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Journal of the American Chemical Society Mar 2013Nuclear receptor binding to coactivator proteins is an obligate first step in the regulation of gene transcription. Nuclear receptors preferentially bind to an LXXLL...
Nuclear receptor binding to coactivator proteins is an obligate first step in the regulation of gene transcription. Nuclear receptors preferentially bind to an LXXLL peptide motif which is highly conserved throughout the 300 or so natural coactivator proteins. This knowledge has shaped current understanding of this fundamental protein-protein interaction, and continues to inspire the search for new drug therapies. However, sequence specificity beyond the LXXLL motif and the molecular functioning of flanking residues still requires urgent addressing. Here, ribosome display has been used to reassess the estrogen receptor for new and enlarged peptide recognition motifs, leading to the discovery of a potent and highly evolved PXLXXLLXXP binding consensus. Molecular modeling and X-ray crystallography studies have provided the molecular insights on the role of the flanking prolines in priming the length of the α-helix and enabling optimal interactions of the α-helix dipole and its surrounding amino acids with the surface charge clamp and the receptor activation function 2. These findings represent new structural parameters for modulating the nuclear receptor-coactivator interaction based on linear sequences of proteinogenic amino acids and for the design of chemically modified inhibitors.
Topics: Amino Acid Motifs; Amino Acid Sequence; Consensus Sequence; Crystallography, X-Ray; Gene Library; Humans; Models, Molecular; Molecular Sequence Data; Peptide Library; Peptides; Proline; Protein Binding; Protein Structure, Secondary; Receptors, Estrogen
PubMed: 23437920
DOI: 10.1021/ja311748r -
Plant Science : An International... Sep 2015Two novel homologous peptides named ToHyp1 and ToHyp2 that show no similarity to any known proteins were isolated from Taraxacum officinale Wigg. flowers by...
Two novel homologous peptides named ToHyp1 and ToHyp2 that show no similarity to any known proteins were isolated from Taraxacum officinale Wigg. flowers by multidimensional liquid chromatography. Amino acid and mass spectrometry analyses demonstrated that the peptides have unusual structure: they are cysteine-free, proline-hydroxyproline-rich and post-translationally glycosylated by pentoses, with 5 carbohydrates in ToHyp2 and 10 in ToHyp1. The ToHyp2 peptide with a monoisotopic molecular mass of 4350.3Da was completely sequenced by a combination of Edman degradation and de novo sequencing via top down multistage collision induced dissociation (CID) and higher energy dissociation (HCD) tandem mass spectrometry (MS(n)). ToHyp2 consists of 35 amino acids, contains eighteen proline residues, of which 8 prolines are hydroxylated. The peptide displays antifungal activity and inhibits growth of Gram-positive and Gram-negative bacteria. We further showed that carbohydrate moieties have no significant impact on the peptide structure, but are important for antifungal activity although not absolutely necessary. The deglycosylated ToHyp2 peptide was less active against the susceptible fungus Bipolaris sorokiniana than the native peptide. Unique structural features of the ToHyp2 peptide place it into a new family of plant defense peptides. The discovery of ToHyp peptides in T. officinale flowers expands the repertoire of molecules of plant origin with practical applications.
Topics: Amino Acid Sequence; Bacteria; Chromatography, High Pressure Liquid; Chromatography, Reverse-Phase; Circular Dichroism; Flowers; Glycopeptides; Hydroxyproline; Microbial Sensitivity Tests; Molecular Sequence Data; Molecular Weight; Proline; Sequence Analysis, Protein; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Taraxacum
PubMed: 26259198
DOI: 10.1016/j.plantsci.2015.07.002 -
Organic Letters Sep 2012A proline-based phosphine template enabling a rapid Staudinger ligation of azide-containing substrates under mild conditions is reported. This reaction has a...
A proline-based phosphine template enabling a rapid Staudinger ligation of azide-containing substrates under mild conditions is reported. This reaction has a second-order rate constant of 1.12 M(-1) s(-1). It is expected that the proline-based Staudinger ligation strategy will be a useful method for bioconjugation and proline based peptide coupling.
Topics: Azides; Chemistry, Organic; Combinatorial Chemistry Techniques; Molecular Structure; Peptides; Proline
PubMed: 22924811
DOI: 10.1021/ol3022484 -
Biochemistry May 2010Although proline residues are incompatible with an alpha-helix conformation, they fit well into the N-terminal end of alpha-helices. Proline can form either a...
Although proline residues are incompatible with an alpha-helix conformation, they fit well into the N-terminal end of alpha-helices. Proline can form either a C(gamma)-exo ring pucker or a C(gamma)-endo ring pucker. An electron-withdrawing substituent on the 4R position of proline favors an exo ring pucker while an endo ring pucker is preferred if the substituent is on the 4S position due to stereoelectronic effects. The villin headpiece subdomain (HP36) is a small helical protein composed of three alpha-helices and contains a proline residue (Pro62) at the N-terminus of its C-terminal alpha-helix. Pro62 has a C(gamma)-exo ring pucker and forms an aromatic-proline interaction, with Trp64 in the native structure. This work reports the use of 4-substituted proline derivatives, including (2S,4R)-4-hydroxyproline (Hyp), (2S,4R)-4-fluoroproline (Flp), (2S,4R)-4-methoxyproline (Mop), (2S,4S)-4-hydroxyproline (hyp), (2S,4S)-4-fluoroproline (flp), and (2S,4S)-4-methoxyproline (mop), to replace Pro62 and study how the pucker conformation affects the proline-aromatic interaction and the stability of HP36. CD and NMR measurements indicate that all of the HP36 variants incorporated with proline derivatives maintain a structure similar to that of the wild type. Thermal unfolding and urea-induced denaturation measurements have shown that all of the mutants with the exception of the one with the flp substitution are less stable than the wild type. Our results reveal that, upon the replacement of Pro62 to proline derivatives, not only do stereoelectronic effects influence the aromatic-proline interaction but the steric and hydrophobic effects induced by the substituents also play an important role in modulating the stability of HP36.
Topics: Amino Acid Sequence; Circular Dichroism; Hydroxyproline; Models, Molecular; Neurofilament Proteins; Peptide Fragments; Proline; Protein Conformation; Protein Folding; Thermodynamics
PubMed: 20405858
DOI: 10.1021/bi100323v -
Chemistry (Weinheim An Der Bergstrasse,... Jan 2014This Concept article summarizes recent progress in the field of hydrogen-bonding aminocatalysis using proline-derived systems. The aminocatalysts available in the...
This Concept article summarizes recent progress in the field of hydrogen-bonding aminocatalysis using proline-derived systems. The aminocatalysts available in the literature are categorized by the incorporated hydrogen-bonding scaffold and its mode of recognition. Both mono- and double-hydrogen-bonding motifs are discussed and examples of their application in asymmetric synthesis are given.
Topics: Catalysis; Hydrogen Bonding; Proline; Pyrrolidines; Stereoisomerism
PubMed: 24311406
DOI: 10.1002/chem.201303982 -
PloS One 2013Proline is an anomalous amino acid. Its nitrogen atom is covalently locked within a ring, thus it is the only proteinogenic amino acid with a constrained phi angle....
Proline is an anomalous amino acid. Its nitrogen atom is covalently locked within a ring, thus it is the only proteinogenic amino acid with a constrained phi angle. Sequences of three consecutive prolines can fold into polyproline helices, structures that join alpha helices and beta pleats as architectural motifs in protein configuration. Triproline helices are participants in protein-protein signaling interactions. Longer spans of repeat prolines also occur, containing as many as 27 consecutive proline residues. Little is known about the frequency, positioning, and functional significance of these proline sequences. Therefore we have undertaken a systematic bioinformatics study of proline residues in proteins. We analyzed the distribution and frequency of 687,434 proline residues among 18,666 human proteins, identifying single residues, dimers, trimers, and longer repeats. Proline accounts for 6.3% of the 10,882,808 protein amino acids. Of all proline residues, 4.4% are in trimers or longer spans. We detected patterns that influence function based on proline location, spacing, and concentration. We propose a classification based on proline-rich, polyproline-rich, and proline-poor status. Whereas singlet proline residues are often found in proteins that display recurring architectural patterns, trimers or longer proline sequences tend be associated with the absence of repetitive structural motifs. Spans of 6 or more are associated with DNA/RNA processing, actin, and developmental processes. We also suggest a role for proline in Kruppel-type zinc finger protein control of DNA expression, and in the nucleation and translocation of actin by the formin complex.
Topics: Actins; Amino Acid Sequence; Computational Biology; Humans; Kruppel-Like Transcription Factors; Microfilament Proteins; Models, Molecular; Molecular Sequence Data; Peptides; Proline; Protein Structure, Secondary; Protein Structure, Tertiary; Proteome
PubMed: 23372670
DOI: 10.1371/journal.pone.0053785 -
Biopolymers Mar 2015Installing an electrophilic amino-acid residue can engender a peptide or protein with chemoselective reactivity. Such a modification to collagen, which is the most...
Installing an electrophilic amino-acid residue can engender a peptide or protein with chemoselective reactivity. Such a modification to collagen, which is the most abundant protein in animals, could facilitate the development of new biomaterials. Collagen has an abundance of proline-like residues. Here, we report on the incorporation of an electrophilic proline congener, (2S)-4-ketoproline (Kep), into a collagen-mimetic peptide (CMP). An ab initio conformational analysis of Kep revealed its potential to be accommodated within a collagen triple helix. A synthetic CMP containing a Kep residue was indeed able to form a stable triple helix. Moreover, the condensation of its carbonyl group with aminooxy-biotin did not compromise the conformational stability of the triple helix. These data encourage the use of 4-ketoproline as an electrophilic congener of proline.
Topics: Collagen; Peptides; Proline; Protein Conformation
PubMed: 25656588
DOI: 10.1002/bip.22620 -
ELife Mar 2020The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic...
The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, -4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to ()-Δ-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.
Topics: Clostridioides difficile; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Hydroxyproline; Models, Molecular; Proline; Protein Conformation; Proteins
PubMed: 32180548
DOI: 10.7554/eLife.51420 -
The Protein Journal Feb 2018Three-dimensional (3D) domain swapping is a mechanism to form protein oligomers. It has been proposed that several factors, including proline residues in the hinge...
Three-dimensional (3D) domain swapping is a mechanism to form protein oligomers. It has been proposed that several factors, including proline residues in the hinge region, may affect the occurrence of 3D domain swapping. Although introducing prolines into the hinge region has been found to promote domain swapping for some proteins, the opposite effect has also been observed in several studies. So far, how proline affects 3D domain swapping remains elusive. In this work, based on a large set of 3D domain-swapped structures, we performed a systematic analysis to explore the correlation between the presence of proline in the hinge region and the occurrence of 3D domain swapping. We further analyzed the conformations of proline and pre-proline residues to investigate the roles of proline in 3D domain swapping. We found that more than 40% of the domain-swapped structures contained proline residues in the hinge region. Unexpectedly, conformational transitions of proline residues were rarely observed upon domain swapping. Our analyses showed that hinge regions containing proline residues preferred more extended conformations, which may be beneficial for the occurrence of domain swapping by facilitating opening of the exchanged segments.
Topics: Molecular Dynamics Simulation; Proline; Protein Domains; Proteins
PubMed: 29119487
DOI: 10.1007/s10930-017-9747-5 -
Biophysical Journal May 2016Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched...
Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.
Topics: Hydrogen Bonding; Models, Molecular; Nitrogen; Proline; Protein Structure, Secondary; Proteins; Quantum Theory
PubMed: 27166805
DOI: 10.1016/j.bpj.2016.03.034