scholarly journals The structural origins of the unusual specificities observed in the isolation of chymopapain M and actinidin by covalent chromatography and the lack of inhibition of chymopapain M by cystatin

1995 ◽  
Vol 306 (1) ◽  
pp. 39-46 ◽  
Author(s):  
M P Thomas ◽  
C Verma ◽  
S M Boyd ◽  
K Brocklehurst
Keyword(s):  
Computer Modelling ◽  
Short Form ◽  
Egg White ◽  
Cysteine Proteinases ◽  
General Technique ◽  
Binding Characteristics ◽  
Modelling Techniques ◽  
Dynamics Simulations ◽  
Active Centres ◽  
Covalent Chromatography

1. The selectivity observed when the potentially general technique for the isolation of fully active forms of cysteine proteinases, covalent chromatography by thiol-disulphide interchange, is applied to chymopapain M and to actinidin was investigated by a combination of experimentation and computer modelling. Neither of these enzymes is able to react with the original Sepharose-GSH-2-dipyridyl disulphide gel, but fully active forms of both enzymes are obtained by using Sepharose-2-hydroxypropyl-2′-dipyridyl disulphide gel, which is both electrically neutral and sterically less demanding than the GSH gel. Electrostatic potential calculations, minimization and molecular-dynamics simulations provide explanations for the unusual, but different, specificities exhibited by actinidin and chymopapain M in the interactions of their active centres with ligands. 2. The unique behaviour of chymopapain M in exerting an almost absolute specificity for substrates with glycine at the P1 position and in resisting inhibition by cystatin was examined by the computer-modelling techniques. A new, modelled, structure of the complete chicken egg-white cystatin molecule based on the crystal structure of a short form of cystatin was deduced as a necessary prerequisite. The results suggest that electrostatic repulsion prevents reaction of actinidin with the GSH gel, whereas a steric ‘cap’ resulting from a unique arginine-65-glutamic acid-23 interaction in chymopapain M prevents reaction of the gel with this enzyme and accounts for the lack of its inhibition by cystatin and its specificity in catalysis. 3. Use of chymopapain M as a structural variant of papain demonstrates the validity of the predictions of Lowe and Yuthavong [Biochem. J. (1971) 124, 107-115] relating to the structural requirements and binding characteristics of the S1 subsite of papain.

scholarly journals Inhibition of cysteine proteinases and dipeptidyl peptidase I by egg-white cystatin

1984 ◽  
Vol 223 (1) ◽  
pp. 245-253 ◽  
Author(s):  
M J H Nicklin ◽  
A J Barrett
Keyword(s):  
Cathepsin B ◽  
Bond Cleavage ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Dipeptidyl Peptidase ◽  
Egg White ◽  
Reversible Inhibitor ◽  
Cysteine Proteinases ◽  
Peptide Bond Cleavage ◽  
Specific Oxidation

The interactions between egg-white cystatin and the cysteine proteinases papain, human cathepsin B and bovine dipeptidyl peptidase I were studied. Cystatin was shown to be a competitive reversible inhibitor of cathepsin B (Ki 1.7 nM, k-1 about 2.3×10(-3) s-1). The inhibition of dipeptidyl peptidase I was shown to be reversible (Ki(app.) 0.22 nM, k-1 about 2.2×10(-3) s-1). Cystatin bound papain too tightly for Ki to be determined, but an upper limit of 5 pM was estimated. The association was a second-order process, with k+1 1.0×10(7) M-1×s-1. Papain was shown to form equimolar complexes with cystatin. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis of complexes formed between papain or cathepsin B and an excess of cystatin showed no peptide bond cleavage after incubation for 72 h. The reaction of the active-site thiol group of papain with 5,5′-dithiobis-(2-nitrobenzoic acid) at pH 8 and 2,2′-dithiobispyridine at pH 4 was blocked by complex-formation. Dipeptidyl peptidase I and papain were found to compete for binding to cystatin, contrary to a previous report. The two major isoelectric forms of cystatin were found to have similar specific inhibitory activities for papain, and similar affinities for papain, cathepsin B and dipeptidyl peptidase I. This, together with specific oxidation of the N-terminal serine residue with periodate, showed the N-terminal amino group of cystatin 1 to be unimportant for inhibition. General citraconylation of amino groups resulted in a large decrease in the affinity of cystatin for dipeptidyl peptidase I. It is concluded that the interaction of cystatin with cysteine proteinases has many characteristics similar to those of an inhibitor such as aprotinin with serine proteinases.

scholarly journals Evidence that the active centre of chymopapain A is different from the active centres of some other cysteine proteinases and that the Brønsted coefficient (βnuc.) for the reactions of thiolate anions with 2,2′-dipyridyl disulphide may be decreased by reagent protonation

1980 ◽  
Vol 189 (1) ◽  
pp. 189-192 ◽  
Author(s):  
K Brocklehurst ◽  
B S Baines ◽  
M S Mushiri
Keyword(s):  
Carica Papaya ◽  
Cysteine Proteinases ◽  
Active Centre ◽  
Pka Values ◽  
Nitrobenzoic Acid ◽  
Specific Reactivity ◽  
Ph Range ◽  
Thiolate Anions ◽  
Active Centres

The active centres of chymopapains A and B (jointly designated EC 3.4.22.6) and papaya (Carica papaya L.) peptidase A were investigated by using 2,2′-dipyridyl disulphide and 5,5′-dithiobis-(2-nitrobenzoic acid) as thiol-specific reactivity probes. Whereas the first active-centre pKa values for chymopapain B and papaya peptidase A are less than 5, is as the case for papain (EC 3.4.22.2) and ficin (EC 3.4.22.3), that for chymopapain A is about 6.8. The reason why the reactions of thiols of pKa approx. 6.5 with 2.2′-dipyridyl disulphide are essentially pH-independent in the pH range around the thiol pKa is delineated. The value of the Brønsted coefficient (beta nuc.) for the reactions of thiolate ions with the 2,2′-dipyridyl disulphide monocation appears to be smaller than its value for the corresponding reactions with the neutral disulphide.

scholarly journals The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.

2000 ◽  
Vol 47 (1) ◽  
pp. 65-78 ◽  
Author(s):  
J Mazerski ◽  
K Muchewicz
Keyword(s):  
Conformational Changes ◽  
Ring System ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Intercalation Complex ◽  
Highly Active ◽  
Antitumor Compounds ◽  
Chemical Constitution ◽  
Modelling Techniques ◽  
Dynamics Simulations

Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.

scholarly journals Colibactin DNA damage signature indicates causative role in colorectal cancer

2019 ◽  
Author(s):  
Paulina J. Dziubańska-Kusibab ◽  
Hilmar Berger ◽  
Federica Battistini ◽  
Britta A. M. Bouwman ◽  
Amina Iftekhar ◽  
...  
Keyword(s):  
Dna Damage ◽  
Human Cancer ◽  
Colorectal Cancers ◽  
Causative Role ◽  
Sequence Motifs ◽  
Dna Double Strand Breaks ◽  
Colon Cells ◽  
Binding Characteristics ◽  
Significant Enrichment ◽  
Dynamics Simulations

AbstractColibactin, a potent genotoxin of Escherichia coli, causes DNA double strand breaks (DSBs) in human cells. We investigated if colibactin creates a particular DNA damage signature in infected cells by identifying DSBs in colon cells after infection with pks+ E.coli. Interestingly, genomic contexts of DSBs were enriched for AT-rich penta-/hexameric sequence motifs, exhibiting a particularly narrow minor groove width and extremely negative electrostatic potential. This corresponded with the binding characteristics of colibactin to double-stranded DNA, as elucidated by docking and molecular dynamics simulations. A survey of somatic mutations at the colibactin target sites of several thousand cancer genomes revealed significant enrichment of the identified motifs in colorectal cancers. Our work provides direct evidence for a role of colibactin in the etiology of human cancer.One sentence summaryWe identify a mutational signature of colibactin, which is significantly enriched in human colorectal cancers.

scholarly journals Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1918 ◽  
Author(s):  
Jordi C. J. Hintzen ◽  
Jordi Poater ◽  
Kiran Kumar ◽  
Abbas H. K. Al Temimi ◽  
Bas J. G. E. Pieters ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Biomolecular Recognition ◽  
Crucial Importance ◽  
Binding Characteristics ◽  
Human Genes ◽  
Health And Disease ◽  
Fundamental Insight ◽  
Dynamics Simulations ◽  
Insight Into ◽  
Epigenetic Processes

Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermodynamic analyses, molecular dynamics simulations and quantum chemical analyses. Collectively, our experimental and computational findings reveal that trimethylthialysine and trimethyllysine exhibit very similar binding characteristics for the association with human reader proteins, thereby justifying the use of trimethylthialysine for studies aimed at dissecting the origin of biomolecular recognition in epigenetic processes that play important roles in human health and disease.

Suction Energy for Double-Stranded DNA Inside Single-Walled Carbon Nanotubes

2017 ◽  
Vol 70 (4) ◽  
pp. 387-400 ◽  
Author(s):  
Mansoor H Alshehri ◽  
James M Hill
Keyword(s):  
Carbon Nanotubes ◽  
Mathematical Modelling ◽  
Molecular Electronics ◽  
Continuum Approximation ◽  
Suction Force ◽  
Dsdna Molecule ◽  
Double Stranded Dna ◽  
Modelling Techniques ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes

Summary Deoxyribonucleic acid (DNA) and carbon nanotubes (CNTs) constitute hybrid materials with the potential to provide new components with many applications in various technology areas, such as molecular electronics, field devices and medical applications. Using classical applied mathematical modelling, we investigate the suction force experienced by a double-stranded DNA (dsDNA) molecule which is assumed to be located on the axis near an open end of a semi-infinite single-walled CNT. We employ both the 6-12 Lennard-Jones potential and the continuum approximation, which assumes that a discrete atomic structure can be replaced by a surface with constant average atomic density. While most research in the area is dominated by molecular dynamics simulations, here we use elementary mechanical principles and classical applied mathematical modelling techniques to formulate explicit analytical criteria and ideal model behaviour. We observe that the suction behaviour depends on the radius of the CNT, and we predict that it is less likely for a dsDNA molecule to be accepted into the CNT when the value of the tube radius is ${<}12.9$ Å. The dsDNA molecule will be accepted into the CNT for radii lager than 13 Å, and we show that the optimal single-walled CNT necessary to fully enclose the DNA molecule has a radius of 13.56 Å, which approximately corresponds to the chiral vector numbers (20, 20). This means that the ideal single-walled CNT to be used to encapsulate a dsDNA is (20, 20) which has the required radius of 13.56 Å.

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