.alpha.-Helix-to-random-coil transitions of two-chain, coiled coils: a theoretical model for the "pretransition" in cysteine-190-cross-linked tropomyosin

Biochemistry ◽  
1986 ◽  
Vol 25 (20) ◽  
pp. 6192-6202 ◽  
Author(s):  
Jeffrey Skolnick ◽  
Alfred Holtzer

1985 ◽  
Vol 18 (6) ◽  
pp. 1083-1086 ◽  
Author(s):  
S. Yukioka ◽  
Ichiro Noda ◽  
Mitsuru Nagasawa ◽  
Marilyn Emerson Holtzer ◽  
Alfred Holtzer




2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.



2010 ◽  
Vol 82 (4) ◽  
pp. 941-951 ◽  
Author(s):  
Cui Yu-bao ◽  
Ying Zhou ◽  
Shi Weihong ◽  
Ma Guifang ◽  
Li Yang ◽  
...  

To obtain the recombinant group 2 allergen product of Dermatophagoides farinae (Der f 2), the Der f 2 gene was synthesized by RT-PCR. The full-length cDNA comprised 441 nucleotides and was 99.3% identical to the reference sequence (GenBank AB195580). The cDNA was bound to vector pET28a to construct plasmid pET28a(+)-Der f 2, which was transformed into E. coli BL21 and induced by IPTG. SDS-PAGE showed a specific band of about 14kDa in the hole cell lysate. s estiated by chroatography, about 3.86 g of the recobinant product as obtained, which conjugated with serum IgE from asthmatic children. The protein had a signal peptide of 17 amino acids. Its secondary structure comprised an alpha helix (19.86%), an extended strand (30.82%), and a random coil (49.32%). The subcellular localization of this allergen was predicted to be at mitochondria. Furthermore, its function was shown to be associated with an MD-2-related lipid-recognition (ML) domain. The results of this study provide a solid foundation for large-scale production of the allergen for clinical diagnosis and treatent of allergic disorders.



2008 ◽  
Vol 105 (40) ◽  
pp. 15275-15280 ◽  
Author(s):  
Ian R. Wheeldon ◽  
Joshua W. Gallaway ◽  
Scott Calabrese Barton ◽  
Scott Banta

Here, we present two bifunctional protein building blocks that coassemble to form a bioelectrocatalytic hydrogel that catalyzes the reduction of dioxygen to water. One building block, a metallopolypeptide based on a previously designed triblock polypeptide, is electron-conducting. A second building block is a chimera of artificial α-helical leucine zipper and random coil domains fused to a polyphenol oxidase, small laccase (SLAC). The metallopolypeptide has a helix–random-helix secondary structure and forms a hydrogel via tetrameric coiled coils. The helical and random domains are identical to those fused to the polyphenol oxidase. Electron-conducting functionality is derived from the divalent attachment of an osmium bis-bipyrdine complex to histidine residues within the peptide. Attachment of the osmium moiety is demonstrated by mass spectroscopy (MS-MALDI-TOF) and cyclic voltammetry. The structure and function of the α-helical domains are confirmed by circular dichroism spectroscopy and by rheological measurements. The metallopolypeptide shows the ability to make electrical contact to a solid-state electrode and to the redox centers of modified SLAC. Neat samples of the modified SLAC form hydrogels, indicating that the fused α-helical domain functions as a physical cross-linker. The fusion does not disrupt dimer formation, a necessity for catalytic activity. Mixtures of the two building blocks coassemble to form a continuous supramolecular hydrogel that, when polarized, generates a catalytic current in the presence of oxygen. The specific application of the system is a biofuel cell cathode, but this protein-engineering approach to advanced functional hydrogel design is general and broadly applicable to biocatalytic, biosensing, and tissue-engineering applications.



1983 ◽  
Vol 16 (3) ◽  
pp. 462-465 ◽  
Author(s):  
Marilyn Emerson Holtzer ◽  
Alfred Holtzer ◽  
Jeffrey Skolnick


2013 ◽  
Vol 647 ◽  
pp. 250-257
Author(s):  
Ling Jie Zuo ◽  
An Chun Cheng ◽  
Ming Shu Wang

Glycoprotein L(gL) is encoded by UL1 gene of duck plague virus (DPV). Through predicting and analyzing the structure and physicochemical properties of DPV gL protein by using some software and online tools to gain more information of DPV gL protein. The phylogenetic tree shows that DPV gL protein has close evolutionary relationship with the genus Simplexvirus. The online analysis of the physicochemical properties demonstrates that the protein has ten potential phosphorylation sites and five potential O-linked glycosylation sites, and without both the signal peptide and the transmembrance region. In addition, the subcellular localization of gL protein largely locates at mitochondrial with 47.8%. The secondary structure results reveal that random coil dominate among secondary structure elements followed by alpha helix, extended strand and β-turn for all sequences. All the data will help a basis for further functional and physiological features study of the DPV gL protein.



2011 ◽  
Vol 282-283 ◽  
pp. 453-456
Author(s):  
Hua Zhong ◽  
Bao Ping Sun ◽  
Fang Ying Zhao

The amino acid sequence of Cation Diffusion Facilitator from Populus trichocarpa, Thlaspi goesingense, Arabidopsis lyrata subsp. Lyrata, Brassica juncea and Medicago sativa, registered in GenBank, were analyzed and researched by the bioinformatic tools in the several aspects, including hydrophobicity / hydrophilicity properties, post-translational modification, secondary structures prediction and transmembrane domain. The results showed that Cation Diffusion Facilitator is a hydrophobic and transmembrane protein, which exists in endoplasmic reticulum and other secretory pathway. The main motifs of predicted secondary structure of Cation Diffusion Facilitator are alpha helix and random coil.



2014 ◽  
Vol 522-524 ◽  
pp. 1109-1116
Author(s):  
Jing Fan ◽  
Ming Yuan Huang ◽  
Xi Yu Zhang ◽  
Zi Liang ◽  
Cheng Hao Xu

Late embryogenesis abundant (LEA) proteins play important roles in enhancing the resistance of plants to adverse stresses and promoting seeds development and maturation. TheOsEmgene in rice is one of LEA protein-encoding genes, however, physical and chemical properties, phylogenetic relationship and protein-protein interaction network of it are still unknown. Here, the full length cDNA ofOsEmwas cloned using nested RT-PCR, the sequencing result was then computational analyzed using bioinformatics approaches. The results showed thatOsEmencoded a high hydrophilic protein with small molecule weight, it is mainly composed of alpha helix, extended strand, beta turn, random coil and contains a conserved region with 20 amino acid residues. Phylogenetic analysis showed that OsEM protein has the nearest phylogenetic relationship to BiEM1, but has the distant phylogenetic relationship to BnEM6. Results of protein-protein interaction network showed the expression ofOsEmgene was regulated by complexes ofVP1/BZ8orVP1/TRAB1. This work is helpful to further define the function ofOsEmgene and provide useful information for improving the adverse stress tolerance of plants in the future.



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