Theoretical examination of competitive β-radical-induced cleavages of N–Cα and Cα–C bonds of peptides

2015 ◽  
Vol 93 (12) ◽  
pp. 1355-1362 ◽  
Author(s):  
Wai-Kit Tang ◽  
Chun-Ping Leong ◽  
Qiang Hao ◽  
Chi-Kit Siu
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Bond Cleavage ◽  
Radical Cations ◽  
Radical Center ◽  
Amino Acid Residues ◽  
Mobile Proton ◽  
Aromatic Side Chain ◽  
Heterolytic Cleavage ◽  
Terminal Fragment

Selective cleavages of N–Cα and Cα–C bonds of β-radical tautomers of amino acid residues in radical peptides have been examined theoretically by means of the density functional theory at the M06-2X/6-311++G(d,p) level. The majority of the bond cleavages are homolytic via β-scission. Their energy barriers depend largely on the ability of the radical being stabilized in the transition structures and the availability of a mobile proton in the vicinity of the β-radical center. The N–Cα bond is less favorably cleaved than the Cα–C bond (except Ser and Thr) for systems without a mobile proton. It is because, firstly, the homolytic cleavage is less favorable for the more polar N–Cα bond than for the less polar Cα–C bond. Secondly, a less stable σ-radical localized on the amide nitrogen atom of the incipient N-terminal fragment is formed for the former, while a more stable radical delocalized in a π*(CO)-like orbital of the incipient C-terminal fragment is formed for the latter. In the presence of a mobile proton N-terminal to the β-radical center, some degrees of heterolytic cleavage character, as preferred by the polar N–Cα bond, are observed. Consequently, its barrier is reduced. If the mobile proton is located at the C-terminal amide oxygen of the β-radical center, the Cα–C bond cleavage will be significantly suppressed. It is because the radical in the incipient C-terminal fragment becomes more localized as a σ-radical on the carbon atom of its protonated amide group. With basic amino acid residues, the Cα–C bond cleavage can be reactivated. Heterolytic cleavage of the polar N–Cα bond can be largely facilitated if a mobile proton N-terminal to the β-radical center is available and the radical in the incipient C-terminal fragment is sufficiently stabilized, for instance, by the aromatic side chain of Trp and Tyr. Therefore, cleavages of the N–Cα bond induced by the β-radical tautomer of Trp and Tyr are often preferred as compared with cleavages of the Cα–C bond in peptide radical cations containing mobile protons.

scholarly journals Explaining SARS-CoV-2 3CL Mpro binding to peptidyl Michael acceptor and a ketone-based inhibitors using Molecular fractionation with conjugate caps method

2020 ◽  
Author(s):  
C Solis-Calero ◽  
PA Morais ◽  
FF Maia Jr ◽  
VN Freire ◽  
HF Carvalho
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Radial Distance ◽  
Amino Acid Residues ◽  
Functional Theory ◽  
Main Protease ◽  
The Density Functional Theory ◽  
Michael Acceptor ◽  
Total Interaction ◽  
Molecular Fractionation

The main protease SARS-CoV-2 3CL Mpro (3CL-Mpro) is an attractive target for developing antiviral inhibitors due to its essential role in processing the polyproteins translated from viral coronavirus RNA. In this work, it was obtained non-covalent complexes of this protease with two distinct ligands, a peptidyl Michael acceptor (N3) and a ketone-based compound (V2M). The complexes were modeled from processed crystallographic data (PDB id: 6LU7 and 6XHM respectively) using combined quantum mechanics/molecular mechanics (QM/MM) calculations. The QM region was treated at the PBE-def2-SV(P) level, while the Amber-ff19SB force field was used to describe the MM region. The obtained models were used to perform calculations for describing the protease/ligand binding, based in the framework of the Density Functional Theory (DFT) and within the Molecular Fractionation with Conjugated Caps (MFCC) scheme. Our results have shown values for the total interaction energies of -111.84 and -111.64 kcal mol-1 having as ligands a N3 and V2M, respectively. Most importantly, it was possible to assess the relative individual amino acid energy contribution for the binding of both ligands considering residues around them up to 10 Å of radial distance. Residues Gln189, Met165, Glu166, His164, and Asn142 were identified as main interacting amino acid residues for both complexes, being their negative interaction energy contributions higher than -5.0 kcal mol-1. In the case of 3CL-Mpro/ V2M complex, we should add His41, Ser144, and Cys145 as main contributing residues. Our data also have shown that interactions of type π-amide, π-alkyl and alkyl-alkyl and carbon hydrogen bonds should be also considered in order to explain the binding of 3CL-Mpro with the selected inhibitors. Our results also determined that the carbonyl-L-leucinamide scaffold of both inhibitors is its main determinant of binding with a contribution to the energy of interaction of 54.51 and 50.69 kcal mol-1 for N3 and V2M, respectively.

THE USE OF REGION SPECIFIC RADIOIMMUNOASSAYS FOR CHARACTERIZATION OF CIRCULATING CALCITONIN IN PATIENTS WITH MEDULLARY CARCINOMA OF THE THYROID GLAND

1979 ◽  
Vol 91 (3) ◽  
pp. 449-461 ◽  
Author(s):  
Lisbeth Myhre ◽  
Kaare M. Gautvik
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Molecular Forms ◽  
Amino Acid Residues ◽  
Terminal Amino Acid ◽  
Amino Terminal ◽  
Terminal Fragment ◽  
Terminal Amino ◽  
Carboxy Terminal ◽  
Amino Terminal Fragment

ABSTRACT Two antisera with known region specificities have been used to characterize calcitonin immunoreactivity (iCT) in serum of patients with medullary thyroid carcinoma (MCT). Antiserum I which was raised against the synthetic hormone (1–32 amino acid residues), contained heterogeneous populations of immunoglobulins directed predominantly against carboxyterminal sequences of the hormone, but the antiserum reacted also with the amino-terminal fragment (1–10 amino acid residues). Antiserum II, which was raised against the carboxy-terminal hormone fragment (11–32 amino acid residues) reached equally well with the intact hormone and the C-terminal fragment, but showed negligible binding of the amino terminal fragment. Antiserum I measured therefore both amino-terminal and carboxy-terminal sequences of calcitonin while antiserum II measured only carboxy-terminal amino acid sequences. In 40 patients with MCT, antiserum I measured usually the highest concentration of serum iCT suggesting the presence of non-uniform hormone immunoreactivity. The different molecular forms of circulating iCT in 7 MCT patients were explored by using antiserum I after gel filtration on Sephadex G-100. The patients who were selected on basis of iCT measurement in serum using antiserum I and II, could be divided into 3 groups which showed characteristic iCT profiles. Group 1, in which antiserum II measured a higher concentration of serum iCT, contained predominantly (60–70 %) small fragments of calcitonin immunoreactivity. On the other hand, in the sera of group 3 in which antisera I measured an equal or the highest concentrations, the dominant form of the hormone consisted of molecular sequences equal to or larger than the intact hormone (90 %). In group 2, the two antisera measured an equal amount of serum iCT and molecular forms consisting mostly of larger hormone fragments dominated (50 %). All the patients were normocalcaemic in spite of frequently grossly elevated serum iCT, and 33 out of 36 patients had normal serum immunoreactive parathyroid hormone. In conclusion: 1. Serum iCT is heterogeneous and represents peptides of quite different molecular size with no or low biological activity. 2. Most of the serum calcitonin immunoreactivity consists of peptides with carboxy-terminal amino acid sequences. 3. Most, if not all, of the amino-terminal calcitonin immunoreactivity is due to monomeric and polymeric hormonal forms.

scholarly journals Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc

1999 ◽  
Vol 19 (9) ◽  
pp. 6020-6028 ◽  
Author(s):  
Fumiko Hirose ◽  
Masamitsu Yamaguchi ◽  
Akio Matsukage
Keyword(s):  
Salivary Gland ◽  
Amino Acid ◽  
Dna Replication ◽  
Heat Shock ◽  
Imaginal Disc ◽  
Ectopic Expression ◽  
Amino Acid Residues ◽  
Terminal Fragment ◽  
Binding Factor ◽  
Eye Imaginal Disc

ABSTRACT The promoters of Drosophila genes encoding DNA replication-related proteins contain transcription regulatory elements consisting of an 8-bp palindromic DNA replication-related element (DRE) sequence (5′-TATCGATA). The specific DRE-binding factor (DREF), a homodimer of the polypeptide with 709 amino acid residues, is a positive trans-acting factor for transcription of DRE-containing genes. Both DRE binding and dimer formation are associated with residues 16 to 115 of the N-terminal region. We have established transgenic flies expressing the full-length DREF polypeptide or its N-terminal fragment (amino acid residues 1 to 125) under the control of the heat shock promoter, the salivary gland-specific promoter, or the eye imaginal disc-specific promoter. Heat shock induction of the N-terminal fragment during embryonic, larval, or pupal stages caused greater than 50% lethality. This lethality was overcome by coexpression of the full-length DREF. In salivary glands of the transgenic larvae expressing the N-terminal fragment, this fragment formed a homodimer and a heterodimer with the endogenous DREF. Ectopic expression of the N-terminal fragment in salivary gland cells reduced the contents of mRNAs for the 180-kDa subunit of DNA polymerase α and for dE2F and the extent of DNA endoreplication. Ectopic expression of the N-terminal fragment in the eye imaginal discs significantly reduced DNA replication in cells at the second mitotic wave. The lines of evidence suggest that the N-terminal fragment can impede the endogenous DREF function in a dominant negative manner and that DREF is required for normal DNA replication in both mitotic cell cycle and endo cycle.

scholarly journals The dimerization of half-molecule fragments of transferrin

1988 ◽  
Vol 251 (3) ◽  
pp. 849-855 ◽  
Author(s):  
J Williams ◽  
K Moreton
Keyword(s):  
Amino Acid ◽  
Molecular Recognition ◽  
Amino Acid Residues ◽  
X Ray ◽  
X Ray Crystallography ◽  
Recognition Sites ◽  
Terminal Fragment

Partial proteolysis was used to prepare half-molecule fragments of hen ovotransferrin. N-Terminal and C-terminal fragments associate to form an N-terminal fragment-C-terminal fragment dimer. Variant forms of the N- and C-terminal fragments can be prepared in which a few amino acid residues are lacking from the C-terminal ends of the fragments. These variant fragments are partially or completely unable to associate; the suggestion that the molecular recognition sites are located in these C-terminal stretches of the N-terminal half-molecule (320-332) and of the C-terminal half-molecule (683-686) is in agreement with X-ray-crystallography data for human lactotransferrin [Anderson, Baker, Dodson, Norris, Rumball, Waters & Baker (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 1769-1773].

Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins

2016 ◽  
Vol 18 (25) ◽  
pp. 16748-16756 ◽  
Author(s):  
Biswajit Sadhu ◽  
Mahesh Sundararajan
Keyword(s):  
Density Functional Theory ◽  
Amino Acid ◽  
Density Functional ◽  
Copper Proteins ◽  
Amino Acid Residues ◽  
Functional Theory ◽  
Copper Protein ◽  
Inner Sphere ◽  
Reorganization Energies

Density functional theory based calculations predict the inner sphere reorganization energies of type zero copper protein is largely modulated by Asn47 and Phe114 amino acid residues.

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