Conformation of branched polypeptides based on poly(L-lysine): Circular dichroism study

1980 ◽  
Vol 45 (3) ◽  
pp. 941-949 ◽  
Author(s):  
Hana Votavová ◽  
Ferenc Hudecz ◽  
Judit Kajtár ◽  
Mária Szekerke ◽  
Jaroslav Šponar ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Amino Acid ◽  
Main Chain ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Cd Spectra ◽  
Circular Dichroïsm

Circular dichroism (CD) spectra of branched (multichain) polypeptides based on poly(L-lysine) with DL-alanine and other amino-acid residues in the side chain have been measured under various conditions of pH. The spectra were interpreted using spectra of poly(L-lysine) as standard. No straightforward correlation between polypeptide CD spectra and their structure could be detected. The contribution of the side chain CD to that of the main chain is additive in some cases, but in other cases qualitatively different CD spectra arise. The reason for this CD behavior is discussed.

Synthesis and conformation of sequential basic polypeptides with branched and linear side chains

1985 ◽  
Vol 50 (12) ◽  
pp. 2925-2936 ◽  
Author(s):  
Štěpánka Štokrová ◽  
Jan Pospíšek ◽  
Jaroslav Šponar ◽  
Karel Bláha
Keyword(s):  
Amino Acid ◽  
Salt Concentration ◽  
Salt Solution ◽  
Theoretical Work ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Cd Spectra ◽  
Low Salt ◽  
Conformational Freedom ◽  
Basic Polypeptides

Polypeptides (Lys-X-Ala)n and (Lys-X-Gly)n in which X represents residues of isoleucine and norleucine, respectively, and polypeptide (Tle-Lys-Ala)n, were synthesized via polymerization of 1-hydroxysuccinimidyl esters of the appropriate tripeptides to complete previously studied series. Circular dichroism (CD) spectra of the respective polymers were measured as a function of pH and salt concentration of the medium. The results were correlated with those obtained previously with the same series containing different amino acid residues at the X-position. The helix forming ability of the polypeptides (Lys-X-Ala)n with linear X side chain was found to be independent of the length. In the series (Lys-X-Gly)n the unordered conformation was the most probable one except (Lys-Ile-Gly)n. This polymer assumed the β conformation even in low salt solution at neutral pH. An agreement with some theoretical work concerned with the restriction of conformational freedom of amino acid residue branching at Cβ atom with our experimental results is evident.

Circular Dichroism, Self Interaction and Side Chain Conformation of Riboflavin and Riboflavin Analogues

1972 ◽  
Vol 27 (9) ◽  
pp. 1044-1046 ◽  
Author(s):  
G. Scola-Nagelschneider ◽  
P. Hemmerich
Keyword(s):  
Circular Dichroism ◽  
Ionic Strength ◽  
Aqueous Solutions ◽  
Chain Conformation ◽  
Side Chain ◽  
Cd Spectra ◽  
Polar Solvents ◽  
Side Chain Conformation ◽  
Vibronic Transitions ◽  
Circular Dichroïsm

The CD-spectra of riboflavin and riboflavin analogues in aqueous solutions differ very little depending on pH and ionic strength, but are extremely sensitive upon solvent changes. The two bands in the region of 300 —500 nm seen in aqueous solutions are split into seven bands in less polar solvents, which can be assigned to seven vibronic transitions. The spectra may be interpreted by “through space” and “through chain” interactions of the sidechain centers of chirality with the flavin chromophore, which influence the two first π —π* transitions in different manner.

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

Analogues of the cholecystokinin octapeptide modified in the central part of the molecule

1991 ◽  
Vol 56 (9) ◽  
pp. 1963-1970 ◽  
Author(s):  
Jan Hlaváček ◽  
Václav Čeřovský ◽  
Jana Pírková ◽  
Pavel Majer ◽  
Lenka Maletínská ◽  
...  
Keyword(s):  
Amino Acid ◽  
Biological Activities ◽  
Point Of View ◽  
Biologically Active ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Cholecystokinin Octapeptide ◽  
Biological Tests ◽  
Biological Potency ◽  
Biologically Active Conformation

In a series of analogues of the cholecystokinin octapeptide (CCK-8) the amino acid residues were gradually modified by substituting Gly by Pro in position 4, Trp by His in position 5, Met by Cle in position 6, or the Gly residue was inserted between Tyr and Met in positions 2 and 3 of the peptide chain, and in the case of the cholecystokinin heptapeptide (CCK-7) the Met residues were substituted by Nle or Aib. These peptides were investigated from the point of view of their biological potency in the peripheral and central region. From the results of the biological tests it follows that the modifications carried out in these analogues and in their Nα-Boc derivatives mean a suppression of the investigated biological activities by 2-3 orders of magnitude (at a maximum dose of the tested substance of 2 . 10-2 mg per animal).This means that a disturbance of the assumed biologically active conformation of CCK-8, connected with a considerable decrease of the biological potency of the molecule, takes place not only after introduction of the side chain into its centre (substitution of Gly4), but also after the modification of the side chains of the amino acids or by extension of the backbone in further positions around this central amino acid.

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