Binding Of Dipeptides Research Articles

Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA

This investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity (Delta {C}_{p}^{o}) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.

Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids.

Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins.

Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases

The functionality of caspase homologs in prokaryotic cell execution has been perceived, yet the dimensions of their metabolic pertinence are still cryptic. Here, a detailed in silico study on putative cyanobacterial caspase homologs, termed orthocaspases, in a sequenced genome of 132 strains was performed. We observed that 473 putative orthocaspases were distributed among 62% cyanobacterial strains subsumed within all the taxonomical orders. However, high diversity among these orthocaspases was also evident as the conventional histidine–cysteine (HC) dyad was present only in 72.03% of orthocaspases (wild-type), whereas the rest 28.18% were pseudo-variants having substituted the catalytic dyad. Besides, the presence of various accessory functional domains with Peptidase C14 probably suggested the multifunctionality of the orthocaspases. Moreover, the early origin and emergence of wild-type orthocaspases were conferred by their presence in Gloeobacter; however, the complex phylogeny displayed by these caspase-homologs perhaps suggested horizontal a gene transfer for their acquisition. However, morpho-physiological advancements and larger genome size favored the acquisition of orthocaspases. Moreover, the conserved caspase hemoglobinase fold not only in the wild-type but also in the pseudo-orthocaspases in Nostoc sp. PCC 7120 ascertained the least effect of catalytic motifs in the protein tertiary structure. Further, the 100-ns molecular dynamic simulation and molecular mechanics/generalized born surface area exhibited stable binding of arginylarginine dipeptide with wild-type orthocaspase of Nostoc sp. PCC 7120, displaying arginine-P1 specificity of wild-type orthocaspases. This study deciphered the distribution, diversity, domain architecture, structure, and basic substrate specificity of putative cyanobacterial orthocaspases, which may aid in functional investigations in the future.

Oligopeptide-CB[8] complexation with switchable binding pathways.

Host-guest complexes exhibiting a 1 : 1 binding stoichiometry need not consist of a single host and guest. A series of oligopeptides, which were previously reported to have abnormally high binding enthalpies were investigated to deduce whether they exist as a 2 : 2 quaternary or a 1 : 1 binary complex with cucurbit[8]uril (CB[8]). Through a systematic study of the sequence-specific binding pathways of peptide-CB[8] association, a phenylalanine-leucine dipeptide was found to be capable of switching from a 1 : 1 stoichiometric complex to a 2 : 1 complex. By studying the differences in size-based diffusion properties of these two binding modes, the presence of a 1 : 1 pairwise inclusion complex was verified for the regime where CB[8] is in excess. Findings in this study can be utilised to 'customise' the precise CB[8]-oligopeptide self-assembly pathway, acting as a useful toolbox in the design of supramolecular systems.

Decision tree for the binding of dipeptides to the thermally fluctuating surface of cathepsin K

The behavior of 15 dipeptides on thermally fluctuating cathepsin K was investigated by molecular dynamics and docking simulations. Four dipeptides were distributed on sites near the active center, and the variations were small. Eleven dipeptides were distributed on sites far from the active center, and the variations were large for nine dipeptides and very large for the other two. The decision tree was constructed using genetic programming, and it accurately classified the 15 dipeptides. The decision tree would accurately estimate the behavior of various peptides, and should significantly contribute to the design of useful peptides.

Role of electrostatic interactions for ligand recognition and specificity of peptide transporters.

BackgroundPeptide transporters are membrane proteins that mediate the cellular uptake of di- and tripeptides, and of peptidomimetic drugs such as β-lactam antibiotics, antiviral drugs and antineoplastic agents. In spite of their high physiological and pharmaceutical importance, the molecular recognition by these transporters of the amino acid side chains of short peptides and thus the mechanisms for substrate binding and specificity are far from being understood.ResultsThe X-ray crystal structure of the peptide transporter YePEPT from the bacterium Yersinia enterocolitica together with functional studies have unveiled the molecular bases for recognition, binding and specificity of dipeptides with a charged amino acid residue at the N-terminal position. In wild-type YePEPT, the significant specificity for the dipeptides Asp-Ala and Glu-Ala is defined by electrostatic interaction between the in the structure identified positively charged Lys314 and the negatively charged amino acid side chain of these dipeptides. Mutagenesis of Lys314 into the negatively charged residue Glu allowed tuning of the substrate specificity of YePEPT for the positively charged dipeptide Lys-Ala. Importantly, molecular insights acquired from the prokaryotic peptide transporter YePEPT combined with mutagenesis and functional uptake studies with human PEPT1 expressed in Xenopus oocytes also allowed tuning of human PEPT1’s substrate specificity, thus improving our understanding of substrate recognition and specificity of this physiologically and pharmaceutically important peptide transporter.ConclusionThis study provides the molecular bases for recognition, binding and specificity of peptide transporters for dipeptides with a charged amino acid residue at the N-terminal position.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0167-8) contains supplementary material, which is available to authorized users.

Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913.

Peptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements. PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr). PsDppA alternates between an "open" and a "closed" form during substrate binding. Structural analyses of the 4 PsDppA-substrate complexes combined with mutational assays indicate that PsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake. Peptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unliganded PsDppA and PsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism of PsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism of PsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.

Crystal structure of the leucine-rich repeat domain of the NOD-like receptor NLRP1: Implications for binding of muramyl dipeptide

The NOD-like receptor NLRP1 (NLR family, pyrin domain containing 1) senses the presence of the bacterial cell wall component l-muramyl dipeptide (MDP) inside the cell. We determined the crystal structure of the LRR domain of human NLRP1 in the absence of MDP to a resolution of 1.65Å. The fold of the structure can be assigned to the ribonuclease inhibitor-like class of LRR proteins. We compared our structure with X-ray models of the LRR domains of NLRX1 and NLRC4 and a homology model of the LRR domain of NOD2. We conclude that the MDP binding site of NLRP1 is not located in the LRR domain.

Pathogen Sensing by Nucleotide-binding Oligomerization Domain-containing Protein 2 (NOD2) Is Mediated by Direct Binding to Muramyl Dipeptide and ATP

Nucleotide binding and oligomerization domain-containing protein 2 (NOD2/Card15) is an intracellular protein that is involved in the recognition of bacterial cell wall-derived muramyl dipeptide. Mutations in the gene encoding NOD2 are associated with inherited inflammatory disorders, including Crohn disease and Blau syndrome. NOD2 is a member of the nucleotide-binding domain and leucine-rich repeat-containing protein gene (NLR) family. Nucleotide binding is thought to play a critical role in signaling by NLR family members. However, the molecular mechanisms underlying signal transduction by these proteins remain largely unknown. Mutations in the nucleotide-binding domain of NOD2 have been shown to alter its signal transduction properties in response to muramyl dipeptide in cellular assays. Using purified recombinant protein, we now demonstrate that NOD2 binds and hydrolyzes ATP. Additionally, we have found that the purified recombinant protein is able to bind directly to muramyl dipeptide and can associate with known NOD2-interacting proteins in vitro. Binding of NOD2 to muramyl dipeptide and homo-oligomerization of NOD2 are enhanced by ATP binding, suggesting a model of the molecular mechanism for signal transduction that involves binding of nucleotide followed by binding of muramyl dipeptide and oligomerization of NOD2 into a signaling complex. These findings set the stage for further studies into the molecular mechanisms that underlie detection of muramyl dipeptide and assembly of NOD2-containing signaling complexes.

Binding of Dipeptides and Amino Acids to Teicoplanin Chiral Stationary Phase: Apparent Homogeneity of Some Heterogeneous Systems

The binding between Teicoplanin glycopeptide antibiotic and some dipeptides and amino acids has been studied by nonlinear liquid chromatography. A Teicoplanin-based chiral stationary phase, specifically designed to achieve maximum selectivity and loading by reducing non-specific interactions, has been prepared and packed into a microbore column. The adsorption isotherms of the enantiomers of proline, alanine, and alanine-alanine (Ala-Ala) have been measured through frontal analysis. The experimental binding data have been interpreted in the context of the ordinary homogeneous Michaelis-Menten model and by considering an heterogeneous model that accounts for a broad adsorption energy distribution (AED). AED has been achieved by the analysis of adsorption isotherms. Besides confirming the importance of the terminal D-Ala-D-Ala moiety in the molecular recognition between the dipeptide and the macrocyclic antibiotic Teicoplanin (it was found that Teicoplanin behaves as a molecular filter toward the enantiomers of Ala-Ala), this study shows that a heterogeneous adsorption model is needed for the correct interpretation of binding data.

The Molecular Recognition of Dipeptide by Oligoglycyl Head Group of Amphiphile: A Quantum Chemical Study

In the present work, we presented an analysis of the unusual recognition specificity exhibited by marked difference in the binding behavior of dipeptide with amphiphilic head group when subtle relative change of N-terminal and C-terminal of the dipeptide are made. Recently, in a series of detailed experiments, binding of aqueous dipeptides, GlyX and X/Gly (X = Leu, Phe, Pro, Ala; X/ = Leu, Phe) with dialkyl oligoglycyl amphiphiles is studied [X. Cha, K. Ariga, M. Onda, and T. Kunitake, J. Am. Chem. Soc. 117, 11833 (1995)]. It is observed that GlyX are specifically bound to 2C18BGly2NH2 while X/Gly are insignificantly bound. We first studied the conformational energy variation of GlyPhe, PheGly and model of 2C18BGly2NH2 amphiphile using semi-empirical and ab-initio methods in vacuum. Using the individual energy optimized monomer structure of amphiphile and peptide, we studied the binding energy of optimized GlyPhe: amphiphile pair and PheGly: amphiphile pair structures at 1:1 and 1:2 ratio at the same level of theory using a population of structures. Binding of GlyPhe is favorable over the binding of PheGly at various levels of theory (semi-empirical and ab-initio). It is noted that the hydrogen bonding pattern in the GlyPhe binding is more effective than that in the PheGly binding. In the population of low energy structures, PheGly: amphiphile structures have more exposed area around the hydrophobic Phe group than the GlyPhe: amphiphile structures. Relatively more PheGly: amphiphile structures have intermolecular orientation unsuitable to contribute to the population of head group structures relevant in aqueous interface. Summarizing, significantly better binding capacity of GlyPhe over the PheGly with amphiphile, is due to the difference in hydrogen bonding interaction pattern, hydrophobic effect and possible orientations of the amphiphile and peptide at interface, relevant to the condensed phase monolayer structure. All the three factors cooperatively lead to favorable recognition of GlyPhe over PheGly as observed in experiment. A calculation of the ratio of the amphiphile-peptide bound complex to the initial concentration of the amphiphile indicates that the diffusional process at the peptide interfaces could be significantly influenced by hydrogen bonding.

Substrate-binding Sites of UBR1, the Ubiquitin Ligase of the N-end Rule Pathway

Substrates of a ubiquitin-dependent proteolytic system called the N-end rule pathway include proteins with destabilizing N-terminal residues. N-recognins, the pathway's ubiquitin ligases, contain three substrate-binding sites. The type-1 site is specific for basic N-terminal residues (Arg, Lys, and His). The type-2 site is specific for bulky hydrophobic N-terminal residues (Trp, Phe, Tyr, Leu, and Ile). We show here that the type-1/2 sites of UBR1, the sole N-recognin of the yeast Saccharomyces cerevisiae, are located in the first approximately 700 residues of the 1,950-residue UBR1. These sites are distinct in that they can be selectively inactivated by mutations, identified through a genetic screen. Mutations inactivating the type-1 site are in the previously delineated approximately 70-residue UBR motif characteristic of N-recognins. Fluorescence polarization and surface plasmon resonance were used to determine that UBR1 binds, with a K(d) of approximately 1 microm, to either type-1 or type-2 destabilizing N-terminal residues of reporter peptides but does not bind to a stabilizing N-terminal residue such as Gly. A third substrate-binding site of UBR1 targets an internal degron of CUP9, a transcriptional repressor of peptide import. We show that the previously demonstrated in vivo dependence of CUP9 ubiquitylation on the binding of cognate dipeptides to the type-1/2 sites of UBR1 can be reconstituted in a completely defined in vitro system. We also found that purified UBR1 and CUP9 interact nonspecifically and that specific binding (which involves, in particular, the binding by cognate dipeptides to the UBR1 type-1/2 sites) can be restored either by a chaperone such as EF1A or through macromolecular crowding.

Synthesis of a new artificial host for the binding of dipeptides in water

An artificial peptide receptor was prepared by a simple procedure. Initial binding studies (UV titrations) in buffered water showed preferential complexation of N-acetyl-dipeptide carboxylates containing alanine in the C-terminal position in comparison with simple amino acids, other dipeptides and two tripeptides.

Sequence‐Dependent Binding of Dipeptides by an Artificial Receptor in Water

An artificial dipeptide receptor (1) was designed and observed to bind the deprotonated dipeptide Ac-D-Ala-D-Ala-OH in buffered water with K = 33,100 M(-1), whereas other dipeptides such as Ac-Gly-Gly-OH or Ac-D-Val-D-Val-OH were bound less efficiently, by factors of more than 10 (K < 3000 M(-1)). The efficient binding and the pronounced sequence selectivity are the result of a combination of strong electrostatic contacts and size-discriminating hydrophobic interactions. To provide such a combination, a guanidiniocarbonylpyrrole cation was attached to a novel cyclotribenzylene-substituted alanine derivative 5, to provide a hydrophobic bowl-shaped cavity just large enough to bind a methyl group but not any larger alkyl chains, thus causing the receptor to prefer alanine to valine. We describe the synthesis of 1 and the evaluation of its complexation properties in UV and fluorescence titration studies.

The study on the interaction between seryl-histidine dipeptide and proteins by circular dichroism and molecular modeling

The selective cleavage of proteins is very important in key biological processes. Chemical (nonenzymatic) reagents such as cyanogen bromide and transition metal complexes are used extensively with great defects. In this paper, the binding of seryl-histidine dipeptide (abbreviated as SH) with bovine serum albumin (BSA) and lysozyme were investigated by the circular dichroism spectroscopy (CD) at 298 K, molecular docking studies and quantum chemical calculations based on the previous results of polyacrylamide gel electrophoresis (PAGE). From the studies of CD, it showed that SH interacted strongly with BSA and lysozyme. The change percentages of the secondary structures of BSA and lysozyme were calculated. The contents of the β-sheets decreased remarkably. It indicated that the interactions between SH and proteins could break the hydrogen bonds of β-sheets selectively. The docking studies between SH and BSA showed that the position of the oxygen atom of the hydroxyl group of SH (O 12) was in favor of a nucleophilic attack on carbon atom of the amide bond of a β-sheet (C 34) because the distance between O 12 and C 34 was 3.37 Å. Natural charges, natural atomic hybrid percentages and square sums of HOMO coefficients calculated by the NBO and population analysis at HF/6-31G* supported the suggested mechanism. And so SH may be an interesting agent for the therapeutic use.

The Membrane-Associated Lipoprotein-9 GmpC from Staphylococcus aureus Binds the Dipeptide GlyMet via Side Chain Interactions,

Bacterial dipeptide ABC transporters function to import a wide range of dipeptide substrates. This ability to transport a wide variety of dipeptides is conferred by the cognate substrate binding protein (SBP) of these transporters. SBPs bind dipeptides with little regard for their amino acid content. Here, we report the 1.7 A resolution structure of lipoprotein-9 (SA0422) of Staphylococcus aureus in complex with the dipeptide glycylmethionine. Experimental characterization of the subcellular location of the protein confirmed that SA0422 is an acylated, peripheral membrane protein. This is the first structure determined for an SBP of a Gram-positive dipeptide ABC transporter. Usually, binding of dipeptides occurs in a binding pocket that is largely hydrated and able to accommodate the side chains of several different amino acid residues. Unlike any other known SBP, lipoprotein-9 binds the side chains of the glycylmethionine dipeptide through very specific interactions. Lipoprotein-9 shares significant structural and sequence homology with the MetQ family of methionine SBP. Sequence comparisons between MetQ-like proteins and lipoprotein-9 suggest that the residues forming the tight interactions with the methionine side chains of the ligand are highly conserved between lipoprotein-9 and MetQ homologues, while the residues involved in coordinating the glycine residue are not. Modeling of the Vibrio cholerae MetQ and lipoprotein-9 binding pockets can account for lipoprotein-9 substrate specificity toward glycylmethionine. For this reason, we have designated lipoprotein-9 GmpC, for glycylmethionine binding protein.

Residue- and sequence-selective binding of nonaromatic dipeptides by bis(beta-cyclodextrin) with a functional tether.

Do you recognise this peptide? Novel 6,6′-(2,2′-dithiobis(2-(benzoylamino)ethylamino))-bridged bis(β-CD), such as the one shown here, showed good to excellent residue selectivities of up to 28 for several nonaromatic dipeptides with the complex stability sequence of Glu-Glu < Gly-Gly < Leu-Gly < Met-Met < Gly-Pro < Gly-Leu, and also a high sequence selectivity of 5.0 for Gly-Leu versus Leu-Gly.

Molecular Mechanics Study of the Steric Structure of the Dipeptides Vilon and Thymogen

Molecular dynamics trajectories of two dipeptides, vilon (Lys-Glu) and thymogen (Glu-Trp), were traced up to 700 ps. Both structures comprise intramolecular salt bridges which make them less conformationally flexibile. Vilon is comparatively more flexible due to the aliphatic side chain of Lys, whereas thymogen is quite a rigid structure, which is defined by the mutual arrangement of salt bridges and aromatic rings in the side chain of Trp. A probable mechanism of ligand-receptor binding of dipeptides with excitable membrane was proposed. The binding can be effected via the nitrogen and oxygen atoms forming the salt bridges.

ChemInform Abstract: Binding of Dipeptides and Tripeptides Containing Lysine or Arginine by p‐Sulfonatocalixarenes in Water: NMR and Microcalorimetric Studies.

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Binding of dipeptides and tripeptides containing lysine or arginine by p-sulfonatocalixarenes in water: NMR and microcalorimetric studiesElectronic supplementary information (ESI) available: chemical shifts experienced by different protons of KK, RR, KKK or RRR in the presence of increasing amounts of 14 or 16; heat effects observed upon titration of 14, 16 or 18 by KK, RR, KKK or RRR; COSY

The water soluble p-sulfonatocalix[n]arenes (n = 4, 6 and 8) (14, 16 and 18) show glycosylaminoglycan (GAG) mimicry, being both active antithrombotics and modulators of lysyloxidase activity. In order to understand how these synthetic receptors interact with GAG receptor sequences, we have undertaken a study to thermodynamically characterize the binding of dipeptides and tripeptides bearing lysine or arginine residues by 14, 16 and 18 in aqueous buffer at pH 8.0 and 298.15 K. The association constants, enthalpies and entropies of complexation have been determined using titration microcalorimetry. The structure of the complexes in solution has been studied by 1H NMR spectroscopy. Combining the microcalorimetric data, the binding shifts and the 2D experiments, the nature of the complexation may be clarified.