Proline | EPFL Graph Search

Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group -NH2 but is rather a secondary amine. The secondary amine nitrogen is in the protonated form (NH2+) under biological conditions, while the carboxyl group is in the deprotonated −COO− form. The "side chain" from the α carbon connects to the nitrogen forming a pyrrolidine loop, classifying it as a aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it from the non-essential amino acid L-glutamate. It is encoded by all the codons starting with CC (CCU, CCC, CCA, and CCG). Proline is the only proteinogenic secondary amino acid which is a secondary amine, as the nitrogen atom is attached both to the α-carbon and to a chain of three carbons that together form a five-membered ring. History and etymology Proline was first isolated in 1900 by Richard Willstätter who obtained the amino a

N-Terminal Selective C-H Azidation of Proline-Containing Peptides: a Platform for Late-Stage Diversification

Emmanuelle Madeline Dominique Allouche, Raphaël Michel Henri Simonet-Davin, Jérôme Waser

A methodology for the C-H azidation of N-terminal proline-containing peptides was developed employing only commercially available reagents. Peptides bearing a broad range of functionalities and containing up to 6 amino acids were selectively azidated at the carbamate-protected N-terminal residue in presence of the numerous other functional groups present on the molecules. Post-functionalizations of the obtained aminal compounds were achieved: cycloaddition reactions or C-C bond formations via a sequence of imine formation/nucleophilic addition were performed, offering an easy access to diversified peptides.

WILEY-V C H VERLAG GMBH2022

Gas-phase probes of kinetically trapped peptides

Liudmila Voronina

Gas-phase techniques are promising for studying intrinsically disordered peptides and proteins, as they can be implemented in a conformer-selective way. One of the issues that prevent them from finding a broader use is the question of to which extent the structure of a biological molecule is preserved when transferring it from solution to the gas phase via electrospray. We focus on cis/trans isomerization of prolyl-peptide bonds, which is known to have high barrier on the potential energy surface. Upon electrospraying, solution-like structures can find themselves kinetically trapped behind these barriers, as we explicitly show for the case of bradykinin 1-5 fragment. Using nuclear magnetic resonance, we determine that it adopts mostly all-trans conformation in solution, while three distinct conformational families are observed in the ion mobility experiment in the gas phase. Cryogenic ion spectroscopy combined with first-principles simulations allows us to identify the major conformers and show that the solution structural preferences of the prolyl-peptide bonds are preserved in the kinetically trapped conformational family, while the lowest-energy gas-phase structures have one of the prolines in the cis conformation. We show how collisional cross-sections and infrared spectra are used to guide and verify the calculations, giving rise to a new type of symbiosis between theory and experiment. This is especially valuable for the kinetically trapped structures, as in this case the energy criterion cannot be decisive. As a next step, we characterize the full nonapeptide bradykinin in the +3 charge state. Using field-asymmetric ion mobility spectrometry combined with cryogenic ion spectroscopy, we demonstrate the presence of three major conformational families in the gas phase, one of which is kinetically trapped. This result is in agreement with the drift-tube ion mobility data published previously, and we propose a correspondence between the conformational families separated by field-asymmetric and drift-tube ion mobility spectrometry. We obtain conformer-specific infrared spectra of the major conformers and assign the vibrational bands using 15N isotopic labeling. Substituting carbon atoms in the phenyl ring with their 13C isotope allows us to separate two types of structures according to their fragmentation pattern upon electronic excitation. This method can serve as a complementary way to introduce conformer-selectivity when studying large molecules. Finally, we assess the result of substituting one or two prolines in the bradykinin sequence with alanine. This method has been used previously to assign the peaks in the drift-time distributions to certain conformations of the prolyl-peptide bonds. We show that the mutants do reproduce a part of the conformers of the original peptide, but also form additional structures due to the higher flexibility of the alanine backbone compared to proline. We conclude that the proline-to-non-proline substitutions are helpful to assign the structures, but have to be used in conjunction with spectroscopic techniques, which allow detailed comparison of the structures of the mutant and the native peptide. In general, this work is one of the first steps towards a database of atomic-resolution peptide structures in the gas phase and a better understanding of the capabilities and limits of spectroscopy and ion mobility in the gas phase applied to intrinsically disordered peptides.

EPFL2016

Synthesis and structure-activity studies of well-defined nickel complexes as catalysts for cross coupling of alkyl electrophiles

Pablo Marcelo Perez Garcia

This dissertation is devoted to the development of well-defined nickel complexes as catalysts for cross coupling processes of alkyl electrophiles. In chapter one, we summarize recent cross coupling methodologies of alkyl electrophiles using nickel based catalysts. The description of each study includes the coupling conditions, the substrate scope and the mechanistic considerations. In chapter two, we report the development of high diastereoselective alkyl-alkyl Kumada coupling method for 1,3- and 1,4-substituted cyclohexyl halides and tetrahydropyrans using an amido bis(amine) nickel complex "Nickamine" as catalyst. The stereochemical properties of the starting materials and of the coupling products were determined by NMR techniques. The mechanistic investigations of the coupling provided evidence of a reversible activation of the alkyl halide. In chapter three, we present the synthesis of new bidentate amido â amine ligands derived from 2,5-dimethylpyrrolidine or Î±-methylbenzylamine. The ligands were used to synthesize well-defined bidentate nickel complexes by transmetallation from the corresponding lithium complexes. A complex having an Î±-methylbenzylamine derived ligand and 2,4-lutidine as co-ligand was an effective catalyst for the coupling of non-activated secondary iodides with alkyl Grignard reagents. An enantiomerically pure version of this complex was synthesized and no racemization was observed during the synthesis. The chiral complex showed no asymmetric induction capacity as a cross coupling catalyst. In chapter four, the synthesis of new amido bis(amine) pincer ligands derived from Î±-methylbenzylamine or pyrrolidine are described. The metallation of a NNN ligand derived from Î±-methylbenzylamine was not possible by transmetallation from the corresponding lithium complex or by oxidative addition from the corresponding chloroamine. A well-defined pincer nickel complex was synthesized by Li â Ni transmetallation using a NNN ligand having dimethyl amino and pyrolidine donors. Crystal structure analysis shows that the pyrrolidine donor is slightly less hindered. This complex is an effective catalyst for alkyl-alkyl and alkyl-aryl Kumada coupling of non-activated primary and secondary alkyl halides. The coupling process shows good functional group tolerance. This is the first time that a well-defined nickel pincer complex shows high catalytic activity for Kumada coupling reactions of sterically hindered alkyl substrates. In chapter 5, a well-defined nickel pincer complex bearing an alkyl amine donor is synthesized. The complex is able to catalyzed direct coupling of non-activated primary halides with terminal alkynes at room temperature. The catalysis has a good substrate scope and high functional group tolerance. Kinetic data suggest that the new pincer ligand is hemilabile, and the dissociation of the alkyl amine donor is the turnover-determining step of the catalysis. An intermediate Ni-alkynyl species has been isolated and structurally characterized. The reactivity of this species gives insight into the nature of the active species for the activation of alkyl halide.