scholarly journals X-ray Crystallographic Structure of α-Helical Peptide Stabilized by Hydrocarbon Stapling at i,i + 1 Positions

2021 ◽  
Vol 22 (10) ◽  
pp. 5364
Author(s):  
Yui Makura ◽  
Atsushi Ueda ◽  
Takuma Kato ◽  
Akihiro Iyoshi ◽  
Mei Higuchi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Crystallographic Analysis ◽  
Crystallographic Structure ◽  
Amino Acid Residues ◽  
X Ray ◽  
Stapled Peptide ◽  
Helical Peptide ◽  
Α Helix ◽  
The Right

Hydrocarbon stapling is a useful tool for stabilizing the secondary structure of peptides. Among several methods, hydrocarbon stapling at i,i + 1 positions was not extensively studied, and their secondary structures are not clarified. In this study, we investigate i,i + 1 hydrocarbon stapling between cis-4-allyloxy-l-proline and various olefin-tethered amino acids. Depending on the ring size of the stapled side chains and structure of the olefin-tethered amino acids, E- or Z-selectivities were observed during the ring-closing metathesis reaction (E/Z was up to 8.5:1 for 17–14-membered rings and up to 1:20 for 13-membered rings). We performed X-ray crystallographic analysis of hydrocarbon stapled peptide at i,i + 1 positions. The X-ray crystallographic structure suggested that the i,i + 1 staple stabilizes the peptide secondary structure to the right-handed α-helix. These findings are especially important for short oligopeptides because the employed stapling method uses two minimal amino acid residues adjacent to each other.

Protein Structure Prediction by Fusion,Bayesian Methods

2011 ◽  
pp. 1330-1336
Author(s):  
Somasheker Akkaladevi ◽  
Ajay K. Katangur ◽  
Xin Luo
Keyword(s):  
Neural Network ◽  
Amino Acids ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Prediction Accuracy ◽  
Protein Secondary Structure ◽  
Decision Fusion ◽  
Amino Acid Residues ◽  
Fusion Methods ◽  
Bayesian Inference Method

Prediction of protein secondary structure (alpha-helix, beta-sheet, coil) from primary sequence of amino acids is a very challenging and difficult task, and the problem has been approached from several angles. A protein is a sequence of amino acid residues and can thus be considered as a one dimensional chain of ‘beads’ where each bead correspond to one of the 20 different amino acid residues known to occur in proteins. The length of most protein sequence ranges from 50 residues to about 1000 residues but longer proteins are also known, e.g. myosin, the major protein of muscle fibers, consists of 1800 residues (Altschul et al. 1997). Many techniques were used many researchers to predict the protein secondary structure, but the most commonly used technique for protein secondary structure prediction is the neural network (Qian et al. 1988). This chapter discusses a new method combining profile-based neural networks (Rost et al. 1993b), Simulated Annealing (SA) (Akkaladevi et al. 2005; Simons et al. 1997), Genetic algorithm (GA) (Akkaladevi et al. 2005) and the decision fusion algorithms (Akkaladevi et al. 2005). Researchers used the neural network (Hopfield 1982) combined with GA and SA algorithms, and then applied the two decision fusion methods; committee method and the correlation methods and obtained improved results on the prediction accuracy (Akkaladevi et al. 2005). Sequence profiles of amino acids are fed as input to the profile-based neural network. The two decision fusion methods improved the prediction accuracy, but noticeably one method worked better in some cases and the other method for some other sequence profiles of amino acids as input (Akkaladevi et al. 2005). Instead of compromising on some of the good solutions that could have generated from either approach, a combination of these two approaches is used for obtaining better prediction accuracy. This criterion is the basis for the Bayesian inference method (Anandalingam et al. 1989; Schmidler et al. 2000; Simons et al. 1997). The results obtained show that the prediction accuracy improves by more than 2% using the combination of the decision fusion approach and the Bayesian inference method.

The stability and screw sense of the α -helix in poly- β -benzyl-L-aspartate

1960 ◽  
Vol 259 (1296) ◽  
pp. 110-128 ◽  
Keyword(s):  
Optical Rotatory Dispersion ◽  
Molecular Models ◽  
X Ray Diffraction ◽  
X Ray ◽  
Left Handed ◽  
The Difference ◽  
Diffraction Patterns ◽  
The Stability ◽  
Α Helix ◽  
The Right

A number of polymers and copolymers containing β -benzyl-L-aspartate has been prepared and their optical rotatory dispersion in a variety of solvents has been measured. The results of these measurements together with studies of infra-red spectra, X-ray diffraction patterns, deuteration rates and molecular models lead to the following conclusions. (i) The α -helical form of poly- β -benzyl-L-aspartate is considerably less stable relative to the solvated randomly coiled form than that of poly- γ -benzyl-L-glutamate. (ii) The left-handed α -helix of poly- β -benzyl-L-aspartate is more stable than the right-handed one. (iii) The difference in stability between the two senses of α -helix is much less in the case of poly- β -benzyl-L-aspartate than in that of poly- γ -benzyl-L-glutamate or poly-L-alanine.

Circular dichroism studies on Mengo virus variants and their constituent ribonucleates

1970 ◽  
Vol 48 (8) ◽  
pp. 940-943 ◽  
Author(s):  
Cyril M. Kay ◽  
John S. Colter ◽  
Kimio Oikawa
Keyword(s):  
Amino Acids ◽  
Viral Protein ◽  
Small Amplitude ◽  
Helical Content ◽  
Mengo Virus ◽  
Α Helix ◽  
The Right ◽  
Circular Dichroïsm ◽  
Circular Dichroic

A comparison of the circular dichroic spectra of three variants of Mengo virus and their constituent ribonucleates shows that the curves are essentially identical to one another, with respect to crossover points and the positions and amplitudes of troughs and peaks. This would suggest that the manner in which the proteins are arranged around the RNA chain in the virus is precise and similar in all three cases, and that there are no significant differences in the density of packing among the virions. By subtracting the RNA contribution from that of the virus, the circular dichroic curve of the protein in situ was obtained. The small amplitude of the ellipticity bands at ~205 and 220 mμ (transitions characteristic of the right-handed α-helix) suggests that the protein, as it exists in the virion, possesses a low α-helical content. This observation is consistent with the fact that the viral protein contains a large content of proline and non-α-helix-forming amino acids.

scholarly journals Isolation, characterization, molecular cloning and molecular modelling of two lectins of different specificities from bluebell (Scilla campanulata) bulbs

1999 ◽  
Vol 340 (1) ◽  
pp. 299-308 ◽  
Author(s):  
Lisa M. WRIGHT ◽  
Els J. M. VAN DAMME ◽  
Annick BARRE ◽  
Anthony K. ALLEN ◽  
Fred VAN LEUVEN ◽  
...  
Keyword(s):  
Molecular Modelling ◽  
Close Relationships ◽  
Crystallographic Analysis ◽  
Amino Acid Residues ◽  
Refined Model ◽  
X Ray ◽  
Mannose Binding ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Binding Lectin

Two lectins have been isolated from bluebell (Scilla campanulata) bulbs. From their isolation by affinity chromatography, they are characterized as a mannose-binding lectin (SCAman) and a fetuin-binding lectin (SCAfet). SCAman preferentially binds oligosaccharides with α(1,3)- and α(1,6)-linked mannopyranosides. It is a tetramer of four identical protomers of approx. 13 kDa containing 119 amino acid residues; it is not glycosylated. The fetuin-binding lectin (SCAfet), which is not inhibited by any simple sugars, is also unglycosylated. It is a tetramer of four identical subunits of approx. 28 kDa containing 244 residues. Each 28 kDa subunit is composed of two 14 kDa domains. Both lectins have been cloned from a cDNA library and sequenced. X-ray crystallographic analysis and molecular modelling studies have demonstrated close relationships in sequence and structure between these lectins and other monocot mannose-binding lectins. A refined model of the molecular evolution of the monocot mannose-binding lectins is proposed.

scholarly journals Crystal Structure of Mox-1, a Unique Plasmid-Mediated Class C β-Lactamase with Hydrolytic Activity towards Moxalactam

2014 ◽  
Vol 58 (7) ◽  
pp. 3914-3920 ◽  
Author(s):  
Takuma Oguri ◽  
Takamitsu Furuyama ◽  
Takashi Okuno ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hydrolytic Activity ◽  
Crystallographic Structure ◽  
Structural Flexibility ◽  
Amino Acid Residues ◽  
Structural Elements ◽  
X Ray ◽  
Binding Cavity ◽  
Class C ◽  
Unique Plasmid

ABSTRACTMox-1 is a unique plasmid-mediated class C β-lactamase that hydrolyzes penicillins, cephalothin, and the expanded-spectrum cephalosporins cefepime and moxalactam. In order to understand the unique substrate profile of this enzyme, we determined the X-ray crystallographic structure of Mox-1 β-lactamase at a 1.5-Å resolution. The overall structure of Mox-1 β-lactamase resembles that of other AmpC enzymes, with some notable exceptions. First, comparison with other enzymes whose structures have been solved reveals significant differences in the composition of amino acids that make up the hydrogen-bonding network and the position of structural elements in the substrate-binding cavity. Second, the main-chain electron density is not observed in two regions, one containing amino acid residues 214 to 216 positioned in the Ω loop and the other in the N terminus of the B3 β-strand corresponding to amino acid residues 303 to 306. The last two observations suggest that there is significant structural flexibility of these regions, a property which may impact the recognition and binding of substrates in Mox-1. These important differences allow us to propose that the binding of moxalactam in Mox-1 is facilitated by the avoidance of steric clashes, indicating that a substrate-induced conformational change underlies the basis of the hydrolytic profile of Mox-1 β-lactamase.

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