scholarly journals Synthesis of trifunctional cyclo-β-tripeptide templates

2012 ◽  
Vol 8 ◽  
pp. 1576-1583
Author(s):  
Frank Stein ◽  
Tahir Mehmood ◽  
Tilman Plass ◽  
Javid H Zaidi ◽  
Ulf Diederichsen
Keyword(s):  
Enzymatic Degradation ◽  
Solid Phase ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structure Stability ◽  
Tubular Structures ◽  
Peptide Fragments ◽  
Efficient Synthesis ◽  
Synthetic Proteins ◽  
Orthogonal Protection

The concept of template-assembled synthetic proteins (TASP) describes a central scaffold that predefines the three dimensional structure for diverse molecules linked to this platform. Cyclic β-tripeptides are interesting candidates for use as templates due to their conformationally defined structure, stability to enzymatic degradation, and ability to form intermolecular stacked tubular structures. To validate the applicability of cyclic β-tripeptides within the TASP concept, an efficient synthesis of the cyclopeptide with orthogonal functionalization of the side chains is desired. A solid-phase-supported route with on-resin cyclization is described, employing the aryl hydrazide linker cleavable by oxidation. An orthogonal protection-group strategy allows functionalization of the central cyclic β-tripeptide with up to three different peptide fragments or fluorescent labels.

Characterization of Monoclonal Anti-human Factor VII Antibody (B101/B1) that Recognized Three-dimensional Structures near Arg at Position 79 in the First EGF-like Domain

1998 ◽  
Vol 79 (01) ◽  
pp. 104-109 ◽  
Author(s):  
Osamu Takamiya
Keyword(s):  
Monoclonal Antibodies ◽  
Tissue Factor ◽  
Human Factor ◽  
Solid Phase ◽  
Three Dimensional ◽  
Coagulation Factors ◽  
Factor Vii ◽  
Dimensional Structure ◽  
Epidermal Growth

SummaryMurine monoclonal antibodies (designated hVII-B101/B1, hVIIDC2/D4 and hVII-DC6/3D8) directed against human factor VII (FVII) were prepared and characterized, with more extensive characterization of hVII-B101/B1 that did not bind reduced FVIIa. The immunoglobulin of the three monoclonal antibodies consisted of IgG1. These antibodies did not inhibit procoagulant activities of other vitamin K-dependent coagulation factors except FVII and did not cross-react with proteins in the immunoblotting test. hVII-DC2/D4 recognized the light chain after reduction of FVIIa with 2-mercaptoethanol, and hVIIDC6/3D8 the heavy chain. hVII-B101/B1 bound FVII without Ca2+, and possessed stronger affinity for FVII in the presence of Ca2+. The Kd for hVII-B101/B1 to FVII was 1.75 x 10–10 M in the presence of 5 mM CaCl2. The antibody inhibited the binding of FVII to tissue factor in the presence of Ca2+. hVII-B101/B1 also inhibited the activation of FX by the complex of FVIIa and tissue factor in the presence of Ca2+. Furthermore, immunoblotting revealed that hVII-B101/B1 reacted with non-reduced γ-carboxyglutaminic acid (Gla)-domainless-FVII and/or FVIIa. hVII-B101/B1 showed a similar pattern to that of non-reduced proteolytic fragments of FVII by trypsin with hVII-DC2/D4 on immunoblotting test. hVII-B101/B1 reacted differently with the FVII from the dysfunctional FVII variant, FVII Shinjo, which has a substitution of Gln for Arg at residue 79 in the first epidermal growth factor (1st EGF)-like domain (Takamiya O, et al. Haemosta 25, 89-97,1995) compared with normal FVII, when used as a solid phase-antibody for ELISA by the sandwich method. hVII-B101/B1 did not react with a series of short peptide sequences near position 79 in the first EGF-like domain on the solid-phase support for epitope scanning. These results suggested that the specific epitope of the antibody, hVII-B101/B1, was located in the three-dimensional structure near position 79 in the first EGF-like domain of human FVII.

The Construction of New Proteins. II. Design, Synthesis and Conformational Studies of Folding Units with βαβ-Topology

1986 ◽  
Vol 41 (10) ◽  
pp. 1315-1322 ◽  
Author(s):  
Manfred Mutter ◽  
Karl-Heinz Altmann ◽  
Thomas Vorherr
Keyword(s):  
Solid Phase ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Spectroscopic Studies ◽  
General Concept ◽  
Dimensional Structure ◽  
Design Synthesis ◽  
Phase Synthesis ◽  
Conformational Studies ◽  
Conformational Effects

The design, synthesis and preliminary conformational studies of two polypeptides exhibiting βαβ-type folding topologies are presented. In the design of the model peptides the general concept for the construction of new proteins developed in the preceeding paper was applied. According to this strategy, amphiphilic helices and β-sheets are linked together via hydrophilic loops to attain three-dimensional structures of higher order (‘supersecondary structures’). Com­puter-assisted molecular modelling served as a valuable tool for minimizing conformational con­straints within the molecules. The 38-residue peptide MI was synthesized using polyethylene glycol (PEG) as solubilizing polymeric support (‘Liquid-Phase synthesis'). Conformationally in­duced changes in the physico-chemical properties of the growing peptide chain stressed the significance of conformational effects in peptide synthesis reported earlier. Similar observations were made during the solid-phase synthesis of the 35-peptide MII. CD and IR spectroscopic studies revealed a high degree of secondary structure for both folding units. The present data strongly support the adoption of a three-dimensional structure for both models.

scholarly journals The three-dimensional structure of the cellobiohydrolase Cel7A fromAspergillus fumigatusat 1.5 Å resolution

2015 ◽  
Vol 71 (1) ◽  
pp. 114-120 ◽  
Author(s):  
Olga V. Moroz ◽  
Michelle Maranta ◽  
Tarana Shaghasi ◽  
Paul V. Harris ◽  
Keith S. Wilson ◽  
...  
Keyword(s):  
Enzymatic Degradation ◽  
Plant Cell Wall ◽  
Three Dimensional ◽  
Biofuel Production ◽  
Industrial Processes ◽  
Dimensional Structure ◽  
Carbohydrate Active Enzymes ◽  
Cazy Database ◽  
Generation Biofuel ◽  
Insight Into

The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of theAspergillus fumigatusCBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts.

Effect of Mutation at Valine 61 on the Three-Dimensional Structure, Stability, and Redox Potential of Cytochromeb5†,⊥

Biochemistry ◽  
1999 ◽  
Vol 38 (37) ◽  
pp. 11961-11972 ◽  
Author(s):  
Lin-Long Xue ◽  
Yun-Hua Wang ◽  
Yi Xie ◽  
Ping Yao ◽  
Wen-Hu Wang ◽  
...  
Keyword(s):  
Redox Potential ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structure Stability ◽  
Three Dimensional Structure

Phytochrome three-dimensional structures and functions

2010 ◽  
Vol 38 (2) ◽  
pp. 710-716 ◽  
Author(s):  
Jon Hughes
Keyword(s):  
Ground State ◽  
Solid Phase ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Specific Domain ◽  
Intimate Contact ◽  
N Terminus ◽  
Structural Differences ◽  
Module Structures

The complete three-dimensional sensory module structures of the Pr ground state of Synechocystis 6803 Cph1 and the unusual Pfr ground state of the bacteriophytochrome PaBphP (PDB codes 2VEA and 3C2W respectively) have now been solved, revealing an asymmetrical dumbbell form made up of a PAS (Period/ARNT/Singleminded)–GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA) bidomain carrying the chromophore and the smaller PHY (phytochrome-specific) domain. The PHY domain is structurally related to the GAF family, but carries an unusual tongue-like structure which contacts the larger lobe to seal the chromophore pocket. In 2VEA, the tongue makes intimate contact with the helical N-terminus; both the N-terminus and the tongue structures are quite different in 3C2W. As expected, the structures reveal ZZZssa and ZZEssa chromophore conformations in 2VEA and 3C2W respectively, associated with tautomeric differences in several nearby tyrosine residues. Two salt bridges on opposite sides of the chromophore, as well as the associations of the C-ring propionates also differ. It is still unclear, however, which of these structural differences are associated with bacteriophytochromes compared with Cph1 and plant-type phytochromes, the unusual 3C2W Pfr ground state functionality compared with the Pr ground state or the Pr compared with Pfr photoisomerism. To access the latter unambiguously, both Pr and Pfr structures of the same molecule are required. New solid-phase NMR data for Cph1 in the Pr, Pfr and freeze-trapped intermediate states reveal unexpected changes in the chromophore during Pfr→Pr photoconversion. These, together with our efforts to solve the three-dimensional structure of a complete phytochrome molecule are also described.

scholarly journals Haemoglobin binding with haptoglobin. Localization of the haptoglobin-binding sites on the β-chain of human haemoglobin by synthetic overlapping peptides encompassing the entire chain

1986 ◽  
Vol 234 (2) ◽  
pp. 453-456 ◽  
Author(s):  
N Yoshioka ◽  
M Z Atassi
Keyword(s):  
Binding Sites ◽  
Solid Phase ◽  
Three Dimensional ◽  
Binding Activity ◽  
Dimensional Structure ◽  
Synthetic Approach ◽  
Protein Chain ◽  
Beta Chain ◽  
Human Haemoglobin ◽  
Β Chain

A synthetic approach was employed to identify the haptoglobin-binding sites on the beta-chain of human haemoglobin. This approach consists of the synthesis of a series of consecutive overlapping peptides that, together, systematically represent the entire protein chain. Fourteen synthetic peptides (beta 1-15, beta 11-25 etc.) were examined for their ability to bind human haptoglobin by quantitative solid-phase radiometric titrations of 125I-labelled haptoglobin. Of these 14 peptides only peptides beta 11-25 and beta 131-146 bound haptoglobin significantly; peptide beta 21-35 exhibited a small binding activity as a consequence of the overlap with peptide beta 11-25. On this basis and by examination of the three-dimensional structure of haemoglobin, it was concluded that the beta-chain of haemoglobin has two binding sites for haptoglobin that reside in, but do not necessarily encompass all of, the regions beta 11-25 and beta 131-146.

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