Difficult Sequences Research Articles

Investigation of crudes of synthesis of [Leu31, Pro34]‐neuropeptide Y by capillary zone electrophoresis/mass spectrometry

[Leu31, Pro34]-Neuropeptide Y is a thirty-six amino-acid peptide which has a measured relative molecular mass of 4222. Solid-phase synthesis of this peptide resulted in complex crudes of synthesis which were examined by capillary zone electrophoresis (CZE)/electrospray ionization mass spectrometry (ES-MS). The separation efficiency of CZE combined with the mass specificity of mass spectrometry yielded rapid and reliable information on the target peptide and a number of associated side products, which were mainly acetylated peptide sequences having relative molecular masses in the range 2240-4101. Such incomplete or, as they are commonly called, difficult sequences are provoked by problems of swelling and aggregation of the growing peptide chains in the course of synthesis. The use of mass spectrometry is indispensable for obtaining reliable information on the inevitable side products. Initial tuning of the ion source and optimization of the coupling between the CZE system and the mass spectrometer were achieved by performing a number of measurements pertaining to artificially made mixtures of commercial neuropeptides.

Successful syntheses of β amyloid-(25–35)-peptide: a difficult sequence by N-(9-fluorenylmethoxycarbonyl) chemistry

Successful syntheses of β amyloid-(25–35)-peptide: a difficult sequence by <i>N</i>-(9-fluorenylmethoxycarbonyl) chemistry

Some ‘difficult sequences’ made easy

Case studies of the solid-phase synthesis of some 'difficult sequences' using continuous-flow Fmoc-polyamide techniques are presented. Solvent change and peptide side chain and backbone modification procedures recently found to reduce association effects are applied, and the results compared to syntheses under standard conditions.

The concept of superactive esters

According to the concept presented, esters forming an amide (peptide) bond by the mechanism SN#DN or SN#*DN involving fast decay of the tetrahedral intermediate may behave as 'superactive acylating reagents'. These should render coupling involving less reactive substrates, i.e. sterically hindered or 'difficult coupling sequences', much faster and more uniform than classic active esters. In extremely cases this advantage could be significant, and the calculated increase in time required for 99.9% coupling substrates 6 pKa units less reactive than the standard ones reaches 2,512,000 tau 1/2 units for classic active esters, but only 631 tau 1/2 units for reaction involving 'superactive esters'. The postulated change of mechanism is expected for esters bearing a leaving group which is able to undergo an additional, synchronous, energetically favored process accompanying its departure, as has been observed in the case of triazine esters. Some advantages of triazine superactive esters in the condensation of sterically hindered substrates are demonstrated.

固相ペプチド合成における“Ｄｉｆｆｉｃｕｌｔ Ｓｅｑｕｅｎｃｅ”とペプチド鎖の溶媒和

Recently, “difficult sequences” have been often found as a key word in solid-phase peptide synthesis. “Difficult sequences” which cause the most serious potential problem during stepwise solid-phase peptide synthesis result from the intermolecular aggregation, namely, the formation of β-sheet structure by intermolecular hydrogen bonds between protected peptide chains. This β-sheet structure hinders the coupling reaction, the deprotection of the N-protecting group, and even the liberation of amino groups at each step for peptide chain elongation and results in the incomplete peptides with the properties similar to the target peptide. In liquid phase peptide synthesis, the “difficult sequence” is closely related to the solubility of protected peptides. The decreasing solubility of protected peptides in organic solvents along with increasing their chain length is due to the intermolecular β-sheet structure formation. The conversion of “difficult sequence” to easy sequence by disrupting the β-sheet structure can be achieved wherether the protected peptides are completely solvated by organic solvents or they are subject to peptide segment separation.

Aggregation of resin-bound peptides during solid-phase peptide synthesis. Prediction of difficult sequences.

Nonrandom incomplete aminoacylation of a pendent peptide chain on an insoluble polymeric support during solid-phase peptide synthesis is sequence-dependent and is caused by aggregation of peptide chains, manifested by a decreased swelling capacity. The volume of the swollen peptidyl-resin after each coupling during the syntheses of 87 sequence unrelated peptides was measured, and for each amino acid an aggregation parameter, <Pa>, was derived that reflects the propensity of the swollen volume of peptidyl-resin to decrease during peptide synthesis. These aggregation parameters were used to predict potentially difficult sequences.

ChemInform Abstract: A Reversible Protecting Group for the Amide Bond in Peptides. Use in the Synthesis of ′Difficult Sequences′.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Reinforced variation and selection

Long-Evans rats were reinforced for generating variable sequences of four left (L) and right (R) leverpress responses. If the current sequence, for example, LLRR, differed from each of the preceding five sequences, then a food pellet was provided. Otherwise, there was a brief time-out. After the rats were generating a variety of sequences, one sequence was concurrently reinforced whenever it occurred, that is, an “always-reinforced” contingency was superimposed. The frequency of that sequence increased significantly from the variable baseline (Experiment 1). The “difficulty” of the always-reinforced sequence influenced the extent to which its frequency increased—“easy” sequences increased greatly, but “difficult” ones increased not at all (Experiment 2, and a replication with pigeons in Experiment 3). However, when reinforcement for baseline variability was systematically decreased while a difficult sequence was always reinforced, that sequence slowly emerged and attained relatively high levels (Experiments 4 and 5). Thus, a technique for training even highly improbable, or difficult-to-learn, behaviors is provided by concurrent reinforcement of variation and selection.

Chemical synthesis of a designed β‐protein through the flow‐polyamide method

A designed, 61-residue long, metal-binding protein was synthesized through the flow-polyamide method. This protein, named Minibody (Mini-antibody), contains a beta-sheet scaffold and two regions corresponding to immunoglobulin hypervariable loops (H1 and H2), onto which a metal binding site was engineered. The protein is extremely hydrophobic, with a 70% beta structure. Accordingly, it was anticipated, and actually found, to be a "difficult sequence" for all its length. Comparison of the standard, "minimum redundancy" protocol (single coupling, low excess of activated species) with a different protocol (double and triple coupling plus capping) showed that the two produced approximately the same amount of full-length product (3.7% after extensive purification). Capping was effective in blocking the unreacted amino groups, converting most failure sequences into truncated ones, a possible aid to implement affinity-type chromatographic protocols. Purification was complicated by the very low solubility of the molecule, coupled to a high tendency to aggregate even in concentrated chaotropic media (8 M urea). Nevertheless, a multi-dimensional purification scheme produced a highly homogeneous product, with the expected Ion Spray mass spectrum. The Minibody produced by recDNA methods showed identical chromatographic, spectroscopic and biochemical properties to those of the synthetic product.

A reversible protecting group for the amide bond in peptides. Use in the synthesis of ‘difficult sequences’

N,O-Bis-Fmoc (fluoren-9-ylmethoxycarbonyl) derivatives of Nα-(2-hydroxy-4-methoxybenzyl)amino acids 5 are useful intermediates for the preparation of peptides with reversibly protected (tertiary) peptide bonds; their value in inhibiting interchain association during solid phase peptide synthesis is demonstrated.

Facilitating science learning by embedded explication

Several features have been identified that enhance learning from text. One of these features is explication. To explicate means to state directly, instead of requiring the reader to infer, organize, or construct relationships. This study investigated the effects of three types of embedded explication on science learning: etymological, causal, and analogical in terms of the Mayer and Greeno information processing model. Subjects read parallel texts containing explications presented in a difficult or easy sequence. Overall, groups receiving causal and analogical explication scored significantly higher than the control groups receiving filler material. This supports the use of causal explication to support organization and the use of analogy to link prior and new knowledge together in long-term memory. This study has implications for the design of text-based science instruction based both on the use of embedded explication and the sequencing of information.

Amino acid structure and "difficult sequences" in solid phase peptide synthesis.

Deprotection peak profiles have been determined as a measure of internal aggregation during Fmoc-polyamide continuous flow solid phase synthesis. The results have been correlated with amino-acid structure and discussed in terms of minimising aggregation during synthesis.

Synthesis of difficult peptide sequences: a comparison of FMOC-and BOC-technique

In comparison with Fmoc-technique the BOC-technique with in situ neutralization proved advantageous for the synthesis of difficult peptides forming β-sheet structures.

Synthesis of difficult peptide sequences: A comparison of Fmoc-and BOC-technique

In comparison with Fmoc-technique the BOC-technique with in situ neutralization proved advantageous for the synthesis of difficult peptides forming β-sheet structures.

Pega: a flow stable polyethylene glycol dimethyl acrylamide copolymer for solid phase synthesis.

A copolymer of bisacrylamido polyethylene glycol, monoacrylamido polyethylene glycol and N,N-dimethyl acrylamide was synthesized by radical polymerization and characterized for peptide synthesis by preparation of the difficult test sequence 65–74 from the acyl carrier protein. Reaction times were recorded and compared with synthesis on kieselguhr supported polydimethyl acrylamide gel.

A new detector for fully automatic peptide synthesis

A new method of monitoring the rate of reactions in solid phase peptide synthesis is described. A conductivity detector in the reaction cell enables the deprotection, washing, and subsequent coupling stages to be examined in detail. The half lives of the reactions can be calculated and hence the optimum reaction times predicted. The aggregation of peptide chains and subsequent collapse of the resin is observed. Difficult sequences are sensed and appropriate action taken completely automatically.

A new detector for fully automatic peptide synthesis

A new method of monitoring the rate of reactions in solid-phase peptide synthesis is described. A conductivity detector in the reaction cell (patent applied for) enables the deprotection, washing and subsequent coupling stages to be examined in detail. The half-lives of the reactions can be calculated and hence the optimum reaction times can be predicted. Difficult sequences are sensed and appropriate action taken completely automatically.

Prediction of difficult sequences in solid-phase peptide synthesis

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrediction of difficult sequences in solid-phase peptide synthesisR. C. de L. Milton, Saskia C. F. Milton, and Paul A. AdamsCite this: J. Am. Chem. Soc. 1990, 112, 16, 6039–6046Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://doi.org/10.1021/ja00172a020RIGHTS & PERMISSIONSArticle Views1811Altmetric-Citations99LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts

Supplementary motor area activation while tapping bimanually different rhythms in musicians

In 15 musicians, cortical DC-potentials were recorded from the scalp before and during the execution of bimanual motor sequences. Subjects (Ss) either tapped with their two index fingers in synchrony (quavers against quavers; "2 against 2") or they tapped quavers against triplets ("2 against 3"). Either the right or the left finger started tapping the quavers (onset time t1), after about 4 s the other finger joined in (t2) either with quavers as well (easy rhythm) or with triplets (difficult rhythm). Ss were free to start the sequences, i.e. to determine the onset times t1 and t2. Shifts of cortical DC potentials were averaged twice; (1) time-locked to t1 and (2) time-locked to t2. When moving in synchrony (easy rhythm) DC-potential shifts and maps of radial current densities across the scalp indicated activations of the two primary motor cortices (MI). When bimanually tapping different rhythms, there was not only an activation of MI cortices, but in addition a very large activation of the mesial, central cortex was observed. It is suggested that this cortical area which mainly contains the supplementary motor area (SMA) has the function of controlling the initiations of movements in the difficult sequence which have to fit into a very precise timing plan. Interestingly, activation of the mesial, central cortex preceded the actual performance of the difficult rhythm by about 4 s. This finding indicates that the preparatory set differs between the two tasks.

Adaptive Program vs. Learner Control Strategy on Computer Aided Learning of Gravimetric Stoichiometry Problems

AbstractThe present study was designed to determine the relative effectiveness of two control strategies: learner control (LC) vs. adaptive program control (PC), in computer aided learning (CAL). The LC strategy allowed learners to decide on the learning sequence of the four tasks and the number of practice examples to work on their own. The PC strategy allowed them to work on an easy to difficult task sequence with the number of examples prescribed. A set of four CAL tasks developed and used involved four conceptual rules of converting (a) mole to mole, (b) mole to mass, (c) mass to mole, and (d) mass to mass units in gravimetric stoichiometry. Thirteen LC and 13 PC grade 11 students worked on the four tasks. LC students attempted significantly more practice examples for longer time than PC students, but less successfully. The less than optimal learning performance seems to be most likely due to the undisciplined sequencing of the tasks. The general and specific self-rating intended as indexing learners’...