epidermal growth factor (EGF), c-erb-B2 and human insulin receptors each contain two large, homologous domains (L) which are probably comprised of at least four short alpha-helices followed by turns of conserved length and beta-strands. In the human and Drosophila EGF and c-erb-B2 receptors these homologous domains are each followed by a series of smaller cystine-rich domains (S) to give a gene-duplicated structure of L1S11S12S13L2S21S22S23. In the human insulin receptor, the second series of cystine domains is replaced by a different sequence. These duplicated structures are probably organised as a pseudo-symmetrical dimer. There are two 'hyper-variable' regions, one at the end of the large domains and one in the cystine-rich sequences, which are candidates for hormone or growth-factor binding.

Amino Acid Sequence↗
PubMed1987

The structure of a synthetic pepsin inhibitor complexed with endothiapepsin.

The conformation of a synthetic polypeptide inhibitor, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 0.20-nm resolution and refined to an agreement factor of 0.20. The inhibitor: Pro Thr Glu Phe-R-Phe Arg Glu (R = -CH2NH-) is based on a chromogenic substrate of pepsin (EC 3.4.23.1). It has, in place of the scissile bond, a reduced peptide group which is resistant to hydrolysis and mimics the tetrahedral transition state. The inhibitor binds in an extended conformation with the reduced bond close to the essential aspartate side-chains of the enzyme. The hydrogen bonds and hydrophobic interactions between the enzyme and the inhibitor do not induce large conformational changes.

Aspartic Acid Endopeptidases↗
PubMed1987

Crystallographic studies of reduced bond inhibitors complexed with an aspartic proteinase.

To aid in the design of an effective inhibitor to human renin, it is essential to have a detailed knowledge of how this aspartic proteinase interacts with its substrate, angiotensinogen. Human renin shows a stringent specificity toward the Leu-Val bond in its natural substrate. The minimal length for an effective substrate has been characterised as an octapeptide sequence derived from the amino terminal portion of angiotensinogen (residues 6----13): His-Pro-Phe-His-Leu-Val-Ile-His (Leu-Val is the scissile bond). This suggests that renin has a fairly extensive active site cleft, as has been observed in homologous enzymes whose three-dimensional structures have been solved using x-ray diffraction methods. The homologous fungal aspartic proteinase, endothiapepsin, has been cocrystallised with human renin inhibitors of the type His-Pro-Phe-His-Leu-R-Val-Ile-His, where R indicates a reduced carbonyl analogue of the scissile peptide bond. The three-dimensional crystallographic structures of two complexes of endothiapepsin with an inhibitor have been solved. The details of inhibitor binding at the active site cleft of endothiapepsin are described. These data allow a rational approach to the design of novel renin inhibitors, through studies of these inhibitors in a three-dimensional model of human renin constructed in our laboratory.

Amino Acid Sequence↗