Sequence cyclization. Medical search. Frequent questions

The Nazarov cyclization reaction (often referred to as simply the Nazarov cyclization) is a chemical reaction used in organic chemistry for the synthesis of cyclopentenones. (wikipedia.org)
As the reaction has been developed, variants involving substrates other than divinyl ketones and promoters other than Lewis acids have been subsumed under the name Nazarov cyclization provided that they follow a similar mechanistic pathway. (wikipedia.org)
The mechanism of the classical Nazarov cyclization reaction was first demonstrated experimentally by Charles Shoppee to be an intramolecular electrocyclization and is outlined below. (wikipedia.org)
In this way, the Nazarov cyclization is a rare example of a stereoselective pericyclic reaction, whereas most electrocyclizations are stereospecific. (wikipedia.org)
Research involving the reaction was relatively quiet in subsequent years, until in the mid-1980s when several syntheses employing the Nazarov cyclization were published. (wikipedia.org)
One-Pot Synthesis of 1,2-Disubstituted 4-, 5-, 6-, and 7-Azaindoles from Amino-o-halopyridines via N-Arylation/Sonogashira/Cyclization Reaction. (acs.org)
The sequence divergence within the class presents a challenge in assigning one of these functions to a given Rieske oxygenase, let alone predict the substrate, site of reactivity, or type of reaction (Fig. 1a ). (nature.com)
The first total syntheses of the chromone-containing natural products chaetoquadrins H and I are reported, using an aldol reaction and an acid-catalyzed deprotection/cyclization/elimination sequence. (thieme-connect.de)
These results lead directly to a conjugation-trapping mechanism, in which a thermodynamically unfavorable cyclization reaction is coupled to an electronic conjugation trapping step, to drive chromophore maturation. (proteopedia.org)
The methodology represents an efficient and simple one-pot procedure, employing a synthetic sequence consisting of an Ugi-4 component reaction, a Boc-deprotection, an intramolecular cyclisation reaction and a final reduction (UDCR). (rsc.org)
A new internal, base-mediated redox-cyclisation reaction has been discovered and developed. (mpg.de)
This observation opened the way to an easy formation of azasugars following the sequence of a ) glycosylamine formation, b) Grignard reaction. (enscada.com)
When a strong acid such as trifluoroacetic acid (TFA) is added to the reaction, it causes cyclization. (psiberg.com)
At the competition , the team confirmed the peptide cyclisation reaction, providing a proof-of-concept and a basis for further research. (lsm.lv)

Three reactions occur in the sequencer i.e. coupling, cyclization or cleavage conversion, and isomerization. (psiberg.com)
Sequencers perform these reactions automatically and repeat them until they get the sequence. (psiberg.com)
Cyclic peptides occur naturally in many plant species, and the molecular mechanism responsible for the cyclisation reactions is the BURP-domain protein. (lsm.lv)

The distinct activity of antimicrobial peptides governs their sequence, namely, the incorporation of these peptides into microbial cell membranes. (genscript.com)
It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein. (rosettacommons.org)
That being said, there are many ways of cyclizing peptides, and to my knowledge, Peptiderive uses a very narrow definition of "compatible with cyclic geometry": it only considers cyclization schemes involving disulfides between terminal residues of linear peptides when the terminal residues are already close enough to gether to make disulfide closure likely. (rosettacommons.org)
Mimotopes supplies custom peptides with fully customisable sequences and modifications, including options for the N and C termini. (nridigital.com)
We offer head-to-tail cyclisation, side-chain cyclisation, stapled, and other constrained peptides. (nridigital.com)
Linear peptides, especially those with long sequences, are particularly unpredictable and susceptible to unintentional folding. (nridigital.com)
It sequences the amino acids in short peptides (50-60 residues). (psiberg.com)

The modular synthesis is based on Suzuki cross-coupling of the aryl substituents as boronic acid precursors with 5,8-dibromo-2-( tert -butyl)-4,9-dimethoxy-2,3-dihydro-1H-phenalen-1-one, and the subsequent transformation of the product to the desired 2,5-diaryl 6-hydroxyphenalenone in a reduction/deprotection sequence. (thieme-connect.com)
Amides 94 were obtained from 87 by deprotection,acetylation and diol protection in sequence in 67\% yield. (kaist.ac.kr)
γ-Lactam 98 and 99 were prepared by deprotection of amide group of 97 and the cyclization of γ-aminoacids. (kaist.ac.kr)

By demonstrating that the BURP-domain protein can cyclicise different peptide sequences, the team hopes to provide a fundamental basis for further development of cyclic peptide products. (lsm.lv)
A cyclic ACP have a cyclic structure with a disulfide bond or head-to-tail cyclization. (prismbiolab.com)

Recently, significant advances have taken place in the use of SmI 2 for the synthesis of nitrogen heterocycles, enabled in large part by the unique combination of high reducing power of this reagent (E 1/2 of up to −2.8 V) with excellent chemoselectivity of the reductive umpolung cyclizations mediated by SmI 2 . (mdpi.com)

Intramolecular cyclization of amines and/or guanidines with carboxy groups can and does happen but it would not be very fast at pH 3. (bio.net)
The loss of 18 sounds like some kind of loss of water molecule - and it can be some kind of intramolecular cyclization - either into a lactone, lactame or some other kind of heterocycle, as long as the local geometry allows it. (bio.net)

The success of the Nazarov cyclization as a tool in organic synthesis stems from the utility and ubiquity of cyclopentenones as both motifs in natural products (including jasmone, the aflatoxins, and a subclass of prostaglandins) and as useful synthetic intermediates for total synthesis. (wikipedia.org)
Novel synthetic methodologies for the synthesis of substituted phenanthridines and oxindoles utilizing tandem cyclizations of β-keto radicals were developed. (purdue.edu)
Sequences for all of the known enzymes involved in TIAs synthesis were identified. (biomedcentral.com)
After various challenges, a short and facile formal total synthesis relying on a cascade cyclization was developed. (jyu.fi)

As a result, these sequences usually consist of >50% hydrophobic residues. (genscript.com)

Non-natural oligonucleotides are valuable probes of biological systems, as they can convey synthetic control of endogenous nucleic acids with high sequence specificity. (cdc.gov)

2010) Identification of candidates for cyclotide biosynthesis and cyclisation by expressed sequence tag analysis of Oldenlandia affinis. (cybase.org.au)

With labels and modifications, changes can be made to a peptide without altering the base amino acid sequence. (nridigital.com)
Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (bvsalud.org)

In addition, they may contain modifications such as cyclization or disulfide bonds. (genscript.com)

Here, we review the sequences, structures, and antimicrobial activities of this family and elucidated the motifs of structural and functional significance, as well as its application in food. (bvsalud.org)

a Sequence similarity network of Rieske oxygenases (Pfam PF00355) generated by the EFI-EST 59 server at an E-value of 5 and alignment score of 65, visualized in Cytoscape v3.7.1 60 . (nature.com)
Using sequence and structural similarity searches, we identified 43 new LFcins from the mammalian LFs deposited in the protein databases, which are grouped into six families according to their origins (Primates, Rodentia, Artiodactyla, Perissodactyla, Pholidota, and Carnivora). (bvsalud.org)
The degree of similarity between sequences. (bvsalud.org)

The present invention also relates to isolated trichodiene synthases and isolated nucleic acid sequences encoding the trichodiene synthases. (justia.com)
The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acid sequences as well as methods for producing the trichodiene synthases. (justia.com)

Similarly, β-substitution directed inward restricts the s-trans conformation so severely that E-Z isomerization has been shown to occur in advance of cyclization on a wide range of substrates, yielding the trans cyclopentenone regardless of initial configuration. (wikipedia.org)

A cascade sequence of metal-assisted beta-carbon elimination to form a metal homoenolate followed by hemiketal formation, carbon monoxide insertion and lactonization forms the oxaspirolactone products. (purdue.edu)

Several MO caging strategies have been devised, employing hairpin structures, 7 intermolecular duplexes, 8 , 9 nucleobase modifications, 10 or oligonucleotide cyclization. (cdc.gov)

Trichothecenes are produced by a sequence of oxygenations, isomerizations, cyclizations, and esterifications leading from trichodiene, which is produced from the cyclization of trans, trans-farnesyl pyrophosphate by the enzyme trichodiene synthase (Desjardins, Hohn, and McCormick, 1993, Microbiological Reviews 57: 595-604). (justia.com)
Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation. (uni-stuttgart.de)

We discovered that these deletions were the result of either HPV integration into the human genome or HPV-HPV sequence junctions. (biomedcentral.com)
2 − 6 These nuclease-resistant polymers persist in live organisms for days and are typically designed to recognize 25-base sequences that span intron-exon junctions or translational start sites. (cdc.gov)

Understanding how the sequence of a DNA molecule affects its dynamic properties is a central problem affecting biochemistry and biotechnology. (utmb.edu)
Correlations along a DNA molecule dictate critical sequence positions that can affect the looping rate. (utmb.edu)

This helped in increasing the sequencing of amino acids in the polypeptide chains up to sixty steps in minimum time. (psiberg.com)
Several devices sequence the amino acids of polypeptide chains based on Edman degradation called sequencers or Edman sequencers. (psiberg.com)
It helps sequence the amino acids of polypeptide chains. (psiberg.com)

A sequence-dependent model is developed to qualitatively predict the relative loop formation time as a function of DNA sequence. (utmb.edu)
I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein. (rosettacommons.org)

Proteins that have blocked N-terminal amino acids cannot be sequenced through Edman-degradation. (psiberg.com)
Edman degradation is used for sequencing amino acids in the proteins. (psiberg.com)

Cyclisation is an optional modification, to aid in the constrained conformation of a peptide with a disulphide bond. (nridigital.com)

These authors have shown, for the first time, that the addition of Grignard reagents to N-benzyl and N-alkyl glycosylamines derived from perbenzylated pentofuranoses or hexopyranoses followed by a simple cyclization procedure afforded a short and convenient approach to imino-C-glycosides in the pyrrolidine and piperidine series [43,44]. (enscada.com)
The procedure is illustrated in Scheme 2 (see compounds 1 6) from a d-arabinofuranosylamine, using octylmagnesium bromide, and from a d-glucopyranosylamine using allylmagnesium bromide, and cyclization promoted by reacting the intermediate amino alditol with triflic anhydride. (enscada.com)

We then examined the sequencing data to characterize the HPV copy number and HPV physical status to determine what effect they have on both HPV and human genome structural changes. (biomedcentral.com)

As originally described, the Nazarov cyclization involves the activation of a divinyl ketone using a stoichiometric Lewis acid or protic acid promoter. (wikipedia.org)
After the invention of the amino acid analyzer by Spackman in 1958, it was easy to sequence larger polypeptides with Edman-degradation. (psiberg.com)
The resultant product of the cyclization step is the 2-anilino-thiazo-linon (ATZ amino acid). (psiberg.com)

Generally speaking, α-helical ACPs have short chain lengths compared to other classes and a variety of sequence patterns are found in them. (prismbiolab.com)

This is the first approach to apply cyclization on apelin, and these results provide the basis for the development of drug-like apelin analogues. (nih.gov)

The GH19 Engineering Database: sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19. (uni-stuttgart.de)

The formal acylation of the benzothiazoles is achieved through a sequence involving formation of an aryl glyoxal, ring-opening of the benzothiazole followed by condensation of the amino group with the aryl glyoxal, cyclization and oxidation. (organic-chemistry.org)

Cyclopropanols readily undergo single-electron oxidation and ring opening to give β-keto radicals which underwent cyclization with biaryl isonitriles and acrylamides followed by homolytic aromatic substitution to give ketoalkylated phenanthridines and oxindoles. (purdue.edu)

The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. (rosettacommons.org)

1qyo is a 1 chain structure with sequence from Aequorea victoria . (proteopedia.org)
Random coil ACPs have no fixed structure and so far the ACP from this class have proline and glycine-rich sequences. (prismbiolab.com)

There are 3 steps in Edman degradation: coupling, cyclization, and conversion. (psiberg.com)

The process of cyclizing short DNA, as a critical step in molecular cloning, lacks a comprehensive picture of the kinetic process containing sequence information. (utmb.edu)

To characterize the physical status of HPV within OPSCC and to determine the effect this has throughout the host genome, we have performed 30-40X whole genome sequencing (WGS) on the BGI sequencing platform on 34 OPSCCs: 28 of which were HPV positive. (biomedcentral.com)

Further, we determine that under aerobic, but not anaerobic, conditions the Gly-Gly-Gly chromophore sequence cyclizes and incorporates an oxygen atom. (proteopedia.org)

Significantly, these distortions eliminate potential helical hydrogen bonds that would otherwise have to be broken at an energetic cost during peptide cyclization and force the G67 nitrogen and S65 carbonyl oxygen atoms within van der Waals contact in preparation for covalent bond formation. (proteopedia.org)

See Interrupted cyclizations below) Along this same vein, allenyl vinyl ketones of the type studied extensively by Marcus Tius of the University of Hawaii show dramatic rate acceleration due to the removal of β-hydrogens, obviating a large amount of steric strain in the s-cis conformer. (wikipedia.org)
Recent advancements in next generation sequencing (NGS) technologies and their utilization to examine large numbers of primary cervical cancers has revealed that the overall model for HPV-driven carcinogenesis needs to be rethought. (biomedcentral.com)

How can the hotspot with least contact points with the protein give the best predicition for interaction upon cyclization. (rosettacommons.org)

A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. (biomedcentral.com)

Organisms4

Chemicals and Drugs44

Analytical, Diagnostic and Therapeutic Techniques and Equipment7

Phenomena and Processes12

Disciplines and Occupations1

Technology, Industry, Agriculture3

Information Science1

Reaction14

Reactions3

Peptides7

Deprotection3

Cyclic2

Reductive1

Intramolecular2

Synthesis4

Residues1

Specificity1

Biosynthesis1

Amino Acid Seq2

Disulfide1

Antimicrobial1

Similarity3

Synthases2

Substrates1

Elimination1

Modifications1

Enzyme2

Junctions2

Molecule2

Polypeptide3

Predict2

Proteins2

Modification1

Procedure2

Structural1

Acid3

Patterns1

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Formal1

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