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Topic: Peptide sequence

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	Stimulation of gonadotropin release by a non-GnRH peptide sequence of the GnRH precursor -- Millar et al. 232 (4746): ...
		Stimulation of gonadotropin release by a non-GnRH peptide sequence of the GnRH precursor -- Millar et al.
		A synthetic peptide comprising the first 13 amino acids (H X Asp-Ala-Glu-Asn-Leu-Ile-Asp-Ser-Phe-Gln-Glu-Ile-Val X OH) of the 59-amino acid peptide was found to stimulate the release of gonadotropic hormones from human and baboon anterior pituitary cells in culture.
		A GnRH antagonist did not inhibit gonadotropin stimulation by the peptide, and the peptide did not compete with GnRH for GnRH pituitary receptors, indicating that the action of the peptide is independent of the GnRH receptor.
	www.sciencemag.org /cgi/content/abstract/232/4746/68 (345 words)

	Peptide sequence Encyclopedia (Site not responding. Last check: )
		Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain in Peptides and Proteins.
		The sequence is generally reported from the N-terminal end containing free amino group to the C-terminal end containing free carboxyl group.
		Peptide sequence is often called protein sequence if it represents the primary structure of a protein.
	www.hallencyclopedia.com /topic/Peptide_sequence.html (316 words)

	Peptide Solubility
		Peptide solubility is sequence dependent and it is for this reason that, if experimentally tolerated, the peptide sequence should contain at least 20% charged residues to facilitate solubilization.
		Peptides that are shorter than 5 residues are generally soluble in aqueous media, except in extreme cases where all the residues are very hydrophobic (W, I, L, F, M, V or Y).
		Peptide sequences containing a very high (>75%) proportion of S, T, E, D, K, R, H, N, Q or Y are capable of forming extensive intermolecular hydrogen bonding network and have a tendency to form gels in concentrated aqueous solutions.
	www.sigmaaldrich.com /Brands/Sigma_Genosys/Custom_Peptides/Key_Resources/Peptide_Solubility.html (553 words)

	Peptide Atlas
		A given peptide sequence may have been found in more than one protein or more than once in the same protein.
		The number of times a peptide sequence has been identified in all experiments.
		If a peptide sequence has not been found in the protein database, this value will be zero and there will not be a Biosequence Name for this peptide.
	www.peptideatlas.org /docs/PA_terms.php (251 words)

	Derivation of Peptide Sequence from Mass Spectral Data
		Peptide sequencing represents a good area for GA application, since the solution space (number of peptides that could match a given spectrum) is large and the traditional approaches [4, 5] are computationally intensive: For example, each step in a stepwise extension algorithm must consider 20 possibilities.
		This representation permits peptides of arbitrary length, yielding a population of various-length peptides.
		Two peptide properties are measured in mass spectrometry: the overall molecular weight of the peptide and the ion series characteristic of fragmentation along the peptide backbone.
	www.abrf.org /JBT/1998/December98/dec98rcstranz.html (3085 words)

	Peptide Synthesis
		Peptides are complex molecules and each peptide sequence is unique with regard to its chemical and physical properties.
		Peptides are slowly degraded particularly the cysteine-containing peptides are oxidized over time at -20°C. The water content of a given peptide powder varies depending on sequence of the peptide, storage conditions, handling, and other factors.
		Maintain peptide in an oxygen-free environment as peptides having cysteine, methionine, trypophan, glutamine, and asparagine residues are susceptible to oxidation and have reduced self-life.
	www.lerner.ccf.org /services/molecbiotech/peptide.php (1175 words)

	Hartwell Center/Macromolecular Synthesis/Peptide Synthesis/Overview
		Peptides are typically rendered as "fluffy" lyophilized powders that are strongly hygroscopic, rapidly absorbing water from the air.
		If the sequence has been typed in SEQED by the investigator or was obtained from a source other than one of the available databases, bring the sequence as a text file on a floppy disk to the Hartwell Center.
		If this peptide is intended to mimic an internal piece of the protein, the ends of the peptide possess charges, which were not present, when the peptide was within the protein.
	www.hartwellcenter.org /bio_services/macsyn/pepservices/index.php (4885 words)

	Peptide Synthesis - Peptide Protein Research Ltd (PPR Ltd) (Site not responding. Last check: )
		Fmoc chemistry is most suitable for simple peptides and sequences prone to oxidation, but the use of Boc chemistry allows us to synthesise difficult sequences, and gives a greater flexibility in the synthesis of modified peptides.
		Most peptide synthesis is carried out in the solid phase, but certain modifications are carried out in solution after peptide synthesis and cleavage from the resin.
		Shorter peptides may be dispatched sooner, difficult peptides sequences or unusual modifications may take longer, and this will be indicated in your quotation if possible.
	www.peptidesynthetics.co.uk /questions (621 words)

	Global Peptide Services, LLC: FAQ
		Ideally, peptide sequences should be 10-30 residues in length, be relatively hydrophilic and possess few or none of the avoidances discussed in Question 2.
		Peptides, unlike oligonucleotides, which can be produced quickly and predictably, are often difficult to synthesize due to their many chemically different residues.
		Each peptide is guaranteed to meet the requirements of the order at the time of delivery or GPS will re-synthesize or re-purify the peptide in question, or refund your money.
	www.globalpeptide.com /faq.html (1357 words)

	Peptide Sequence Databases: Research: Nathan Edwards
		The protein sequence databases used by tandem mass spectra search engines are designed to be useful as possible to as many researchers as possible.
		Fortunately, it is possible to construct a new sequence database that contains all peptide sequences from the original without introducing new ones, by considering all "words" of length 30 (30-mers) from the sequence database.
		Sequence database compression for peptide identification from tandem mass spectra" describes the process by which this new sequence database can be constructed, and gives compression rates for commonly used protein sequence databases.
	www.umiacs.umd.edu /~nedwards/research/pepseqdb.html (712 words)

	Peptide Design
		Peptide sequence selection is likely the most difficult step in the development of anti-peptide antibodies.
		Although the design of peptides for use as antigens is not exact, several tips can help maximize the likelihood of success in producing antibodies.
		It is important to select sequences which are found on the surface of the native protein, contain both hydrophilic and hydrophobic residues, and preferably have antigenic amino acids (e.g.
	www.ucalgary.ca /antibody/peptidedesign.htm (234 words)

	PUBLICATION GUIDELINES FOR THE ANALYSIS AND DOCUMENTATION OF PEPTIDE AND PROTEIN IDENTIFICATIONS
		Authors are required to present representative spectra of posttranslationally modified peptides in the body of the text and the remaining annotated spectra as supplemental material.
		Identical peptide sequences can be included in multiple unique protein sequences due to biological variation such as single amino acid variants, alternative splice forms, homologs, orthologs and paralogs.
		Detection of shared peptides introduces an uncertainty between the possibility that a shared peptide can be mapped to more than one protein sequence (bioinformatics redundancy) versus the possibility that more than one precursor is in the original protein mixture (physical redundancy).
	www.mcponline.org /misc/ParisReport_Final.shtml (1594 words)

	Peptide sequence tag-based blind identification of post-translational modifications with point process model -- Liu et ...
		Peptide sequence tag-based blind identification of post-translational modifications with point process model -- Liu et al.
		spectra with theoretical spectra from peptides in a peptide
		peptide sequence tags (PSTs) from an extended spectrum graph.
	bioinformatics.oxfordjournals.org /cgi/content/abstract/22/14/e307 (348 words)

	Peptide software
		If you are interested in software that would lead you to the identification of peptides or proteins based on a peptide sequence, please see our page on proteomics software.
		Peptide Builder Lite - an application that simplifies generation of text representations for simple peptides and proteins.
		Peptide Companion from CSPS Pharmaceuticals - This software is capable of performing a wide range of peptide analysis: HPLC behavior of peptides, difficult sequences to synthesize, enzymatic or chemical degradation, conformation predictions of peptides and proteins, and much more.
	www.peptideresource.com /software.html (514 words)

	BioMed Central \| Full text \| A geometric and algebraic view of MHC-peptide complexes and their binding properties
		The space of sequence properties (having a particular amino acid at a particular position) of MHC-peptide complexes conveys a geometric structure to these sequence properties in the form of a distance measure, which reveals the peptide binding requirements imposed by the polymorphic sequence characteristics of the MHC molecules.
		Therefore, nonamers are characterised by 180 sequence properties, one for each of the 20 amino acids at each of the nine positions; and MHC alleles are characterised by 207 sequence properties for each of the possible amino acids at each one of the 73 polymorphic positions in the alpha-1 and alpha-2 domains.
		Future progress in elucidating how peptides are selected for their presentation to T cells depends on the development of algorithms to analyse peptide binding data in a combinatorial way that would account for the possibility that the effect of MHC sequence variables is interrelated.
	www.biomedcentral.com /1472-6807/1/2 (6004 words)

	ELIZABETH HALEN CORP.
		Modification of this peptide sequence generated a novel peptide signal sequence, which in turn was complexed to two cofactors known to be integral components in the collagen synthetic pathway; namely, ascorbic palmitale and electron iron.
		By applying the properties of peptide signal sequences as genetic and metabolic feedback messengers, a novel peptide signal sequence complex was generated that significantly affects dermal metabolism and structure.
		Tests using this sequence have demonstrated a dose-dependent increase in fibroblast proliferation and an enhanced ability of the fibroblast to thrive in a stressful environment.
	www.ellazen.com /m2peptide/technology.html (1163 words)

	Matrix Science - Help - Sequence Query
		The sequence query, in which one or more peptide molecular masses are combined with sequence, composition and fragment ion data, is potentially the most powerful search of all.
		They defined a sequence tag derived from an MS/MS spectrum as the mass of the precursor peptide, the mass of the first peak of the identified sequence ladder, a stretch of interpreted sequence, and the mass of the final peak of the ladder.
		The sequence tag qualifier consists of the observed mass of the first peak of an identified sequence ladder, a stretch of interpreted amino acid sequence, and the observed mass of the final peak of the ladder.
	www.matrixscience.com /help/sq_help.html (1548 words)

	a letterhead ccr memo (Site not responding. Last check: )
		The peptide fraction of the crude material consists of the ideal peptide, traces of deletion peptides and modified peptides created during side chain deprotection and cleavage from the starting resin.
		The coupling method and the carrier used for conjugation are dependent on the chemical structure of the peptide, the species inoculated, and the use for the antiserum.
		In a typical run, between 0 to 5% of the peptides fail to synthesize properly due to difficulties in coupling caused by the specific amino acid sequence of the peptide.
	web.mit.edu /biopolymers/www/peptide_synthesis.html (2894 words)

	Frequently Asked Questions
		Peptide sequence is crucial to creating an antibody that will specifically recognize native proteins with high affinity.
		In general, peptide sequences that are rich in hydrophobic amino acids can be difficult to dissolve in aqueous solutions, and may be unsuitable for use in biological systems.
		An inter- or intra- peptide disulphide bonds may be formed due to the presence of additional cysteine residue in the sequence, thus leading to insolubility and structural alteration of the peptide.
	www.abgent.com /doc/faqs (1536 words)

	Peptide Synthesis : linear peptide, linear sequence, custom service, amino acid, research (Site not responding. Last check: )
		The charges are specific for the sequence and varies depending on the purity level, length of the sequence, modification required, amount supplied etc.
		After the synthesis the peptide is subjected to Mass Spec analysis (the result of which is given to the customer).
		It may be for addition of a particular group (Phospho group) on the peptide, addition of carboxyl group on the C Term, developing a peptide for Antibody synthesis and other modification required.
	www.vardabiotech.com /PeptideSynthesis.php (480 words)

	Peptide Sequencing and Synthesis
		When peptides and proteins larger than 20 to 40 amino acid units are to be sequenced, they are first broken into smaller fragments either by chemical or enzymatic partial hydrolysis.
		Of course, angiotensin II (a peptide involved in blood pressure regulation) is small enough that a protein sequenator could give its sequence directly, but the example illustrates the way fragments may be overlapped to give a complete sequence for a larger protein.
		When we are thinking of a peptide's sequence it is convenient to think of it as a chain which is stretched out, peptides are more commonly coiled (alpha helix, Brown p 518) or folded (beta sheet, Brown p 519).
	chemistry2.csudh.edu /rpendarvis/AmAcSeqSyn.html (1592 words)

	MSCI Module 4
		The specific difference from the previous module is the use of peptide sequence data input to the search engine.
		There are 20 amino acid side chains, or R groups, therefore, amino acid sequence of a peptide can be interpreted from the fragments created in the mass spectrometer.
		The parent or "precursor" peptide that was fragmented is shown in the upper mass spectrum, and the fragments of that mass are shown in the lower spectrum.
	drnelson.utmem.edu /module6/module6.htm (741 words)

	New England Peptide Frequently Asked Questions (Site not responding. Last check: )
		When a peptide is “cut out” from a protein, charges on the ends of the fragment peptide will be different than the parent.
		Peptides in solution are less stable, so it is strongly recommended that you use sterile water or sterile filtration during reconstitution.
		This tier is appropriate when the peptide sequences are very similar, sequences are short (7-8 amino acids) or the research is in a very general or early stage.
	www.newenglandpeptide.com /web/html/faq.html (1474 words)

	NIAID: Research Technologies Branch: Peptide Synthesis
		Synthetic peptides are either procured from commercial sources or made in-house based on the criteria presented earlier (see Technology Section).
		In the absence of the naturally occurring Cysteine in the peptide of interest, an extra Cysteine may be added to the sequence at either N-term or C-term to serve as an attachment point.
		This HPLC purity of peptide reflects a ratio (in %) of area of the correct peak versus the sum of areas for all detected peaks at the given UV wavelength (typically 215nm or 220nm).
	www.niaid.nih.gov /dir/services/rtb/peptide/faqs.asp (1163 words)

	Custom Peptide Services
		These peptides are used for the study of platelet aggregation, release of serotonin from platelets, calcium mobilization, tyrosine phosphorylation, and protein kinase C activation.
		Cationic amphiphilic peptides can be synthesized with D-amino acids to reduce their lability to proteases, formulated with lipids to increase stability or formulated with an altered sequence to increase the diversity of the peptides.
		Neuromedin N is a neurotensin-like peptide and causes hypotension in rats.
	www.qcb.com /services/cps.htm (2220 words)

	Class Definition for Class 930 - PEPTIDE OR PROTEIN SEQUENCE
		In digests 550-772 and 780-822, sequences modified by removal or addition of amino acids, by substitution of amino acids by others, or by a combination of these modifications, are classified as the parent peptide when the combined number of modifications totals less than 50% of the parent fragment.
		Such a peptide can be one whose structure corresponds to at least half the amino acid residues of the named peptide, or one which is the product of side chain substitution, C or N terminal chain extension and insertion, or a replacement reaction, or a removal reaction.
		A series of peptide repeating units is intended to mean that an amino acid sequence of two or more amino acid residues is sequentially repeated two or more times in the peptide or protein in uninterrupted sucession.
	www.uspto.gov /go/classification/uspc930/defs930.htm (4959 words)

	Membrane Fusion Is Induced by a Distinct Peptide Sequence of the Sea Urchin Fertilization Protein Bindin -- Ulrich et ...
		Membrane Fusion Is Induced by a Distinct Peptide Sequence of the Sea Urchin Fertilization Protein Bindin -- Ulrich et al.
		Membrane Fusion Is Induced by a Distinct Peptide Sequence of the Sea Urchin Fertilization Protein Bindin
		The peptide was found to mimic the behavior of its parent protein
	www.jbc.org /cgi/content/abstract/273/27/16748 (424 words)

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