Which type of sponge cake roll resembles the protein fold introduced by Jane S. Richardson?
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Jelly roll fold The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins. Taken together, the jelly roll and Greek key structures comprise around 30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database.
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Swiss roll A Swiss roll, jelly roll, or cream roll is a type of sponge cake roll filled with whipped cream, jam, or icing.
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Jelly slice A jelly slice is a New Zealand and Australian dessert consisting of three layers: the top layer being jelly, the middle layer being custard or cream, and the bottom layer being biscuits.
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Arem-arem Arem-arem is an Indonesian Javanese snack made of compressed rice cake in the form of a cylinder wrapped inside a banana leaf, filled with diced vegetables, "tempeh" or "oncom", sometimes also filled with minced meat or "abon" (beef floss), and eaten as snack. Arem-arem is often described as a smaller size "lontong" snack with fillings, thus sometimes also called lontong isi (lit. "filled lontong").
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Frederic M. Richards Frederic Middlebrook Richards (August 19, 1925 – January 11, 2009), commonly referred to as Fred Richards, was an American biochemist and biophysicist known for solving the pioneering crystal structure of the ribonuclease S enzyme in 1967 and for defining the concept of solvent-accessible surface. He contributed many key experimental and theoretical results and developed new methods, garnering over 20,000 journal citations in several quite distinct research areas. In addition to the protein crystallography and biochemistry of ribonuclease S, these included solvent accessibility and internal packing of proteins, the first side-chain rotamer library, high-pressure crystallography, new types of chemical tags such as biotin/avidin, the nuclear magnetic resonance (NMR) chemical shift index, and structural and biophysical characterization of the effects of mutations.
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Pi helix A pi helix (or π-helix) is a type of secondary structure found in proteins. Although once thought to be rare, short π-helices are found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix. Because such insertions are highly destabilizing, the formation of π-helices would tend to be selected against unless it provided some functional advantage to the protein. π-helices therefore are typically found near functional sites of proteins.
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Bread roll A roll is a small, often round loaf of bread served as a meal accompaniment (eaten plain or with butter). A roll can be served and eaten whole or cut transversely and dressed with filling between the two halves. Rolls are also commonly used to make sandwiches similar to those produced using slices of bread.
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Octyl glucoside Octyl glucoside ("n"-octyl-β--glucoside) is a nonionic surfactant frequently used to solubilise integral membrane proteins for studies in biochemistry. Structurally, it is a glycoside derived from glucose and octanol. Like Genapol X-100 and Triton X-100, it is a nonphysiological amphiphile that makes lipid bilayers less "stiff".
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Black bun Black bun is a type of fruit cake completely covered with pastry. It is Scottish in origin, originally eaten on Twelfth Night but now enjoyed at Hogmanay. The cake mixture typically contains raisins, currants, almonds, citrus peel, allspice, ginger, cinnamon and black pepper. It had originally been introduced following the return of Mary, Queen of Scots from France, but its original use at Twelfth Night ended with the Scottish Reformation. It was subsequently used for first-footing over Hogmanay.
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Sponge reef Sponge reefs are reefs formed by Hexactinellid sponges, which have a skeleton made of silica, and are often referred to as "glass sponges". Such reefs are now very rare, and found only on the western Canadian continental shelf. Although common in the late Jurassic period, sponge reefs were believed to have gone extinct during or shortly after the Cretaceous period, until the existing reefs were discovered in 1987–1988 - hence these sometimes being dubbed living fossils.
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Chaperone (protein) In molecular biology, molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures. Chaperones are present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly. The chaperones are concerned primarily with protein folding. The first protein to be called a chaperone assists the assembly of nucleosomes from folded histones and DNA and such assembly chaperones, especially in the nucleus, are concerned with the assembly of folded subunits into oligomeric structures.
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Papuamide Papuamides A and B are depsipeptides which appear to protect T cells from HIV. They were isolated from the sponge Theonella, and are part of a larger group of structurally similar depsipeptides—also isolated from sponges—including neamphamide A, callipeltin A, and mirabamides A-D.
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Callystatin A Callystatin A is a polyketide natural product from the leptomycin family of antibiotics. It was first isolated in 1997 from the marine sponge "Callyspongia truncata" which was collected from the Goto Islands in the Nagasaki Prefecture of Japan by the Kobayashi group. Since then its absolute configuration has been elucidated and callystatin A was discovered to have anti-fungal and anti-tumor activities with extreme potency against the human epidermoid carcinoma KB cells (IG = 10 pg/ml) and the mouse lymphocytic leukemia Ll210 cells (IG = 20 pg/ml).
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Proteinoid Proteinoids, or thermal proteins, are protein-like, often cross-linked molecules formed abiotically from amino acids. Sidney W. Fox initially proposed that they may have been precursors to the first living cells (protocells). The term was also in the 1960s to describe peptides that are shorter than twenty amino acids found in hydrolysed protein, but this term is no longer commonly used.
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Folding funnel The folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single well-defined tertiary structure. The term was coined by José Onuchic in a 1992 article.
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Francisco J. Blanco Francisco Jose Blanco is a structural biologist working as Group Leader at the Centro de investigación Cooperativa en biociencias CIC bioGUNE, Biscay, Spain. His research utilizes Nuclear Magnetic Resonance spectroscopy to characterize protein structure and protein folding. His major contributions to the field of protein folding include the study of the formation and stability of isolated β-hairpin structures, and the analysis of the folding pathway of the SH3 domain from the α-spectrin protein. His 68 structural biology papers listed in Web of Science have been cited over 2500 times, giving him an h-index of 27.
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Solenoid protein domain Solenoid protein domains are a highly modular type of protein domains. They consist of a chain of nearly identical folds, often simply called "repeats". They are extremely common among all types of proteins, though exact figures are unknown.
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Oscarella nathaliae Oscarella nathaliae is a species of sponge in the order Homosclerophorida, first found in vertical walls of reef caves at depths of about 23 to in the Caribbean Sea. It has a leaf-like flat body, which is loosely attached to the substrate and a perforated, unlobate surface; it contains two bacterial wikt:morphotypes and is characterized by two mesohylar cell types with inclusions.
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Jane Stephens Jane Stephens was an Irish zoologist who was considered a leading authority on sponges in Ireland with specialised knowledge in other marine life who identified and named over 40 sponges new to science. From 1905 to 1920 she was employed in the Natural History Division of the National Museum of Ireland working primarily on the collections of marine invertebrates, including taking part in the Clare Island Survey. Robert Lloyd Praeger testified to her knowledge of and work with Irish sponges stating that "Most of what we know of this group, whether marine or fresh-water, in Ireland, or off the Irish coasts, is due to her work."
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PKD domain PKD (Polycystic Kidney Disease) domain was first identified in the polycystic kidney disease protein, polycystin-1 (PKD1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein–protein and protein–carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.
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Crp domain In molecular biology, the CRP domain is a protein domain consisting of a helix-turn-helix (HTH) motif. It is found at the C-terminus of numerous bacterial transcription regulatory proteins. These proteins bind DNA via the CRP domain. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including ANR, CRP, CLP, CysR, FixK, Flp, FNR, FnrN, HlyX and NtcA.
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Peptide-mass fingerprint In bio-informatics, a peptide-mass fingerprint or peptide-mass map is a mass spectrum of a mixture of peptides that comes from a digested protein being analyzed. The mass spectrum serves as a fingerprint in the sense that it is a pattern that can serve to identify the protein. The method for forming a peptide-mass fingerprint, developed in 1993, consists of isolating a protein, breaking it down into individual peptides, and determining the masses of the peptides through some form of mass spectrometry. Once formed, a peptide-mass fingerprint can be used to search in databases for related protein or even genomic sequences, making it a powerful tool for annotation of protein-coding genes.