Journal articles: 'Proline residues'

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McDONNELL, MAEVE, RICHARD FITZGERALD, IDE NI FHAOLÁIN, P. VINCENT JENNINGS, and GERARD O'CUINN. "Purification and characterization of aminopeptidase P from Lactococcus lactis subsp. cremoris." Journal of Dairy Research 64, no. 3 (August 1997): 399–407. http://dx.doi.org/10.1017/s0022029997002318.

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Aminopeptidase P was purified 65·3-fold from the cytoplasm of Lactococcus lactis subsp. cremoris AM2 with a 5·8% yield. The purified enzyme was found to consist of one polypeptide chain with a relative molecular mass of 41600. Metal chelating agents were found to be inhibitory and Mn2+ and Co2+ stimulated activity 7-fold and 6-fold respectively. The purified enzyme removed the N-terminal amino acid from peptides only where proline (and in one case alanine) was present in the penultimate position. No hydrolysis was observed either with dipeptides even when proline was present in the C-terminal position or when either N-terminal proline or pyroglutamate was present preceding a proline residue in the penultimate position of longer peptides. On the basis of this substrate specificity either aminopeptidase P or post-proline dipeptidyl aminopeptidase are necessary along with a broad specificity aminopeptidase to effect complete hydrolysis of casein-derived peptides containing a single internally placed proline residue. However, both aminopeptidase P and post-proline dipeptidyl aminopeptidase would be required together with a broad specificity aminopeptidase in order to completely hydrolyse casein-derived peptides that contain two internally placed consecutive proline residues. As bitter casein-derived peptides are likely to contain either single prolines or pairs of prolines, aminopeptidase P appears to be an important enzyme for debittering.

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Nishimura, Akira, Yurie Takasaki, Shota Isogai, Yoichi Toyokawa, Ryoya Tanahashi, and Hiroshi Takagi. "Role of Gln79 in Feedback Inhibition of the Yeast γ-Glutamyl Kinase by Proline." Microorganisms 9, no. 9 (September 7, 2021): 1902. http://dx.doi.org/10.3390/microorganisms9091902.

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Awamori, the traditional distilled alcoholic beverage of Okinawa, Japan, is brewed with the yeast Saccharomyces cerevisiae. During the distillation process after the fermentation, enormous quantities of distillation residues containing yeast cells must be disposed of, and this has recently been recognized as a major problem both environmentally and economically. Proline, a multifunctional amino acid, has the highest water retention capacity among amino acids. Therefore, distillation residues with large amounts of proline could be useful in cosmetics. Here, we isolated a yeast mutant with high levels of intracellular proline and found a missense mutation (Gln79His) on the PRO1 gene encoding the γ-glutamyl kinase Pro1, a limiting enzyme in proline biosynthesis. The amino acid change of Gln79 to His in Pro1 resulted in desensitization to the proline-mediated feedback inhibition of GK activity, leading to the accumulation of proline in cells. Biochemical and in silico analyses showed that the amino acid residue at position 79 is involved in the stabilization of the proline binding pocket in Pro1 via a hydrogen-bonding network, which plays an important role in feedback inhibition. Our current study, therefore, proposed a possible mechanism underlying the feedback inhibition of γ-glutamyl kinase activity. This mechanism can be applied to construct proline-accumulating yeast strains to effectively utilize distillation residues.

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Belova, Elena, Oksana Maksimenko, Pavel Georgiev, and Artem Bonchuk. "The Essential Role of Prolines and Their Conformation in Allosteric Regulation of Kaiso Zinc Finger DNA-Binding Activity by the Adjacent C-Terminal Loop." International Journal of Molecular Sciences 23, no. 24 (December 7, 2022): 15494. http://dx.doi.org/10.3390/ijms232415494.

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Kaiso is a methyl-DNA-binding protein containing three C2H2 zinc fingers with a C-terminal extension that participates in DNA binding. The linker between the last zinc finger and the DNA-binding portion of the extension contains two prolines that are highly conserved in vertebrates and in cognate ZBTB4 and ZBTB38 proteins. Prolines provide chain rigidity and can exist in cis and trans conformations that can be switched by proline isomerases, affecting protein function. We found that substitution of the conserved proline P588, but not of P577, to alanine, negatively affected KaisoDNA-binding according to molecular dynamics simulation and in vitro DNA-binding assays. Molecular dynamics simulations of the Kaiso DNA-binding domain with P588 either substituted to alanine or switched to the cis-conformation revealed similar alterations in the H-bonding network and uncovered allosteric effects leading to structural rearrangements in the entire domain that resulted in the weakening of DNA-binding affinity. The substitution of proline with a large hydrophobic residue led to the same negative effects despite its ability to partially rescue the intrinsic DNA-binding activity of the C-terminal loop. Thus, the presence of the C-terminal extension and cis-conformation of proline residues are essential for efficient Kaiso–DNA binding, which likely involves intramolecular tension squeezing the DNA chain.

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Deber, Charles M., Barbara J. Sorrell, and Guang-Yi Xu. "Conformation of proline residues in bacteriorhodopsin." Biochemical and Biophysical Research Communications 172, no. 2 (October 1990): 862–69. http://dx.doi.org/10.1016/0006-291x(90)90755-c.

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SHELDEN, Megan C., Patrick LOUGHLIN, M. Louise TIERNEY, and Susan M. HOWITT. "Proline residues in two tightly coupled helices of the sulphate transporter, SHST1, are important for sulphate transport." Biochemical Journal 356, no. 2 (May 24, 2001): 589–94. http://dx.doi.org/10.1042/bj3560589.

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The sulphate transporter SHST1, from Stylosanthes hamata, features three tightly coupled transmembrane helices which include proline residues that are conserved in most related transporters. We used site-directed mutagenesis and expression of the mutant transporters in yeast to test whether these proline residues are important for function. Four proline residues were replaced by both alanine and leucine. Only one of these proline residues, Pro-144, was essential for sulphate transport. However, mutation of either Pro-133 or Pro-160 resulted in a severe decrease in sulphate transport activity; this was due more to a decrease in transport activity than to a decrease in the amount of mutant SHST1 in the plasma membrane. These results suggest that all three proline residues are important for transport, and that the conformation of the three tightly coupled helices may play a critical role in sulphate transport. We also show that SHST1 undergoes a post-translational modification that is required for trafficking to the plasma membrane.

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Nakajima, Yoshitaka, Kiyoshi Ito, Makoto Sakata, Yue Xu, Kanako Nakashima, Futoshi Matsubara, Susumi Hatakeyama, and Tadashi Yoshimoto. "Unusual Extra Space at the Active Site and High Activity for Acetylated Hydroxyproline of Prolyl Aminopeptidase from Serratia marcescens." Journal of Bacteriology 188, no. 4 (February 15, 2006): 1599–606. http://dx.doi.org/10.1128/jb.188.4.1599-1606.2006.

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ABSTRACT The prolyl aminopeptidase complexes of Ala-TBODA [2-alanyl-5-tert-butyl-(1, 3, 4)-oxadiazole] and Sar-TBODA [2-sarcosyl-5-tert-butyl-(1, 3, 4)-oxadiazole] were analyzed by X-ray crystallography at 2.4 Å resolution. Frames of alanine and sarcosine residues were well superimposed on each other in the pyrrolidine ring of proline residue, suggesting that Ala and Sar are recognized as parts of this ring of proline residue by the presence of a hydrophobic proline pocket at the active site. Interestingly, there was an unusual extra space at the bottom of the hydrophobic pocket where proline residue is fixed in the prolyl aminopeptidase. Moreover, 4-acetyloxyproline-βNA (4-acetyloxyproline β-naphthylamide) was a better substrate than Pro-βNA. Computer docking simulation well supports the idea that the 4-acetyloxyl group of the substrate fitted into that space. Alanine scanning mutagenesis of Phe139, Tyr149, Tyr150, Phe236, and Cys271, consisting of the hydrophobic pocket, revealed that all of these five residues are involved significantly in the formation of the hydrophobic proline pocket for the substrate. Tyr149 and Cys271 may be important for the extra space and may orient the acetyl derivative of hydroxyproline to a preferable position for hydrolysis. These findings imply that the efficient degradation of collagen fragment may be achieved through an acetylation process by the bacteria.

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Homareda, Haruo, Kiyoshi Kawakami, Kei Nagano, and Hideo Matsui. "Stabilization in microsomal membranes of the fifth transmembrane segment of the Na+,K+-ATPase α subunit with proline to leucine mutation." Biochemistry and Cell Biology 71, no. 7-8 (July 1, 1993): 410–15. http://dx.doi.org/10.1139/o93-060.

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We have reported that the fifth transmembrane segment of the Na+,K+-ATPase α subunit could not be inserted into microsomal membranes when it was synthesized from the truncated α1 cDNA. In this study, three proline residues in the segment were changed into leucine residues by site-directed mutagenesis. Replacement of all three proline residues by leucine residues allowed the insertion of this segment and its translocation. This result confirms our previous finding and demonstrates that three proline residues in the fifth transmembrane segment prevent insertion of the segment into the membrane.Key words: Na+,K+-ATPase, transmembrane segment, membrane insertion, site-directed mutagenesis.

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Delos, S. E., J. M. Gilbert, and J. M. White. "The Central Proline of an Internal Viral Fusion Peptide Serves Two Important Roles." Journal of Virology 74, no. 4 (February 15, 2000): 1686–93. http://dx.doi.org/10.1128/jvi.74.4.1686-1693.2000.

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ABSTRACT The fusion peptide of the avian sarcoma/leukosis virus (ASLV) envelope protein (Env) is internal, near the N terminus of its transmembrane (TM) subunit. As for most internal viral fusion peptides, there is a proline near the center of this sequence. Robson-Garnier structure predictions of the ASLV fusion peptide and immediate surrounding sequences indicate a region of order (β-sheet), a tight reverse turn containing the proline, and a second region of order (α-helix). Similar motifs (order, turn or loop, order) are predicted for other internal fusion peptides. In this study, we made and analyzed 12 Env proteins with substitutions for the central proline of the fusion peptide. Env proteins were expressed in 293T cells and in murine leukemia virus pseudotyped virions. We found the following. (i) All mutant Envs form trimers, but when the bulky hydrophobic residues phenylalanine or leucine are substituted for proline, trimerization is weakened. (ii) Surprisingly, the proline is required for maximal processing of the Env precursor into its surface and TM subunits; the amount of processing correlates linearly with the propensity of the substituted residue to be found in a reverse turn. (iii) Nonetheless, proteolytically processed forms of all Envs are preferentially incorporated into pseudotyped virions. (iv) All Envs bind receptor with affinity greater than or equal to wild-type affinity. (v) Residues that support high infectivity cluster with proline at intermediate hydrophobicity. Infectivity is not supported by mutant Envs in which charged residues are substituted for proline, nor is it supported by the trimerization-defective phenylalanine and leucine mutants. Our findings suggest that the central proline in the ASLV fusion peptide is important for the formation of the native (metastable) Env structure as well as for membrane interactions that lead to fusion.

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Doerfel, Lili K., Ingo Wohlgemuth, Christina Kothe, Frank Peske, Henning Urlaub, and Marina V. Rodnina. "EF-P Is Essential for Rapid Synthesis of Proteins Containing Consecutive Proline Residues." Science 339, no. 6115 (December 13, 2012): 85–88. http://dx.doi.org/10.1126/science.1229017.

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Elongation factor P (EF-P) is a translation factor of unknown function that has been implicated in a great variety of cellular processes. Here, we show that EF-P prevents ribosome from stalling during synthesis of proteins containing consecutive prolines, such as PPG, PPP, or longer proline strings, in natural and engineered model proteins. EF-P promotes peptide-bond formation and stabilizes the peptidyl–transfer RNA in the catalytic center of the ribosome. EF-P is posttranslationally modified by a hydroxylated β-lysine attached to a lysine residue. The modification enhances the catalytic proficiency of the factor mainly by increasing its affinity to the ribosome. We propose that EF-P and its eukaryotic homolog, eIF5A, are essential for the synthesis of a subset of proteins containing proline stretches in all cells.

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Heidenreich, Steffi, Pamela Weber, Heike Stephanowitz, Konstantin M. Petricek, Till Schütte, Moritz Oster, Antti M. Salo, et al. "The glucose-sensing transcription factor ChREBP is targeted by proline hydroxylation." Journal of Biological Chemistry 295, no. 50 (October 6, 2020): 17158–68. http://dx.doi.org/10.1074/jbc.ra120.014402.

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Cellular energy demands are met by uptake and metabolism of nutrients like glucose. The principal transcriptional regulator for adapting glycolytic flux and downstream pathways like de novo lipogenesis to glucose availability in many cell types is carbohydrate response element–binding protein (ChREBP). ChREBP is activated by glucose metabolites and post-translational modifications, inducing nuclear accumulation and regulation of target genes. Here we report that ChREBP is modified by proline hydroxylation at several residues. Proline hydroxylation targets both ectopically expressed ChREBP in cells and endogenous ChREBP in mouse liver. Functionally, we found that specific hydroxylated prolines were dispensable for protein stability but required for the adequate activation of ChREBP upon exposure to high glucose. Accordingly, ChREBP target gene expression was rescued by re-expressing WT but not ChREBP that lacks hydroxylated prolines in ChREBP-deleted hepatocytes. Thus, proline hydroxylation of ChREBP is a novel post-translational modification that may allow for therapeutic interference in metabolic diseases.

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Harris, Diondra C., Yenni A. Garcia, Cheryl Storer Samaniego, Veronica W. Rowlett, Nina R. Ortiz, Ashley N. Payan, Tatsuya Maehigashi, and Marc B. Cox. "Functional Comparison of Human and Zebra Fish FKBP52 Confirms the Importance of the Proline-Rich Loop for Regulation of Steroid Hormone Receptor Activity." International Journal of Molecular Sciences 20, no. 21 (October 28, 2019): 5346. http://dx.doi.org/10.3390/ijms20215346.

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Previous studies demonstrated that the 52-kDa FK506-binding protein (FKBP52) proline-rich loop is functionally relevant in the regulation of steroid hormone receptor activity. While zebra fish (Danio rerio; Dr) FKBP52 contains all of the analogous domains and residues previously identified as critical for FKBP52 potentiation of receptor activity, it fails to potentiate activity. Thus, we used a cross-species comparative approach to assess the residues that are functionally critical for FKBP52 function. Random selection of gain-of-function DrFKBP52 mutants in Saccharomyces cerevisiae identified two critical residues, alanine 111 (A111) and threonine 157 (T157), for activation of receptor potentiation by DrFKBP52. In silico homology modeling suggests that alanine to valine substitution at position 111 in DrFKBP52 induces an open conformation of the proline-rich loop surface similar to that observed on human FKBP52, which may allow for sufficient surface area and increased hydrophobicity for interactions within the receptor–chaperone complex. A second mutation in the FKBP12-like domain 2 (FK2), threonine 157 to arginine (T157R), also enhanced potentiation, and the DrFKBP52-A111V/T157R double mutant potentiated receptor activity similar to human FKBP52. Collectively, these results confirm the functional importance of the FKBP52 proline-rich loop, suggest that an open conformation on the proline-rich loop surface is a predictor of activity, and highlight the importance of an additional residue within the FK2 domain.

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Morimoto, Akira, Kazuhiro Irie, Kazuma Murakami, Yuichi Masuda, Hajime Ohigashi, Masaya Nagao, Hiroyuki Fukuda, Takahiko Shimizu, and Takuji Shirasawa. "Analysis of the Secondary Structure of β-Amyloid (Aβ42) Fibrils by Systematic Proline Replacement." Journal of Biological Chemistry 279, no. 50 (September 30, 2004): 52781–88. http://dx.doi.org/10.1074/jbc.m406262200.

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Amyloid fibrils in Alzheimer's disease mainly consist of 40- and 42-mer β-amyloid peptides (Aβ40 and Aβ42) that exhibit aggregative ability and neurotoxicity. Although the aggregates of Aβ peptides are rich in intermolecular β-sheet, the precise secondary structure of Aβ in the aggregates remains unclear. To identify the amino acid residues involved in the β-sheet formation, 34 proline-substituted mutants of Aβ42 were synthesized and their aggregative ability and neurotoxicity on PC12 cells were examined. Prolines are rarely present in β-sheet, whereas they are easily accommodated in β-turn as a Pro-Xcorner. Among the mutants at positions 15-32, only E22P-Aβ42 extensively aggregated with stronger neurotoxicity than wild-type Aβ42, suggesting that the residues at positions 15-21 and 24-32 are involved in the β-sheet and that the turn at positions 22 and 23 plays a crucial role in the aggregation and neurotoxicity of Aβ42. The C-terminal proline mutants (A42P-, I41P-, and V40P-Aβ42) hardly aggregated with extremely weak cytotoxicity, whereas the C-terminal threonine mutants (A42T- and I41T-Aβ42) aggregated potently with significant cytotoxicity. These results indicate that the hydrophobicity of the C-terminal two residues of Aβ42 is not related to its aggregative ability and neurotoxicity, rather the C-terminal three residues adopt the β-sheet. These results demonstrate well the large difference in aggregative ability and neurotoxicity between Aβ42 and Aβ40. In contrast, the proline mutants at the N-terminal 13 residues showed potent aggregative ability and neurotoxicity similar to those of wild-type Aβ42. The identification of the β-sheet region of Aβ42 is a basis for designing new aggregation inhibitors of Aβ peptides.

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Song, Il Keun, and Young Kee Kang. "Puckering Transition of 4-Substituted Proline Residues." Journal of Physical Chemistry B 109, no. 35 (September 2005): 16982–87. http://dx.doi.org/10.1021/jp044337p.

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NARITA, MITSUAKI, NORIHIRO OHKAWA, SATOSHI NAGASAWA, and SHIZUKO ISOKAWA. "Conformation of sequential peptides containing proline residues." International Journal of Peptide and Protein Research 24, no. 2 (January 12, 2009): 129–34. http://dx.doi.org/10.1111/j.1399-3011.1984.tb00937.x.

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Agah, Sayeh, John D. Larson, and Michael T. Henzl. "Impact of Proline Residues on Parvalbumin Stability†." Biochemistry 42, no. 37 (September 2003): 10886–95. http://dx.doi.org/10.1021/bi034721x.

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Deber, Charles M., Mira Glibowicka, and G. Andrew Woolley. "Conformations of proline residues in membrane environments." Biopolymers 29, no. 1 (January 1990): 149–57. http://dx.doi.org/10.1002/bip.360290120.

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MacArthur, Malcolm W., and Janet M. Thornton. "Influence of proline residues on protein conformation." Journal of Molecular Biology 218, no. 2 (March 1991): 397–412. http://dx.doi.org/10.1016/0022-2836(91)90721-h.

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Schmitt, Anthony P., George P. Leser, Eiji Morita, Wesley I. Sundquist, and Robert A. Lamb. "Evidence for a New Viral Late-Domain Core Sequence, FPIV, Necessary for Budding of a Paramyxovirus." Journal of Virology 79, no. 5 (March 1, 2005): 2988–97. http://dx.doi.org/10.1128/jvi.79.5.2988-2997.2005.

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ABSTRACT Enveloped virus budding has been linked to both the ubiquitin-proteasome pathway and the vacuolar protein-sorting pathway of cells. We show here for the paramyxovirus SV5 that proteasome inhibitors and expression of dominant-negative VPS4(E228Q) ATPase blocks budding. The SV5 matrix (M) protein lacks previously defined late domains (e.g., P[T/S]AP, PPxY, YPDL) that recruit cellular factors. We identified a new motif for budding (core sequence FPIV) that can compensate functionally for lack of a PTAP late domain in budding human immunodeficiency virus type 1 virus-like particles (VLPs). Mutagenesis experiments suggest the more general sequence Ø-P-x-V. The proline residue was found to be critically important for function of this sequence, as substitution of this proline in the SV5 M protein resulted in poor budding of SV5 VLPs and failure of recombinant SV5 virus to replicate normally. Adaptation of mutant virus occurred rapidly, resulting in new proline residues elsewhere in the M protein. We hypothesize that these proline residues act to partially restore virus budding by generation of new motifs that act as suboptimal late domains.

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Roigaard-Petersen, H., C. Jacobsen, and M. I. Sheikh. "Transport of L-proline by luminal membrane vesicles from pars recta of rabbit proximal tubule." American Journal of Physiology-Renal Physiology 254, no. 5 (May 1, 1988): F628—F633. http://dx.doi.org/10.1152/ajprenal.1988.254.5.f628.

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The mechanism of renal transport of L-proline by luminal membrane vesicles prepared from proximal straight tubules (pars recta) of rabbit kidney was investigated. The following picture emerges from transport studies: an electrogenic and Na+-requiring system confined to this region of nephron exists for transport of L-proline with a high affinity (Km = 0.16 mM) and low capacity (Vmax = 3.5 nmol.mg protein-1.15 S-1). Lowering the pH from 7.5 to 5.5 increased the affinity (Km lowered from 0.16 mM at pH 7.5 to 0.08 mM at pH 5.5) without changing the maximal capacity of this system. Modification of histidyl residues of the intact luminal membrane vesicles by diethyl-pyrocarbonate (DEP) completely abolished the transient renal accumulation of L-proline. Simultaneous presence of Na+ and L-proline (10 mM) protects against DEP inactivation of renal transport of radioactive L-proline. We propose that a histidyl residue may be at or close to the active site of L-proline transporter in vesicles from the pars recta.

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Wu, Chuan Fen, Ruoning Wang, Qianjin Liang, Jianjiao Liang, Wenke Li, Sung Yun Jung, Jun Qin, Sue-Hwa Lin, and Jian Kuang. "Dissecting the M Phase–specific Phosphorylation of Serine–Proline or Threonine–Proline Motifs." Molecular Biology of the Cell 21, no. 9 (May 2010): 1470–81. http://dx.doi.org/10.1091/mbc.e09-06-0486.

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M phase induction in eukaryotic cell cycles is associated with a burst of protein phosphorylation, primarily at serine or threonine followed by proline (S/TP motif). The mitotic phosphoprotein antibody MPM-2 recognizes a significant subset of mitotically phosphorylated S/TP motifs; however, the required surrounding sequences of and the key kinases that phosphorylate these S/TP motifs remain to be determined. By mapping the mitotic MPM-2 epitopes in Xenopus Cdc25C and characterizing the mitotic MPM-2 epitope kinases in Xenopus oocytes and egg extracts, we have determined that phosphorylation of TP motifs that are surrounded by hydrophobic residues at both −1 and +1 positions plays a dominant role in M phase–associated burst of MPM-2 reactivity. Although mitotic Cdk and MAPK may phosphorylate subsets of these motifs that have a basic residue at the +2 position and a proline residue at the −2 position, respectively, the majority of these motifs that are preferentially phosphorylated in mitosis do not have these features. The M phase–associated burst of MPM-2 reactivity can be induced in Xenopus oocytes and egg extracts in the absence of MAPK or Cdc2 activity. These findings indicate that the M phase–associated burst of MPM-2 reactivity represents a novel type of protein phosphorylation in mitotic regulation.

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GARRIGA, Judit, Edy SEGURA, Xavier MAYOL, Charles GRUBMEYER, and Xavier GRAÑA. "Phosphorylation site specificity of the CDC2-related kinase PITALRE." Biochemical Journal 320, no. 3 (December 15, 1996): 983–89. http://dx.doi.org/10.1042/bj3200983.

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PITALRE is a human protein kinase belonging to the cell division cycle 2 (CDC2) kinase family, and is the catalytic subunit of a multimeric complex that contains several cellular proteins. PITALRE complexes from several cell lines and tissues phosphorylate retinoblastoma protein and myelin basic protein (MBP). In the present work, we have found that MBP is phosphorylated by PITALRE complexes on both Ser and Thr residues. Two different antibodies raised to PITALRE purified virtually identical kinase activities, as analysed by MBP phosphopeptide mapping and phosphoamino acid analysis. We have identified the proline-directed residue Ser-162 of MBP as a major phosphorylation site for PITALRE. In addition, our results suggest that one of the two MBP proline-directed threonine residues, Thr-97, is also selectively phosphorylated by PITALRE. These data, together with analysis of different peptide substrates derived from sites on MBP that are phosphorylated by PITALRE, indicate that PITALRE is a Ser/Thr proline-directed kinase. In addition, our results show that PITALRE has a substrate site specificity distinguishable from those of the CDC2 and cyclin-dependent kinase 2 (CDK2).

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Block, D. A., D. Yu, D. A. Armstrong, and A. Rauk. "On the influence of secondary structure on the α-C→H bond dissociation energy of proline residues in proteins: a theoretical study." Canadian Journal of Chemistry 76, no. 7 (July 1, 1998): 1042–49. http://dx.doi.org/10.1139/v98-107.

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Ab initio computations (B3LYP/6-31G(D), coupled with isodesmic reactions) were used to predict αC→H bond dissociation energies (BDEs) for proline as a residue in a model peptide, intended to mimic the environment in proteins. The environment was further constrained to mimic common proline positions in turns of different types. The BDEs were found to be very dependent on the structural constraints imposed by the turn type, implying different structure-mediated susceptibilities to free radical damage to proline residues. Unnatural repair of proline (inversion of chirality) was found to be thermodynamically unfavourable. The predicted BDEs for the proline αC→H bond, in kJ mol-1, to an estimated accuracy of ±10 kJ mol-1 are as follows: fully optimized trans rotamer, 368.6; fully optimized cis rotamer, 357.7; ß turn type I, 380.7; ß turn type II, 397.8; ß turn type II', 385.4; ß turn type VIa, 374.0; ß turn type VIb, 355.0. Key words: proline, ß -turns, free radical, bond dissociation energy, molecular structure, oxidative damage.<

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Proudfoot, Sarah C., and Daisy Sahoo. "Proline residues in scavenger receptor-BI's C-terminal region support efficient cholesterol transport." Biochemical Journal 476, no. 6 (March 22, 2019): 951–63. http://dx.doi.org/10.1042/bcj20180831.

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Abstract High-density lipoproteins (HDLs) facilitate reverse cholesterol transport, a process in which HDL removes cholesterol from circulation and carries it to the liver for biliary excretion. Reverse cholesterol transport is also facilitated by HDL's high-affinity receptor, scavenger receptor-BI (SR-BI), by mechanisms that are not fully understood. To improve our understanding of SR-BI function, we previously solved the NMR (nuclear magnetic resonance) structure of a peptide encompassing amino acids 405–475 of SR-BI. This segment of SR-BI, that includes the functionally critical C-terminal transmembrane domain and part of the extracellular domain, also contains four conserved proline (Pro) residues. We hypothesized that these proline residues support SR-BI in a conformation that allows for efficient cholesterol transport. To test this, we generated individual Pro-to-alanine mutations in full-length SR-BI and transiently expressed the mutant receptors in COS-7 cells to measure the effects on SR-BI-mediated cholesterol transport functions. Our findings reveal that HDL cell association and uptake of HDL-cholesteryl esters are impaired by mutation of Pro-412, Pro-438, or the transmembrane proline kink residue (Pro-459). In addition, SR-BI-mediated cholesterol efflux and membrane cholesterol distribution are impaired by mutation of Pro-412 or Pro-438, indicating that these residues are essential for a fully functional SR-BI receptor. Furthermore, we demonstrate that Pro-408 is necessary for proper SR-BI expression, but mutation of Pro-408 does not cause SR-BI to become misfolded or rapidly degraded by the proteasome or the lysosome. We conclude that key proline residues play an important role in SR-BI function by allowing for the efficient transport of cholesterol between cells and HDL.

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Melnikov, Sergey, Justine Mailliot, Lukas Rigger, Sandro Neuner, Byung‐Sik Shin, Gulnara Yusupova, Thomas E. Dever, Ronald Micura, and Marat Yusupov. "Molecular insights into protein synthesis with proline residues." EMBO reports 17, no. 12 (November 8, 2016): 1776–84. http://dx.doi.org/10.15252/embr.201642943.

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PANASIK, NICHOLAS, ERIC S. EBERHARDT, ARTHUR S. EDISON, DOUGLAS R. POWELL, and RONALD T. RAINES. "Inductive effects on the structure of proline residues." International Journal of Peptide and Protein Research 44, no. 3 (January 12, 2009): 262–69. http://dx.doi.org/10.1111/j.1399-3011.1994.tb00169.x.

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Baker, Benjamin W., Dennis A. Dougherty, and Sarah C. R. Lummis. "Proline Residues Contribute to Efficient GABAp Receptor Function." ACS Chemical Neuroscience 11, no. 24 (November 17, 2020): 4215–22. http://dx.doi.org/10.1021/acschemneuro.0c00483.

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Orzáez, Mar, Jesús Salgado, Ana Giménez-Giner, Enrique Pérez-Payá, and Ismael Mingarro. "Influence of Proline Residues in Transmembrane Helix Packing." Journal of Molecular Biology 335, no. 2 (January 2004): 631–40. http://dx.doi.org/10.1016/j.jmb.2003.10.062.

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Schönbach, C., M. Ibe, H. Shiga, Y. Takamiya, K. Miwa, K. Nokihara, and M. Takiguchi. "Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues." Journal of Immunology 154, no. 11 (June 1, 1995): 5951–58. http://dx.doi.org/10.4049/jimmunol.154.11.5951.

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Abstract The prerequisites of peptide HLA-B*3501 interactions have been revisited by quantitative peptide binding assays with 190 chemically synthesized peptide possessing two anchor residues corresponding to the HLA-B*3501 peptide motif and a statistical residue-position analysis of binding and nonbinding peptides. According to the peptide motif of HLA-B*3501, aliphatic hydrophobic (Leu, Ile, and Met) or aromatic residues (Tyr and Phe) specify the main anchor at the C terminus, and position 2 renders an auxiliary anchor for proline. The importance of these residues was confirmed as a minimum requirement for peptide binding. Moreover, we demonstrated that high affinity peptide binding requires more than one favorable position of positions 3, 4, and 7. Aliphatic hydrophobic residues and residues that contain -OH or -SH side chains in position 3, 7, and 4 significantly enhance binding. Positions 1 and 5, or 7 may deteriorate peptide binding if these positions are held by proline and small residues (Ala and Gly) or basic residues carrying positively charged side chains (Arg and Lys), respectively. Positions 6 and 8 were statistically free of constrains. Yet, bulky aromatic residues and basic residues with a positively charged side chain at position 8 decreased the binding affinity. These findings were used to assess the predictability of binding and nonbinding peptides. Our binding predictions of 28 nonamers were verified by experimental data. Taking into account the importance of anchor and nonanchor positions in peptide binding and their practical value in peptide binding prediction, the search for peptide epitopes becomes more efficient.

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Bergseng, Elin, Jiang Xia, Chu-Young Kim, Chaitan Khosla, and Ludvig M. Sollid. "Main Chain Hydrogen Bond Interactions in the Binding of Proline-rich Gluten Peptides to the Celiac Disease-associated HLA-DQ2 Molecule." Journal of Biological Chemistry 280, no. 23 (April 12, 2005): 21791–96. http://dx.doi.org/10.1074/jbc.m501558200.

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Binding of peptide epitopes to major histocompatibility complex proteins involves multiple hydrogen bond interactions between the peptide main chain and major histocompatibility complex residues. The crystal structure of HLA-DQ2 complexed with the αI-gliadin epitope (LQPFPQPELPY) revealed four hydrogen bonds between DQ2 and peptide main chain amides. This is remarkable, given that four of the nine core residues in this peptide are proline residues that cannot engage in amide hydrogen bonding. Preserving main chain hydrogen bond interactions despite the presence of multiple proline residues in gluten peptides is a key element for the HLA-DQ2 association of celiac disease. We have investigated the relative contribution of each main chain hydrogen bond interaction by preparing a series of N-methylated αI epitope analogues and measuring their binding affinity and off-rate constants to DQ2. Additionally, we measured the binding of αI-gliadin peptide analogues in which norvaline, which contains a backbone amide hydrogen bond donor, was substituted for each proline. Our results demonstrate that hydrogen bonds at P4 and P2 positions are most important for binding, whereas the hydrogen bonds at P9 and P6 make smaller contributions to the overall binding affinity. There is no evidence for a hydrogen bond between DQ2 and the P1 amide nitrogen in peptides without proline at this position. This is a unique feature of DQ2 and is likely a key parameter for preferential binding of proline-rich gluten peptides and development of celiac disease.

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Booth, Mary, Ide Ni Fhaoláin, P. Vincent Jennings, and Gerard O'Cuinn. "Purification and characterization of a post-proline dipeptidyl aminopeptidase fromStreptococcus cremorisAM2." Journal of Dairy Research 57, no. 1 (February 1990): 89–99. http://dx.doi.org/10.1017/s0022029900026649.

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SummaryThe present study describes the purification of a post-proline dipeptidyl aminopeptidase from the cytoplasm ofStreptococcus cremorisAM2. On the basis of its elution from a calibrated Sephadex G200 column, the enzyme had a molecular weight of 117000 and exhibited a broad pH optimum activity between 6·0 and 9·0. The activity was most comprehensively inhibited by phenylmethylsulphonylfluoride and more modestly inhibited by 1,10-phenanthroline and 8-hydroxyquinoline but not by EDTA. A range of peptides containing either proline or alanine as the penultimate amino acid residue could act as substrates. The presence of proline on the carboxy side of the scissile bond prevented hydrolysis. However the enzyme could release Pro-Pro from Pro-Pro-Gly-Phe-Ser-Pro. The significance of this substrate specificity is considered in the context of removal of either single proline residues or prolylproline sequences from oligopeptides during cheese ripening.

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Suzuki, Yuichiro J., and Jian-Jiang Hao. "Evidence for the oxidant-mediated amino acid conversion, a naturally occurring protein engineering process, in human cells." F1000Research 6 (April 28, 2017): 594. http://dx.doi.org/10.12688/f1000research.11376.1.

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Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through proteasome-dependent degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure are interchangeable. In support of this hypothesis, mass spectrometry demonstrated that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule can be converted into glutamic acid in cultured human cells, establishing a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

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Suzuki, Yuichiro J., and Jian-Jiang Hao. "Results supporting the concept of the oxidant-mediated protein amino acid conversion, a naturally occurring protein engineering process, in human cells." F1000Research 6 (September 28, 2018): 594. http://dx.doi.org/10.12688/f1000research.11376.2.

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Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure can be converted to each other. Mass spectrometry provided results supporting that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule may be converted into glutamic acid in cultured human cells, opening up a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

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Tiennault-Desbordes, Emmanuelle, Yves Cenatiempo, and Soumaya Laalami. "Initiation Factor 2 of Myxococcus xanthus, a Large Version of Prokaryotic Translation Initiation Factor 2." Journal of Bacteriology 183, no. 1 (January 1, 2001): 207–13. http://dx.doi.org/10.1128/jb.183.1.207-213.2001.

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ABSTRACT We have isolated the structural gene for translation initiation factor IF2 (infB) from the myxobacterium Myxococcus xanthus. The gene (3.22 kb) encodes a 1,070-residue protein showing extensive homology within its G domain and C terminus to the equivalent regions of IF2 from Escherichia coli. The protein cross-reacts with antibodies raised against E. coliIF2 and was able to complement an E. coli infB mutant. TheM. xanthus protein is the largest IF2 known to date. This is essentially due to a longer N-terminal region made up of two characteristic domains. The first comprises a 188-amino-acid sequence consisting essentially of alanine, proline, valine, and glutamic acid residues, similar to the APE domain observed in Stigmatella aurantiaca IF2. The second is unique to M. xanthusIF2, is located between the APE sequence and the GTP binding domain, and consists exclusively of glycine, proline, and arginine residues.

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Kaspari, A., T. Diefenthal, G. Grosche, A. Schierhorn, and H. U. Demuth. "Substrates containing phosphorylated residues adjacent to proline decrease the cleavage by proline-specific peptidases." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1293, no. 1 (March 1996): 147–53. http://dx.doi.org/10.1016/0167-4838(95)00238-3.

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Tie, Jian-Kie, Mei-Yan Zheng, Darrel W. Stafford, and David L. Straight. "Expression of a Two Chain Gamma-Glutamyl Carboxylase: Importance of Disulfide Bond Formation and Transmembrane Domain Interactions." Blood 108, no. 11 (November 16, 2006): 1694. http://dx.doi.org/10.1182/blood.v108.11.1694.1694.

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Abstract The vitamin K-dependent carboxylase is an integral membrane protein with five transmembrane domains (TMDs). It catalyzes the post-translational modification of specific glutamic acid residues of vitamin K-dependent proteins to gamma-carboxyglutamic acid residues. This posttranslational modification is critical for the biological functions of blood coagulation. The native enzyme is a single chain molecule with one disulfide bond. In this study, we have expressed carboxylase as two chains: residues 1–345 and 346–758 in the same insect cells. Our results show that these two fragments are assembled into a fully active enzyme and are joined by a disulfide. Affinity purification of the carboxylase C-terminal fragment (346–758) results in co-purification of the N-terminal fragment (1–345) even under reducing condition. This indicates that, in addition to the disulfide linkage between these two fragments, they are also linked by non-covalent interactions. One possibility is that the hydrophobic interactions between the TMDs play a role. According to carboxylase membrane topology, there are four TMDs (1–4) in the N-terminal fragment and one TMD (fifth) in the C-terminal fragment. The C-terminal fragment contains all glycosylation sites. When we introduced two prolines to disrupt the transmembrane helix in the wild type carboxylase’s fifth TMD, glycosylation was eliminated. This indicates that the domain is not inserted into the lumen of the ER, but remains in the cytoplasm. Therefore, as our results demonstrate, in the two chain carboxylase with its fifth TMD disrupted, the two chains do not form a disulfide bound nor do they associate through essential non-covalent TMD interactions. While proline residues can disrupt membrane helices as described above, they often occur at the interface between the membrane and the lumenal surface of ER; these prolines appear to affect the chain orientation as it exits the membrane. There is a proline at residue 378 near the lumenal surface of the fifth TMD helix of carboxylase. To examine P378’s effect on disulfide bond formation, we mutated it to leucine. Results show that less disulfide bond formed in the two chain mutant carboxylase and the protein was significantly degraded when compared to the unmutated two chain molecule. Based on our results, we conclude the following: 1) the two chain carboxylase is assembled into a single molecule in vivo and the two chains are joined by a disulfide bond, the enzyme carboxylates gla-containing substrates and binds propeptide with affinity similar to that of wild type enzyme. Therefore, this molecule is a good model for structural studies of TMD interactions and disulfide bond formation; 2) TMD association in the membrane is important for the orientation of the N- and C-terminal portions of carboxylase to be assembled into the active enzyme; 3) and finally proline residue 378 at the lumenal interface of the fifth TMD plays a key role in the conformation which promotes disulfide formation.

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Lee, Schuyler, Chao Wang, Haolin Liu, Jian Xiong, Renee Jiji, Xia Hong, Xiaoxue Yan, et al. "Hydrogen bonds are a primary driving force forde novoprotein folding." Acta Crystallographica Section D Structural Biology 73, no. 12 (November 10, 2017): 955–69. http://dx.doi.org/10.1107/s2059798317015303.

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The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID153), an optimizedin vitrofolding procedure was derived to obtain large amounts of AID153, which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution ofcisandtransconfigurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome thecis-to-transproline isomerization, orvice versa, during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein foldingin vivo. It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force forde novoprotein folding.

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LIANG, Zhimin, Timothy MATHER, and Guangpu LI. "GTPase mechanism and function: new insights from systematic mutational analysis of the phosphate-binding loop residue Ala30 of Rab5." Biochemical Journal 346, no. 2 (February 22, 2000): 501–8. http://dx.doi.org/10.1042/bj3460501.

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Structural and biochemical data indicate the importance of the phosphate-binding loop residues Gly12 and Gly13 of Ras both in the GTP hydrolysis reaction and in biological activity, but these two residues are not conserved in other Ras-related GTPases. To gain a better understanding of this region in GTP hydrolysis and GTPase function, we used the Ras-related Rab5 GTPase as a model for comparison, and substituted the Ala30 residue (the equivalent of Gly13 of Ras) with all the other 19 amino acids. The resulting mutants were analysed for GTP hydrolysis, GTP binding, GTP dissociation and biological activity. Only the substitution of alanine with proline reduced the GTPase activity by an order of magnitude. This effect is in sharp contrast with the observation that a proline substitution at the neighbouring position (Gly12 of Ras) has little effect on the GTPase activity. Whereas most other substitutions showed either a small negative effect or no effect on the GTPase activity, the arginine substitution surprisingly stimulated the GTPase activity by 5-fold. Molecular modelling suggests that this built-in arginine mimics the catalytic arginine residues found in trimeric GTPases and GTPase-activating proteins in providing the positive charge to facilitate the GTP hydrolysis reaction. We investigated further the biological activity of the Rab5 mutants in relation to stimulating endocytosis. When expressed in cultured baby hamster kidney cells, both arginine and proline mutants, like wild-type Rab5, stimulated endocytosis. However, the arginine mutant was a more potent stimulator than the proline mutant (3-fold stimulation as against 1.7-fold). The tryptophan mutant, on the other hand, was completely deficient in activity in terms of the stimulation of endocytosis, demonstrating the importance of the phosphate-binding loop in Rab GTPase function.

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Okada, Masahiro, Tomotoshi Sugita, and Ikuro Abe. "Posttranslational isoprenylation of tryptophan in bacteria." Beilstein Journal of Organic Chemistry 13 (February 22, 2017): 338–46. http://dx.doi.org/10.3762/bjoc.13.37.

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Posttranslational isoprenylation is generally recognized as a universal modification of the cysteine residues in peptides and the thiol groups of proteins in eukaryotes. In contrast, the Bacillus quorum sensing peptide pheromone, the ComX pheromone, possesses a posttranslationally modified tryptophan residue, and the tryptophan residue is isoprenylated with either a geranyl or farnesyl group at the gamma position to form a tricyclic skeleton that bears a newly formed pyrrolidine, similar to proline. The post-translational dimethylallylation of two tryptophan residues of a cyclic peptide, kawaguchipeptin A, from cyanobacteria has also been reported. Interestingly, the modified tryptophan residues of kawaguchipeptin A have the same scaffold as that of the ComX pheromones, but with the opposite stereochemistry. This review highlights the biosynthetic pathways and posttranslational isoprenylation of tryptophan. In particular, recent studies on peptide modifying enzymes are discussed.

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Cadieux, Nathalie, Clive Bradbeer, and Robert J. Kadner. "Sequence Changes in the Ton Box Region of BtuB Affect Its Transport Activities and Interaction with TonB Protein." Journal of Bacteriology 182, no. 21 (November 1, 2000): 5954–61. http://dx.doi.org/10.1128/jb.182.21.5954-5961.2000.

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ABSTRACT Uptake of cobalamins by the transporter protein BtuB in the outer membrane of Escherichia coli requires the proton motive force and the transperiplasmic protein TonB. The Ton box sequence near the amino terminus of BtuB is conserved among all TonB-dependent transporters and is the only known site of mutations that confer a transport-defective phenotype which can be suppressed by certain substitutions at residue 160 in TonB. The crystallographic structures of the TonB-dependent transporter FhuA revealed that the region near the Ton box, which itself was not resolved, is exposed to the periplasmic space and undergoes an extensive shift in position upon binding of substrate. Site-directed disulfide bonding in intact cells has been used to show that the Ton box of BtuB and residues around position 160 of TonB approach each other in a highly oriented and specific manner to form BtuB-TonB heterodimers that are stimulated by the presence of transport substrate. Here, replacement of Ton box residues with proline or cysteine revealed that residue side chain recognition is not important for function, although replacement with proline at four of the seven Ton box positions impaired cobalamin transport. The defect in cobalamin utilization resulting from the L8P substitution was suppressed by cysteine substitutions in adjacent residues in BtuB or in TonB. This suppression did not restore active transport of cobalamins but may allow each transporter to function at most once. The uncoupled proline substitutions in BtuB markedly affected the pattern of disulfide bonding to TonB, both increasing the extent of cross-linking and shifting the pairs of residues that can be joined. Cross-linking of BtuB and TonB in the presence of the BtuB V10P substitution became independent of the presence of substrate, indicating an additional distortion of the exposure of the Ton box in the periplasmic space. TonB action thus requires a specific orientation for functional contact with the Ton box, and changes in the conformation of this region block transport by preventing substrate release and repeated transport cycles.

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Pi, Jing, C. Dogovski, and A. J. Pittard. "Functional Consequences of Changing Proline Residues in the Phenylalanine-Specific Permease ofEscherichia coli." Journal of Bacteriology 180, no. 21 (November 1, 1998): 5515–19. http://dx.doi.org/10.1128/jb.180.21.5515-5519.1998.

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ABSTRACT The PheP protein is a high-affinity phenylalanine-specific permease of the bacterium Escherichia coli. A topological model based on genetic analysis involving the construction of protein fusions with alkaline phosphatase has previously been proposed in which PheP has 12 transmembrane segments with both N and C termini located in the cytoplasm (J. Pi and A. J. Pittard, J. Bacteriol. 178:2650–2655, 1996). Site-directed mutagenesis has been used to investigate the functional importance of each of the 16 proline residues of the PheP protein. Replacement of alanine at only three positions, P54, P341, and P442, resulted in the loss of 50% or more activity. Substitutions at P341 had the most dramatic effects. None of these changes in transport activity were, however, associated with any defect of the mutant protein in inserting into the membrane, as indicated by [35S]methionine labelling and immunoprecipitation using anti-PheP serum. A possible role for each of these three prolines is discussed. Inserting a single alanine residue at different sites within span IX and the loop immediately preceding it also had major effects on transport activity, suggesting an important role for a highly organized structure in this region of the protein.

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Robinson, R. A., and D. R. Lee. "Studies of tum- peptide analogs define an alternative anchor that can be utilized by Ld ligands lacking the consensus P2 anchor." Journal of Immunology 156, no. 11 (June 1, 1996): 4266–73. http://dx.doi.org/10.4049/jimmunol.156.11.4266.

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Abstract To determine how peptides that lack a consensus binding motif interact with class I molecules, we have studied the binding of the tumor-associated tum- P91A 14-22 (tum-) peptide to Ld. Previously, a proline at position 2 (P2) and a hydrophobic residue at P9 had been defined as anchors for Ld ligands. However, the tum- peptide lacks the P2 proline anchor. To compare how peptides with and without the P2 proline anchor bind to Ld, we analyzed the binding of monosubstituted analogues of the murine cytomegalovirus (MCMV) pp89 168-176 and the tum- peptides to Ld. As expected, the binding of both peptides was inhibited by substitutions at P9, the carboxyl-terminal anchor. As also predicted, the MCMV peptide was found to be dependent upon its P2 proline for binding to Ld. By contrast, the binding of the tum- peptide to Ld is dependent primarily on a P8 aspartate residue. Interestingly, the p2Ca peptide that is immunodominant in allorecognition of Ld also lacks the P2 proline anchor and has been shown to depend on residues near the carboxyl terminus for binding to Ld. Furthermore, both the p2Ca and the tum- peptides can bind to Ld as octamers. These combined studies suggest that there are at least two alternative manners by which peptides can bind to Ld. Although most Ld ligands bind using a P2 proline anchor, the tum- and p2Ca peptides bind using alternative anchors in the carboxyl-terminal region.

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Kurz, E. M., T. W. Holstein, B. M. Petri, J. Engel, and C. N. David. "Mini-collagens in hydra nematocytes." Journal of Cell Biology 115, no. 4 (November 15, 1991): 1159–69. http://dx.doi.org/10.1083/jcb.115.4.1159.

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We have isolated and characterized four collagen-related c-DNA clones (N-COL 1, N-COL 2, N-COL 3, N-COL 4) that are highly expressed in developing nematocytes in hydra. All four c-DNAs as well as their corresponding transcripts are small in size (600-1,000 bp). The deduced amino acid sequences show that they contain a central region consisting of 14 to 16 Gly-X-Y triplets. This region is flanked amino-terminal by a stretch of 14-23 proline residues and carboxy-terminal by a stretch of 6-9 prolines. At the NH2- and COOH-termini are repeated patterns of cysteine residues that are highly conserved between the molecules. A model is proposed which consists of a central stable collagen triple helix of 12-14 nm length from which three 9-22 nm long polyproline II type helices emerge at both ends. Disulfide linkage between cysteine-rich segments in these helices could lead to the formation of oligomeric network structures. Electrophoretic characterization of nematocyst extracts allows resolution of small proline-rich polypeptides that correspond in size to the cloned sequences.

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Kropshofer, H., H. Max, T. Halder, M. Kalbus, C. A. Muller, and H. Kalbacher. "Self-peptides from four HLA-DR alleles share hydrophobic anchor residues near the NH2-terminal including proline as a stop signal for trimming." Journal of Immunology 151, no. 9 (November 1, 1993): 4732–42. http://dx.doi.org/10.4049/jimmunol.151.9.4732.

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Abstract Naturally processed MHC class II-associated peptides proved to be heterogeneous in size, varying from 13 to 25 amino acids. Truncation variants suggested sequence motifs that afford the amino termini to be shifted for obtaining an alignment: a 9- to 11-residue core region that is bordered by primary anchor residues is surrounded by extra sequences of variable lengths and hitherto unknown functions. Herein we present bulk sequencing analyses of self-peptides from four HLA-DR alleles and HLA-DQw7 clearly showing that the length of most of the NH2-terminal preanchor sequence is limited to 1 to 3 residues. Most strikingly, proline is the dominant residue reappearing at positions 2 and 3 in any allele. Proline revealed to function as a stop signal for NH2-terminal trimming as well as a secondary anchor: crude cytosolic and endosomal peptide fractions could be processed by aminopeptidases in vitro, whereupon DR1 binding peptides with increased affinity were generated. In addition, aminopeptidase treatment of DR1: self-peptide complexes implied that proline together with sterical constraints of the MHC molecule do protect the peptides' NH2-termini from further processing, whereas their COOH-termini were accessible to cathepsin B processing. Finally, bulk sequencing profiles contained signals from further putative anchor residues clustering in the NH2-terminal region:tyrosine, phenylalanine, leucine, isoleucine, and valine are enriched at positions 2 to 4 in DR1, DR5, and DR6, however, at positions 4 to 6 in DR3. Isotype-specificity is demonstrated by DQw7 displaying glutamine and asparagine at position 2. Obviously, the degenerate occurrence of aromatic or aliphatic side chains close to the NH2-terminal guarantees for essential interactions with a hydrophobic pocket of the investigated DR molecules. Most probably, this pocket is located in the nonpolymorphic DR alpha-chain rationalizing previous findings of promiscuous peptide binding to different DR alleles.

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Zhao, Zihan, Xuejiao Xu, Hairong Cheng, Michelle C. Miller, Zhen He, Hongming Gu, Zhongyu Zhang, et al. "Galectin-3 N-terminal tail prolines modulate cell activity and glycan-mediated oligomerization/phase separation." Proceedings of the National Academy of Sciences 118, no. 19 (May 5, 2021): e2021074118. http://dx.doi.org/10.1073/pnas.2021074118.

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Galectin-3 (Gal-3) has a long, aperiodic, and dynamic proline-rich N-terminal tail (NT). The functional role of the NT with its numerous prolines has remained enigmatic since its discovery. To provide some resolution to this puzzle, we individually mutated all 14 NT prolines over the first 68 residues and assessed their effects on various Gal-3–mediated functions. Our findings show that mutation of any single proline (especially P37A, P55A, P60A, P64A/H, and P67A) dramatically and differentially inhibits Gal-3–mediated cellular activities (i.e., cell migration, activation, endocytosis, and hemagglutination). For mechanistic insight, we investigated the role of prolines in mediating Gal-3 oligomerization, a fundamental process required for these cell activities. We showed that Gal-3 oligomerization triggered by binding to glycoproteins is a dynamic process analogous to liquid–liquid phase separation (LLPS). The composition of these heterooligomers is dependent on the concentration of Gal-3 as well as on the concentration and type of glycoprotein. LLPS-like Gal-3 oligomerization/condensation was also observed on the plasma membrane and disrupted endomembranes. Molecular- and cell-based assays indicate that glycan binding–triggered Gal-3 LLPS (or LLPS-like) is driven mainly by dynamic intermolecular interactions between the Gal-3 NT and the carbohydrate recognition domain (CRD) F-face, although NT–NT interactions appear to contribute to a lesser extent. Mutation of each proline within the NT differentially controls NT–CRD interactions, consequently affecting glycan binding, LLPS, and cellular activities. Our results unveil the role of proline polymorphisms (e.g., at P64) associated with many diseases and suggest that the function of glycosylated cell surface receptors is dynamically regulated by Gal-3.

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Ferrario, Eugenio, Riccardo Miggiano, Menico Rizzi, and Davide M. Ferraris. "Structure of Thermococcus litoralis Δ1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline." Acta Crystallographica Section D Structural Biology 76, no. 5 (April 29, 2020): 496–505. http://dx.doi.org/10.1107/s2059798320004866.

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L-Hydroxyproline (L-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. L-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-L-proline (T3LHyp) and trans-4-hydroxy-L-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and L-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.

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SIEMION, IGNACY Z., KATARZYNA SOBCZYK, and MAREK LISOWSKI. "Comparison of conformational properties of proline and threonine residues." International Journal of Peptide and Protein Research 27, no. 2 (January 12, 2009): 127–37. http://dx.doi.org/10.1111/j.1399-3011.1986.tb01802.x.

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Williams, Karen A., and Charles M. Deber. "Proline residues in transmembrane helixes: structural or dynamic role?" Biochemistry 30, no. 37 (September 1991): 8919–23. http://dx.doi.org/10.1021/bi00101a001.

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Woolfson, Derek N., and Dudley H. Williams. "The influence of proline residues on α-helical structure." FEBS Letters 277, no. 1-2 (December 17, 1990): 185–88. http://dx.doi.org/10.1016/0014-5793(90)80839-b.

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Gupta, Shaweta, Prasad Purohit, and Anthony Auerbach. "Proline Residues at the Nicotinic Acetylcholine Transmitter Binding Sites." Biophysical Journal 104, no. 2 (January 2013): 275a. http://dx.doi.org/10.1016/j.bpj.2012.11.1543.

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Tamaki, Makoto, Sadatoshi Akabori, and Ichiro Muramatsu. "Conformation of a cyclic tetrapeptide containing two proline residues." Biopolymers 39, no. 2 (December 6, 1998): 129–32. http://dx.doi.org/10.1002/(sici)1097-0282(199608)39:2<129::aid-bip1>3.0.co;2-r.

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Journal articles on the topic 'Proline residues'

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