Dynamic aspect of bacteriorhodopsin as viewed from13C NMR: Conformational elucidation, surface dynamics and information transfer from the surface to inner residues

We demonstrate here how dynamic as well as conformational features of bacteriorhodopsin (bR) in purple membrane (PM) as a typical membrane protein are revealed by extensive13C NMR studies on [3-13C]-, [2-13C]-, [1-13C]Ala or [1-13C]Val-labeled bR and a variety of site-directed mutants. A number of13C NMR peaks were well-resolved for [3‒13C]Ala‒ and [1-13C]Val-bR under the condition of fully hydrated PM at ambient temperature and assigned to individual amino-acid residues, initially by regio-specific manner with reference to the data of the conformation-dependent displacements of peaks from model polypeptides and subsequently by site-specific manner with reference to the specifically reduced peak-intensities of site-directed mutant as compared with those of wild type. It is noticeable that the revealed bR structure at ambient temperature by13C NMR is not static as anticipated from the data of diffraction studies at cryo-temperature but is dynamically heterogeneous undergoing motional fluctuations with various frequencies (102–108Hz) depending upon the domains of interest. We further applied this approach to reveal how charged state of surface residues, especially at the side-chain of exracellular Glu residues (Glu 194 and 204), could be transmitted to the inner part of the helices such as Ala 53, 84, and 215 to alter their local conformations of transmembrane helices near at the Schiff base through side-chain interactions. We also analyzed how information of the protonation at Asp 85 from helix C is initially transmitted to helices B (Val 49) and G (Val 213) though modified helix‒helix interactions through the side-chains of Arg 82.

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Artificial granule suspensions of long side chain poly(3-hydroxyalkanoate)

Canadian Journal of Microbiology ◽

10.1139/m95-180 ◽

1995 ◽

Vol 41 (13) ◽

pp. 138-142 ◽

Cited By ~ 25

Author(s):

R. H. Marchessault ◽

F. G. Morin ◽

S. Wong ◽

I. Saracovan

Keyword(s):

Enzymatic Degradation ◽

Room Temperature ◽

Aqueous Suspension ◽

Side Chain ◽

Nmr Studies ◽

Continuous Film ◽

Enzyme Model ◽

C Nmr

In vitro preparation of long side chain poly(3-hydroxyalkanoate) artificial granule suspensions that mimic the "as biosynthesized" inclusions in vivo is reported. Elastomeric poly(3-hydroxyalkanoate) can be made into an aqueous suspension of noncrystalline, submicron-sized particles. Light-scattering measurements on these suspensions showed polymer particles in the range of 90–200 nm in diameter. High-resolution 13C-NMR studies demonstrated the noncrystalline character of the in vitro artificial granules. Upon drying at room temperature, the suspensions yielded a continuous film resulting from the coalescence of these polymers with a low glass transition temperature and low Young's modulus. Aqueous suspensions of poly(3-hydroxyoctanoate) are ideal substrates for enzymatic degradation studies because of their stability and purity, since they are self-stabilized. The range of poly(3-hydroxyalkanoates) that can be converted to artificial granules and the methods of preparation are described.Key words: poly(3-hydroxyalkanoate), artificial granules, in vitro bacterial inclusions, enzyme model substrates, poly(3-hydroxyoctanoate).

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Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.15.162 ◽

2019 ◽

Vol 15 ◽

pp. 1581-1591

Author(s):

Małgorzata Urbańczyk ◽

Michał Jewgiński ◽

Joanna Krzciuk-Gula ◽

Jerzy Góra ◽

Rafał Latajka ◽

...

Keyword(s):

Amino Acid ◽

Mechanism Of Action ◽

Freezing Point ◽

The Body ◽

Side Chain ◽

Amino Acid Residues ◽

Nmr Studies ◽

Antifreeze Glycoproteins ◽

Conformational Preferences ◽

Antifreeze Activity

Antifreeze glycoproteins are a class of biological agents which enable living at temperatures below the freezing point of the body fluids. Antifreeze glycopeptides usually consist of repeating tripeptide unit (-Ala-Ala-Thr*-), glycosylated at the threonine side chain. However, on the microscopic level, the mechanism of action of these compounds remains unclear. As previous research has shown, antifreeze activity of antifreeze glycopeptides strongly relies on the overall conformation of the molecule as well an on the stereochemistry of amino acid residues. The desired monoglycosylated analogues with acetylated amino termini and the carboxy termini in form of N-methylamide have been synthesized. Conformational nuclear magnetic resonance (NMR) studies of the designed analogues have shown a strong influence of the stereochemistry of amino acid residues on the peptide chain stability, which could be connected to the antifreeze activity of these compounds. A better understanding of the mechanism of action of antifreeze glycopeptides would allow applying these materials, e.g., in food industry and biomedicine.

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

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190708103132 ◽

2020 ◽

Vol 16 (4) ◽

pp. 451-459 ◽

Cited By ~ 1

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.

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

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19852925 ◽

1985 ◽

Vol 50 (12) ◽

pp. 2925-2936 ◽

Cited By ~ 2

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.

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13C nuclear magnetic resonance study of cyclodipeptides containing 13C enriched hydrophobic amino acids

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19800482 ◽

1980 ◽

Vol 45 (2) ◽

pp. 482-490 ◽

Cited By ~ 10

Author(s):

Jaroslav Vičar ◽

François Piriou ◽

Pierre Fromageot ◽

Karel Bláha ◽

Serge Fermandjian

Keyword(s):

Amino Acids ◽

Nuclear Magnetic Resonance ◽

Nuclear Magnetic Resonance Study ◽

Coupling Constants ◽

Side Chain ◽

Amino Acid Residues ◽

Magnetic Resonance Study ◽

Side Chain Conformation ◽

13C Nuclear Magnetic Resonance ◽

Hydrophobic Amino Acids

The diastereoisomeric pairs of cyclodipeptides cis- and trans-cyclo(Ala-Ala), cyclo(Ala-Phe), cyclo(Val-Val) and cyclo(Leu-Leu) containing 85% 13C enriched amino-acid residues were synthesized and their 13C-13C coupling constants were measured. The combination of 13C-13C and 1H-1H coupling constants enabled to estimate unequivocally the side chain conformation of the valine and leucine residues.

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

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19911963 ◽

1991 ◽

Vol 56 (9) ◽

pp. 1963-1970 ◽

Cited By ~ 3

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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Structural Investigations of C-Nitrosobenzenes. Part 3.1 Solid-state and Solution 13C NMR Studies, and Crystal Structure of E-(4-CIC6H4NO)2

Journal of Chemical Research ◽

10.1177/174751989902300316 ◽

1999 ◽

Vol 23 (3) ◽

pp. 202-203

Author(s):

Daniel A. Fletcher ◽

Brian G. Gowenlock ◽

Keith G. Orrell ◽

David C. Apperley ◽

Michael B. Hursthouse ◽

...

Keyword(s):

Crystal Structure ◽

Solid State ◽

13C Nmr ◽

Nmr Studies ◽

Structural Investigations ◽

Nmr Data ◽

C Nmr

Solid-state and solution 13C NMR data for the monomers and dimers of 3- and 4-substituted nitrosobenzenes, and the crystal structure of E-(4-CIC6H4NO)2 are reported.

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Effect of roasting temperature on lipid and protein oxidation and amino acid residue side chain modification of beef patties

RSC Advances ◽

10.1039/d1ra03151a ◽

2021 ◽

Vol 11 (35) ◽

pp. 21629-21641

Author(s):

Chao Xia ◽

Pingping Wen ◽

Yaming Yuan ◽

Xiaofan Yu ◽

Yijing Chen ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Residue ◽

Protein Oxidation ◽

Relative Number ◽

Side Chain ◽

Amino Acid Residues ◽

Beef Patties ◽

Lipid And Protein Oxidation ◽

Roasting Temperature

The relative number of peptides modified by the amino acid residues of actin from raw beef patties and those cooked at different roasting temperatures.

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Development of Antimicrobial Stapled Peptides Based on Magainin 2 Sequence

Molecules ◽

10.3390/molecules26020444 ◽

2021 ◽

Vol 26 (2) ◽

pp. 444

Author(s):

Motoharu Hirano ◽

Chihiro Saito ◽

Hidetomo Yokoo ◽

Chihiro Goto ◽

Ryuji Kawano ◽

...

Keyword(s):

Antimicrobial Activity ◽

Amino Acid ◽

Hemolytic Activity ◽

Helical Structure ◽

Antimicrobial Activities ◽

Side Chain ◽

Membrane Disruption ◽

Amino Acid Residues ◽

Electrophysiological Measurements ◽

Cell Membrane Disruption

Magainin 2 (Mag2), which was isolated from the skin of the African clawed frog, is a representative antimicrobial peptide (AMP) that exerts antimicrobial activity via microbial membrane disruption. It has been reported that the helicity and amphipathicity of Mag2 play important roles in its antimicrobial activity. We investigated and recently reported that 17 amino acid residues of Mag2 are required for its antimicrobial activity, and accordingly developed antimicrobial foldamers containing α,α-disubstituted amino acid residues. In this study, we further designed and synthesized a set of Mag2 derivatives bearing the hydrocarbon stapling side chain for helix stabilization. The preferred secondary structures, antimicrobial activities, and cell-membrane disruption activities of the synthesized peptides were evaluated. Our analyses revealed that hydrocarbon stapling strongly stabilized the helical structure of the peptides and enhanced their antimicrobial activity. Moreover, peptide 2 stapling between the first and fifth position from the N-terminus showed higher antimicrobial activity than that of Mag2 against both gram-positive and gram-negative bacteria without exerting significant hemolytic activity. To investigate the modes of action of tested peptides 2 and 8 in antimicrobial and hemolytic activity, electrophysiological measurements were performed.

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