scholarly journals The folding and assembly of the dodecameric type II dehydroquinases

1999 ◽  
Vol 338 (1) ◽  
pp. 195-202 ◽  
Author(s):  
Nicholas C. PRICE ◽  
Deborah J. BOAM ◽  
Sharon M. KELLY ◽  
Doris DUNCAN ◽  
Tino KRELL ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Streptomyces Coelicolor ◽  
Type Ii ◽  
Efficient Manner ◽  
Low Concentrations ◽  
Permeation Studies ◽  
Time Courses ◽  
Outline Model

The dodecameric type II dehydroquinases (DHQases) have an unusual quaternary structure in which four trimeric units are arranged with cubic 23 symmetry. The unfolding and refolding behaviour of the enzymes from Streptomyces coelicolor and Mycobacterium tuberculosis have been studied. Gel-permeation studies show that, at low concentrations (0.5 M) of guanidinium chloride (GdmCl), both enzymes dissociate into trimeric units, with little or no change in the secondary or tertiary structure and with a 15% loss (S. coelicolor) or a 55% increase (M. tuberculosis) in activity. At higher concentrations of GdmCl, both enzymes undergo sharp unfolding transitions over narrow ranges of the denaturant concentration, consistent with co-operative unfolding of the subunits. When the concentration of GdmCl is lowered by dilution from 6 M to 0.55 M, the enzyme from S. coelicolor refolds in an efficient manner to form trimeric units, with more than 75% regain of activity. Using a similar approach the M. tuberculosis enzyme regains less than 35% activity. From the time courses of the changes in CD, fluorescence and activity of the S. coelicolor enzyme, an outline model for the refolding of the enzyme has been proposed. The model involves a rapid refolding event in which approximately half the secondary structure is regained. A slower folding process follows within the monomer, resulting in acquisition of the full secondary structure. The major changes in fluorescence occur in a second-order process which involves the association of two folded monomers. Regain of activity is dependent on a further associative event, showing that the minimum active unit must be at least trimeric. Reassembly of the dodecameric S. coelicolor enzyme and essentially complete regain of activity can be accomplished if the denatured enzyme is dialysed extensively to remove GdmCl. These results are discussed in terms of the recently solved X-ray structures of type II DHQases from these sources.

scholarly journals LeuRS can leucylate type I and type II tRNALeus in Streptomyces coelicolor

2019 ◽  
Vol 47 (12) ◽  
pp. 6369-6385
Author(s):  
Jia-Yi Fan ◽  
Qian Huang ◽  
Quan-Quan Ji ◽  
En-Duo Wang
Keyword(s):  
Tertiary Structure ◽  
Streptomyces Coelicolor ◽  
Catalytic Efficiency ◽  
Type I ◽  
Type Ii ◽  
Specific Domain ◽  
Recognition Mechanism ◽  
Variable Loop

Abstract Transfer RNAs (tRNAs) are divided into two types, type I with a short variable loop and type II with a long variable loop. Aminoacylation of type I or type II tRNALeu is catalyzed by their cognate leucyl-tRNA synthetases (LeuRSs). However, in Streptomyces coelicolor, there are two types of tRNALeu and only one LeuRS (ScoLeuRS). We found that the enzyme could leucylate both types of ScotRNALeu, and had a higher catalytic efficiency for type II ScotRNALeu(UAA) than for type I ScotRNALeu(CAA). The results from tRNA and enzyme mutagenesis showed that ScoLeuRS did not interact with the canonical discriminator A73. The number of nucleotides, rather than the type of base of the variable loop in the two types of ScotRNALeus, was determined as important for aminoacylation. In vitro and in vivo assays showed that the tertiary structure formed by the D-loop and TψC-loop is more important for ScotRNALeu(UAA). We showed that the leucine-specific domain (LSD) of ScoLeuRS could help LeuRS, which originally only leucylates type II tRNALeu, to aminoacylate type I ScotRNALeu(CAA) and identified the crucial amino acid residues at the C-terminus of the LSD to recognize type I ScotRNALeu(CAA). Overall, our findings identified a rare recognition mechanism of LeuRS to tRNALeu.

Characterization of Tamm-Horsfall Urinary Glycoprotein

1973 ◽  
Vol 31 ◽  
pp. 420-421
Author(s):  
John P. Robinson ◽  
J. David Puett
Keyword(s):  
Electron Microscopy ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Quaternary Structure ◽  
Normal Adult ◽  
Morphological Properties ◽  
Adult Males ◽  
Circular Dichroïsm ◽  
Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

scholarly journals Effects of High Hydrostatic Pressure on the Conformational Structure and Gel Properties of Myofibrillar Protein and Meat Quality: A Review

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1872
Author(s):  
Huipeng Liu ◽  
Yiyuan Xu ◽  
Shuyu Zu ◽  
Xuee Wu ◽  
Aimin Shi ◽  
...  
Keyword(s):  
Hydrostatic Pressure ◽  
High Hydrostatic Pressure ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Meat Products ◽  
Myofibrillar Protein ◽  
Conformational Structure ◽  
Gel Properties ◽  
The Relationship

In meat processing, changes in the myofibrillar protein (MP) structure can affect the quality of meat products. High hydrostatic pressure (HHP) has been widely utilized to change the conformational structure (secondary, tertiary and quaternary structure) of MP so as to improve the quality of meat products. However, a systematic summary of the relationship between the conformational structure (secondary and tertiary structure) changes in MP, gel properties and product quality under HHP is lacking. Hence, this review provides a comprehensive summary of the changes in the conformational structure and gel properties of MP under HHP and discusses the mechanism based on previous studies and recent progress. The relationship between the spatial structure of MP and meat texture under HHP is also explored. Finally, we discuss considerations regarding ways to make HHP an effective strategy in future meat manufacturing.

scholarly journals Type II thioesterase ScoT is required for coelimycin production by the modular polyketide synthase Cpk of Streptomyces coelicolor A3(2).

2014 ◽  
Vol 61 (1) ◽  
Author(s):  
Magdalena Kotowska ◽  
Jarosław Ciekot ◽  
Krzysztof Pawlik
Keyword(s):  
Culture Medium ◽  
Polyketide Synthase ◽  
Streptomyces Coelicolor ◽  
Acyl Chain ◽  
No Production ◽  
Type I ◽  
Type Ii ◽  
Peptide Synthetases ◽  
Modular Polyketide Synthase ◽  
Editing Enzyme

Type II thioesterases were shown to maintain efficiency of modular type I polyketide synthases and nonribosomal peptide synthetases by removing acyl residues blocking extension modules. We found that thioesterase ScoT from Streptomyces coelicolor A3(2) is required for the production of the yellow-pigmented coelimycin by the modular polyketide synthase Cpk. No production of coelimycin was observed in cultures of scoT disruption mutant. Polyketide production was restored upon complementation with an intact copy of the scoT gene. An enzymatic assay showed that ScoT thioesterase can hydrolyse a 12-carbon acyl chain but the activity is too low to play a role in product release from the polyketide synthase. We conclude that ScoT is an editing enzyme necessary to maintain the activity of polyketide synthase Cpk. We provide a HPLC based method to measure the amount of coelimycin P2 in a culture medium.

Modified S-transform as a tool to identify secondary structure elements in RNA

2017 ◽  
Vol 13 (4) ◽  
Author(s):  
Nancy Singh ◽  
Sunil Datt Sharma ◽  
Ragothaman M. Yennamalli
Keyword(s):  
Signal Processing ◽  
Secondary Structure ◽  
Dna Sequences ◽  
Tertiary Structure ◽  
Processing Method ◽  
Rna Sequences ◽  
Signal Processing Method ◽  
S Transform ◽  
Highly Correlated ◽  
Signal Processing Methods

AbstractIn this article, we describe the applicability of a signal processing method, specifically the modified S-transform (MST) method, on RNA sequences to identify periodicities between 2 and 11. MicroRNAs (miRNA) are associated with gene regulation and gene silencing and thus have wide applications in biological sciences. Also, the functionality of miRNA is highly associated with its secondary structures (stem, bulge and loop). Signal processing methods have been previously applied on genomic data to reveal the periodicities that determine a wide variety of biological functions, ranging from exon detection to microsatellite identification in DNA sequences. However, there has been less focus on RNA-based signal processing. Here, we show that the signal processing method can be successfully applied to miRNA sequences. We observed that these periodicities are highly correlated with the secondary structure of miRNA and such methods could possibly be used as indicators of secondary and tertiary structure formation.

RNA Structure Analysis: A Multifaceted Approach

1999 ◽  
Author(s):  
Bruce A. Shapiro ◽  
Wojciech Kasprzak
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Hammerhead Ribozyme ◽  
3D Structure ◽  
Computer Prediction ◽  
Rna Molecules ◽  
Tertiary Interactions ◽  
The One ◽  
Secondary And Tertiary Structure

Genomic information (nucleic acid and amino acid sequences) completely determines the characteristics of the nucleic acid and protein molecules that express a living organism’s function. One of the greatest challenges in which computation is playing a role is the prediction of higher order structure from the one-dimensional sequence of genes. Rules for determining macromolecule folding have been continually evolving. Specifically in the case of RNA (ribonucleic acid) there are rules and computer algorithms/systems (see below) that partially predict and can help analyze the secondary and tertiary interactions of distant parts of the polymer chain. These successes are very important for determining the structural and functional characteristics of RNA in disease processes and hi the cell life cycle. It has been shown that molecules with the same function have the potential to fold into similar structures though they might differ in their primary sequences. This fact also illustrates the importance of secondary and tertiary structure in relation to function. Examples of such constancy in secondary structure exist in transfer RNAs (tRNAs), 5s RNAs, 16s RNAs, viroid RNAs, and portions of retroviruses such as HIV. The secondary and tertiary structure of tRNA Phe (Kim et al., 1974), of a hammerhead ribozyme (Pley et al., 1994), and of Tetrahymena (Cate et al., 1996a, 1996b) have been shown by their crystal structure. Currently little is known of tertiary interactions, but studies on tRNA indicate these are weaker than secondary structure interactions (Riesner and Romer, 1973; Crothers and Cole, 1978; Jaeger et al., 1989b). It is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules. Therefore, a logical place to start in determining the 3D structure of RNA is computer prediction of the secondary structure. The sequence (primary structure) of an RNA molecule is relatively easy to produce. Because experimental methods for determining RNA secondary and tertiary structure (when the primary sequence folds back on itself and forms base pairs) have not kept pace with the rapid discovery of RNA molecules and their function, use of and methods for computer prediction of secondary and tertiary structures have increasingly been developed.

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