Detection and Analysis of Chimeric Tertiary Structures by Backbone Thioester Exchange: Packing of an α Helix against an α/β‐Peptide Helix

The steric behaviour of the α-Helix has been investigated using an elastic molecule-model made of solid rubber balls and steel pins. Shortening of the hydrogen-bonds, which is possible at least in the range from 2.91 to 2.67 A in real α-Helices, has the following effects:1. The α-Helix contracts proportionally to the length of the hydrogen-bonds (figs. 3, 4).2. A torsional force arises leading in the case of longer α-Helices to torsional revolutions of the free ends of the helix (figs. 3 a. 4 a).3. Tertiary structures (superhelices. flattened superhelices. planar wavy lines, planar arcs) superpose the α-Helix if only specific hydrogen-bonds (e. g. indicated by arrows in fig. 5) will be shortened and if the distance between them is repeated in the sequence of the polypeptide chain (Tab. I). Some of the sequence-distances show similar tertiary structures and the same pitches of the superhelices (Tab. II). A general variation in the length of the hydrogen-bonds causes alterations in the superstructure and can also change the coiling direction of the superhelix.4. The Cα— Cβ; bonds incline slightly to the axis of the helix (fig. 11) through which the α-Helix with side chains becomes a little thinner. Because of the torsion (see item 2) the distance between the side chains changes also (fig. 12). The distances increase between specific positions of the side chains and decrease between others (Tab. III).Possible reasons for the shortening of the hydrogen-bonds are briefly discussed. The importance of the described behaviour for biological movements, enzymatic catalysis (“allosteric effect”) and active transport is emphasized.

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Stability of Secondary and Tertiary Structures of Virus-Like Particles Representing Noroviruses: Effects of pH, Ionic Strength, and Temperature and Implications for Adhesion to Surfaces

Applied and Environmental Microbiology ◽

10.1128/aem.01278-15 ◽

2015 ◽

Vol 81 (22) ◽

pp. 7680-7686 ◽

Cited By ~ 17

Author(s):

Idrissa Samandoulgou ◽

Riadh Hammami ◽

Rocio Morales Rayas ◽

Ismail Fliss ◽

Julie Jean

Keyword(s):

Ionic Strength ◽

Structural Rearrangement ◽

Tertiary Structures ◽

Hydrophobic Residues ◽

Virus Like Particles ◽

Nacl Concentration ◽

Effects Of Ph ◽

The Stability ◽

Α Helix ◽

Fresh Foods

ABSTRACTLoss of ordered molecular structure in proteins is known to increase their adhesion to surfaces. The aim of this work was to study the stability of norovirus secondary and tertiary structures and its implications for viral adhesion to fresh foods and agrifood surfaces. The pH, ionic strength, and temperature conditions studied correspond to those prevalent in the principal vehicles of viral transmission (vomit and feces) and in the food processing and handling environment (pasteurization and refrigeration). The structures of virus-like particles representing GI.1, GII.4, and feline calicivirus (FCV) were studied using circular dichroism and intrinsic UV fluorescence. The particles were remarkably stable under most of the conditions. However, heating to 65°C caused losses of β-strand structure, notably in GI.1 and FCV, while at 75°C the α-helix content of GII.4 and FCV decreased and tertiary structures unfolded in all three cases. Combining temperature with pH or ionic strength caused variable losses of structure depending on the particle type. Regardless of pH, heating to pasteurization temperatures or higher would be required to increase GII.4 and FCV adhesion, while either low or high temperatures would favor GI.1 adhesion. Regardless of temperature, increased ionic strength would increase GII.4 adhesion but would decrease GI.1 adhesion. FCV adsorption would be greater at refrigeration, pasteurization, or high temperature combined with a low salt concentration or at a higher NaCl concentration regardless of temperature. Norovirus adhesion mediated by hydrophobic interaction may depend on hydrophobic residues normally exposed on the capsid surface at pH 3, pH 8, physiological ionic strength, and low temperature, while at pasteurization temperatures it may rely more on buried hydrophobic residues exposed upon structural rearrangement.

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Two divergent leptin paralogues in zebrafish (Danio rerio) that originate early in teleostean evolution

Journal of Endocrinology ◽

10.1677/joe-09-0034 ◽

2009 ◽

Vol 201 (3) ◽

pp. 329-339 ◽

Cited By ~ 142

Author(s):

Marnix Gorissen ◽

Nicholas J Bernier ◽

Sander B Nabuurs ◽

Gert Flik ◽

Mark O Huising

Keyword(s):

Danio Rerio ◽

Amino Acid Identity ◽

Class I ◽

Conserved Synteny ◽

Disulphide Bridge ◽

Vertebrate Lineage ◽

Tertiary Structures ◽

High Bootstrap ◽

Α Helix ◽

Bundle Structure

We describe duplicate leptin genes in zebrafish (Danio rerio) that share merely 24% amino acid identity with each other and only 18% with human leptin. We were also able to retrieve a second leptin gene in medaka (Oryzias latipes). The presence of duplicate leptin genes in these two distantly related teleosts suggests that duplicate leptin genes are a common feature of teleostean fishes. Despite low primary sequence conservation, we are confident in assigning orthology between mammalian and zebrafish leptins for several reasons. First, both zebrafish leptins share their characteristic gene structure and display key features of conserved synteny with mammalian leptin genes. Secondly, the cysteine residues that make up leptin's single disulphide bridge are equally spaced in mammalian and zebrafish leptins and are unique among all members of the class-I helical cytokine family. Thirdly, the zebrafish leptins cluster with other fish leptins and mammalian leptins in phylogenetic analysis, supported by high bootstrap values. Within the leptin cluster, leptin-b forms a separate clade with the leptin-b orthologue from medaka. Finally, our prediction of the tertiary structures shows that both leptins conform to the typical four α-helix bundle structure of the class-I α-helical cytokines. The zebrafish leptins are differentially expressed; the liver shows high leptin-a expression (in concordance with what we observed for carp leptins), while leptin-b is expressed at much lower levels, which are downregulated further upon fasting. The finding of duplicate leptin genes in teleosts adds to our understanding of the evolution of leptin physiology in the early vertebrate lineage.

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Denaturant Induced Equilibrium Unfolding and Conformational Transitional Studies of Germinated Fenugreek β-Amylase Revealed Molten Globule like State at Low pH

Protein and Peptide Letters ◽

10.2174/0929866527666200403082721 ◽

2020 ◽

Vol 27 (10) ◽

pp. 1046-1057

Author(s):

Dinesh Chand Agrawal ◽

Anjali Yadav ◽

Mohd. Asim Khan ◽

Suman Kundu ◽

Arvind M. Kayastha

Keyword(s):

Circular Dichroism ◽

Catalytic Domain ◽

Molten Globule ◽

Intrinsic Fluorescence ◽

Tertiary Structures ◽

Near Ultraviolet ◽

Equilibrium Unfolding ◽

Α Helix ◽

Far Ultraviolet ◽

Circular Dichroïsm

Background: β-Amylase (EC 3.2.1.2) is a maltogenic enzyme, which releases β-maltose from the non-reducing end of the substrates. The enzyme plays important roles for the production of vaccine, maltiol and maltose rich syrups. Apart from these applications the enzyme protects cells from abiotic as well as oxidative damage. The enzyme is βwell characterized in βplants and microbes and crystal structures of β-amylases βhave been βobtained from sweet potato, soybean and Bacillus cereus. Objective: Find out correlation between structural and functional stability induced by change in pH, temperature and chaotropes. Methods: Activity, intrinsic fluorescence, extrinsic fluorescence, near- and far- ultraviolet circular dichroism spectroscopic measurements were performed. Results: Peaks about 208 nm and 222 nm obtained by near-ultraviolet circular dichroism correspond to α-helix whereas peak at 215 nm shows presence of β-sheet. At pH 2.0, absence of tertiary structures, exposed of hydrophobic regions and presence of substantial secondary structures, revealed the existence of molten globule like state. Temperature induced denaturation studies showed that the enzyme was stable up to 75 ºC and the process was found to be irreversible in nature. Chaotropes dependent equilibrium unfolding studies revealed that at low concentration of chaotropes, ellipticity and intrinsic fluorescence βintensity were βdecreased βwhereas βenzymatic activity remained unchanged, which revealed fenugreek β-amylase is multi-domains enzyme and catalytic βdomain βis more βstable compare to non-catalytic domain. Moreover, the transition was sigmoidal and non-coincidental. Conclusion: Results indicate the probable existence of intermediate states that might perform significant role in physiological process and biotechnological applications.

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Effect of Active Coatings Containing Lippa citriodora Kunth. Essential Oil on Bacterial Diversity and Myofibrillar Proteins Degradation in Refrigerated Large Yellow Croaker

Polymers ◽

10.3390/polym13111787 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1787

Author(s):

Bo Li ◽

Xuesong Wang ◽

Xin Gao ◽

Jun Mei ◽

Jing Xie

Keyword(s):

Essential Oil ◽

Bacterial Diversity ◽

Carbonyl Compounds ◽

Large Yellow Croaker ◽

Myofibrillar Proteins ◽

Refrigerated Storage ◽

Tertiary Structures ◽

Transmission Electron ◽

Α Helix ◽

Β Sheet

The research evaluated the effects of locust bean gum (LBG) and sodium alginate (SA) active coatings containing 0.15, 0.30 or 0.60% lemon verbena (Lippa citriodora Kunth.) essential oil (LVEO) on the bacterial diversity and myofibrillar proteins (MPs) of large yellow croaker during refrigerated storage at 4 °C for 18 days. Variability in the dominant bacterial community in different samples on the 0, 9th and 18th day was observed. Pseudomonas and Shewanella were the two major genera identified during refrigerated storage. At the beginning, the richness of Pseudomonas was about 37.31% and increased for control (CK) samples during refrigerated storage, however, the LVEO-treated samples increased sharply from day 0 to the 9th day and then decreased. LBG-SA coatings containing LVEO treatments significantly delayed MPs oxidation by retarding the formation of free carbonyl compounds and maintaining higher sulfhydryl content, higher Ca2+-ATPase activity, better organized secondary (higher contents of α-helix and β-sheet) and tertiary structures during refrigerated storage. The transmission electron microscope (TEM) images showed that the integrity of the sarcomere was damaged; the boundaries of the H-, A-, and I-bands, Z-disk, and M-line were fuzzy in the CK samples at the end of storage. However, the LVEO-treated samples were still regular in appearance with distinct dark A-bands, light I-bands, and Z-disk. In brief, LBG-SA active coatings containing LVEO treatments suggested a feasible method for protecting the MPs of large yellow croaker during refrigerated storage.

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TACKLING THE MULTIPLE-MINIMA PROBLEM IN PROTEIN FOLDING BY MONTE CARLO SIMULATED ANNEALING AND GENERALIZED-ENSEMBLE ALGORITHMS

International Journal of Modern Physics C ◽

10.1142/s0129183199001352 ◽

1999 ◽

Vol 10 (08) ◽

pp. 1571-1582 ◽

Cited By ~ 6

Author(s):

YUKO OKAMOTO

Keyword(s):

Monte Carlo ◽

Simulated Annealing ◽

Sequence Information ◽

Tertiary Structures ◽

C Peptide ◽

Pancreatic Trypsin Inhibitor ◽

Multiple Minima ◽

Monte Carlo Simulated Annealing ◽

Α Helix ◽

Ensemble Algorithms

Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained have α-helix structure and β-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.

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Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100119430 ◽

1985 ◽

Vol 43 ◽

pp. 522-523

Author(s):

George C. Ruben ◽

Kenneth A. Marx

Keyword(s):

Tertiary Structure ◽

Dna Complexes ◽

Tertiary Structures ◽

Self Assembling ◽

Double Stranded Dna ◽

Calf Thymus ◽

Dna Organization ◽

Condensed Dna ◽

Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

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