Optimization of aromatic side chain size complementarity in the hydrophobic core of a designed coiled-coil

2008 ◽  
Vol 66 (6) ◽  
pp. 387-394 ◽  
Author(s):  
Y. Sakurai ◽  
T. Mizuno ◽  
H. Hiroaki ◽  
J.-I. Oku ◽  
T. Tanaka
2009 ◽  
Vol 102 (09) ◽  
pp. 479-486 ◽  
Author(s):  
Zuzana Reicheltová ◽  
Martin Malý ◽  
Jiří Suttnar ◽  
Alžbòta Sobotková ◽  
Peter Salaj ◽  
...  

SummaryCongenital dysfibrinogenemia is a rare disease characterised by inherited abnormality in the fibrinogen molecule, resulting in functional defects. Two patients, a 26-year-old woman and a 61-year-old man, both with history of thrombotic events, had abnormal coagulation test results. DNA sequencing showed the heterozygous γY363N mutation (Fibrinogen Praha III) and the heterozygous Aα N106D mutation (Fibrinogen Plzeň), respectively. Fibrin polymerisation, after addition of either thrombin or reptilase, showed remarkably delayed polymerisation in both cases. Fibrinolysis experiments showed slower tPA initiated lysis of clots. SDS-PAGE did not show any difference between normal and Praha III and Plzeň fibrinogens. Both mutations had a significant effect on platelet aggregation. In the presence of either ADP or TRAP, both mutations caused the decrease of platelet aggregation. SEM revealed abnormal clot morphology, with a large number of free ends and narrower fibres of both fibrin Praha III and Plzeň. Praha III mutation was situated in the polymerisation pocket “a”. The replacement of the bulky aromatic side chain of tyrosine by the polar uncharged small side chain of asparagine may lead to a conformational change, possibly altering the conformation of the polymerisation pocket. The Plzeň mutation is situated in the coiled-coil connector and this replacement of polar uncharged asparagine residue by polar acidic aspartate changes the alpha-helical conformation of the coiled-coil connector;and may destabilise hydrogen bonds in its neighborhood. Although both mutations are situated in different regions of the molecule, both mutations have a very similar effect on fibrinogen functions and both are connected with thromboses.


Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 656
Author(s):  
Vincent Van Deuren ◽  
Yin-Shan Yang ◽  
Karine de Guillen ◽  
Cécile Dubois ◽  
Catherine Anne Royer ◽  
...  

Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CH groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CH, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CH when compared to amide groups.


Biochemistry ◽  
2008 ◽  
Vol 47 (33) ◽  
pp. 8566-8576 ◽  
Author(s):  
Matthew J. Whitley ◽  
Jun Zhang ◽  
Andrew L. Lee

2021 ◽  
Vol 18 ◽  
Author(s):  
Monika Kakadiya ◽  
Yunus Pasha ◽  
Malleshappa Noolvi ◽  
Ashish Patel

: Tuberculosis remains a highly infectious disease across the world. In the identification of new antitubercular agents, coumarin clubbed thiadiazole amides have been synthesized and evaluated for in vitro antitubercular activity. Due to the growing concern about chemicals and their impact on the environment, greener and faster reaction conditions needed to be incorporated. Therefore, we used TBTU as a coupling reagent for efficient and facile synthesis of substituted-N-(5-((7-methyl-2-oxo-2H-chromes-4-yl)-methyl)-1,3, 4 - thiadiazol-2-yl)-benzamide 4a-j with good yields up to 95% in mild reaction condition. All the synthesized compounds were evaluated in vitro for antitubercular activity against the H37Rv strain of M.Tuberculosis. Compounds 4c, 4f, and 4j were found active at 25 µg/mL against M. tb H37Rv. Electron withdrawing substituents present on aromatic side-chain showed promising anti-tubercular activity.


2021 ◽  
Vol 18 ◽  
Author(s):  
Sarah Kappler ◽  
Andreas Siebert ◽  
Uli Kazmaier

Introduction: Miuraenamides belong to marine natural compounds with interesting biological properties. Materials and Methods: They initiate polymerization of monomeric actin and therefore show high cytotoxicity by influencing the cytoskeleton. New derivatives of the miuraenamides have been synthesized containing a N-methylated amide bond instead of the more easily hydrolysable ester in the natural products. Results: Incorporation of an aromatic side chain onto the C-terminal amino acid of the tripeptide fragment also led to highly active new miuraenamides. Conclusion: We could show that the ester bond of the natural product miuraenamide can be replaced by an N-methyl amide. The yields in the cyclization step are high and generally much better that with the corresponding esters. On the other hand, the biological activity of the new amide analogs are lower compared to the natural products, but the activity can significantly be increased by incorporation of a p-nitrophenyl group at the C-terminus of the peptide fragment.


1989 ◽  
Vol 9 (2) ◽  
pp. 860-864
Author(s):  
E Lazar ◽  
E Vicenzi ◽  
E Van Obberghen-Schilling ◽  
B Wolff ◽  
S Dalton ◽  
...  

Site-directed mutagenesis has been performed in the human transforming growth factor alpha gene. When tyrosine 38 is mutated into phenylalanine or tryptophane, biological activity is retained. In contrast, other alterations between cysteine 34 and cysteine 43 and disruption of disulfide bonds 8 to 21 and 34 to 43 resulted in loss of activities. The presence of an aromatic side chain at position 38 of transforming growth factor alpha seems to be essential for its activity.


1972 ◽  
Vol 27 (5) ◽  
pp. 530-532 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Axel Wollmer

The origin of the positive Soret Cotton effect of myoglobin was calculated by Hsu and WOODY on the basis of a mechanism taking into account the coupling of the Soret and aromatic side-chain π—π* transitions. HUBER and coworkers have worked out the atomic coordinates of a monomeric insect hemoglobin which exhibits a negative Soret Cotton effect.It seemed of some importance to examine the capability of this mechanism to explain the observed inversion of sign. The calculations resulted indeed in a negative total rotational strength (—0,2 DBM), the main contributions arising from phenylalanine residues.


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