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PubMed2006

The peptide-binding and ATPase domains of recombinant hsc70 are required to interact with rotavirus and reduce its infectivity.

The heat shock cognate protein hsc70 has been implicated as a postattachment cell receptor for rotaviruses. Here we show that hsc70 interacts specifically with rotaviruses through its peptide-binding domain, since a recombinant full-length hsc70 protein and its peptide-binding domain, but not its ATPase domain, bound triple-layered particles in a solid-phase assay, and known ligands of hsc70 competed this binding. The peptide ligands of hsc70 were also shown to block rotavirus infectivity when added to cells before virus infection, suggesting that hsc70 on the surface of MA104 cells also interacts with the virus through its peptide-binding domain and that this interaction is important for virus entry. When purified infectious virus was incubated with soluble hsc70 in the presence of the cochaperone hsp40 and ATP and then pelleted through a sucrose cushion, the recovered virus had lost 60% of its infectivity, even though hsc70 was not detected in the pellet fraction. The hsc70-treated virus showed slightly different reactivities with monoclonal antibodies and was more susceptible to heat and basic pHs than the untreated virus, suggesting that hsc70 induces a subtle conformational change in the virus that results in a reduction of its infectivity. The relevance of the ATPase activity of hsc70 for reducing virus infectivity was demonstrated by the finding that in the presence of a nonhydrolyzable analogue of ATP, virus infectivity was not affected, and a mutant protein lacking ATPase activity failed to reduce virus infection. Altogether, these results suggest that during cell infection, the interaction of the virus with hsc70 on the surface of MA104 cells results in a conformational change of virus particles that facilitates their entry into the cell cytoplasm.

Adenosine Triphosphatases↗

PubMed1995

Structural features of the invariant chain fragment CLIP controlling rapid release from HLA-DR molecules and inhibition of peptide binding.

The invariant chain (Ii) prevents binding of ligands to major histocompatibility complex (MHC) class II molecules in the endoplasmic reticulum and during intracellular transport. Stepwise removal of the Ii in a trans-Golgi compartment renders MHC class II molecules accessible for peptide loading, with CLIP (class II-associated Ii peptides) as the final fragment to be released. Here we show that CLIP can be subdivided into distinct functional regions. The C-terminal segment (residues 92-105) of the CLIP-(81-105) fragment mediates inhibition of self- and antigenic peptide binding to HLA-DR2 molecules. In contrast, the N-terminal segment CLIP-(81-98) binds to the Staphylococcus aureus enterotoxin B contact site outside the peptide-binding groove on the alpha 1 domain and does not interfere with peptide binding. Its functional significance appears to lie in the contribution to CLIP removal: the dissociation of CLIP-(81-105) is characterized by a fast off-rate, which is accelerated at endosomal pH, whereas in the absence of the N-terminal CLIP-(81-91), the off-rate of C-terminal CLIP-(92-105) is slow and remains unaltered at low pH. Mechanistically, the N-terminal segment of CLIP seems to prevent tight interactions of CLIP side chains with specificity pockets in the peptide-binding groove that normally occurs during maturation of long-lived class II-peptide complexes.

Amino Acid Sequence↗

PubMed1993

Identification of human immunodeficiency virus type 1 subtypes and their distribution in the Commonwealth of Independent States (Former Soviet Union) by serologic V3 peptide-binding assays and V3 sequence analysis.

Serologic V3 loop peptide-binding assays have been used to predict divergent human immunodeficiency virus type 1 (HIV-1) strains from the Commonwealth of Independent States (former Soviet Union) that have been subsequently confirmed by sequencing of the V3 region. Initial screening was done by MN V3 peptide binding; 12 parenterally infected HIV-1-positive subjects from Elista and Rostov (group 1) with low-titer MN binding and 6 heterosexually infected HIV-1-positive adults from Byelorussia (group 2) with high-titer MN binding were selected. A consensus sequence from the Elista and Rostov areas was generated; a corresponding 14-mer peptide was synthesized and used in an indirect ELISA to screen sera from 392 individuals from diverse geographic areas. Reactivity to the consensus peptide was 82% in subjects from the homologous areas and 11%-38% in other areas. Antibody binding to a panel of synthetic V3 peptides may be used to predict the presence of diverse strains of HIV-1 within virally heterogenous populations.

Amino Acid Sequence↗

PubMed1996

Alanine substitutions in calmodulin-binding peptides result in unexpected affinity enhancement.

Calmodulin is a calcium-binding protein that regulates a wide range of enzymes. It is also one of the few examples of a small protein capable of binding to peptides with very high affinity, and is therefore an interesting candidate for biotechnological applications and a good model system for studying how proteins associate. We have synthesized a complete series of peptides derived from the recognition sequence of skeletal muscle myosin light-chain kinase, corresponding to single-point amino acid mutations to alanine. These peptides bind to calmodulin with a biphasic kinetic: a fast association step followed by a slow intramolecular isomerisation. We have measured the isomerisation rate (k(isom)) of these peptides for calmodulin by stopped-flow analysis, and their association and dissociation kinetic constants (k(on) and k(off)) by real-time interaction analysis using surface plasmon resonance detection. In addition, k(off) constants were measured by competition experiments using a high-sensitivity luminescence analyser and native polyacrylamide gels. We have observed that all the alanine-scanning peptides bound to calmodulin with better affinity than the wild-type. In one case, a Asn-->Ala substitution resulted in a 1000-fold improvement in affinity, owing to a slower off-rate. Our results indicate that naturally occurring calmodulin binders may have evolved to have high affinities, but far from the maximum. Our affinity data are in contrast with recently published predictions of interactions responsible for high-affinity calmodulin binding based on modelling and energy calculations.

Alanine↗

PubMed2001

Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations.

Peptides are key immune targets. They are generated by fragmentation of antigenic proteins, selected by major histocompatibility complex (MHC) molecules and subsequently presented to T cells. One of the most selective requirements is that of peptide binding to MHC. Accurate descriptions and predictions of peptide-MHC interactions are therefore important. Quantitative matrices representing MHC class I specificity can be used to search any query protein for the presence of MHC binding peptides. Assuming that each peptide residue contributes to binding in an additive and sequence independent manner, such "crude" matrix-driven predictions can be expressed as a quantitative estimates of binding strength. Crude matrix-driven predictions are reasonably uniform (i.e. precise), however, there is a general tendency towards overestimating binding (i.e. being inaccurate). To evaluate and possibly improve predictions, we have measured the MHC class I binding of a large number of peptides. In an attempt to further improve predictions and to include sequence dependency, we subdivided the panel of peptides according to whether the peptides had zero, one or two primary anchor residues. This allowed us to define unique anchor-stratified calibrations, which led to predictions of improved precision and accuracy.

Animals↗

PubMed1996

Identification of calmodulin-binding peptide consensus sequences from a phage-displayed random peptide library.

The calcium-binding protein, calmodulin (CaM), was used to screen a phage library displaying random peptides 26 amino acids (aa) in length. Twenty CaM-binding peptides were identified, 17 of which contained one of three consensus sequence motifs: + W-OlambdaR, WRAAV or WRXXAAAL, where +, -, O, lambda and X are positively charged, negatively charged, hydrophobic, leucine or valine, and any residue, respectively. The Trp residue in these motifs is located within 14 aa of the N-terminus of the displayed peptide. Previous studies [Dedman et al., J. Biol. Chem. 268 (1993) 23025-23030] using a library displaying random peptides 15 aa in length identified CaM-binding peptides which contained a Trp-Pro dipeptide motif. These results suggest that the type of CaM-binding motif identified can vary between different types of combinatorial peptides.

Amino Acid Sequence↗

PubMed1984

[Determination of enzymatic catalysis for the cis-trans-isomerization of peptide binding in proline-containing peptides].

The rates of cis to trans interconversion of Glt-(Ala)n-Pro-Phe-4-nitroanilides (n = 1-3) were estimated by means of a two-step process with chymotrypsin as the trans-substrate cleaving activity. By the aid of this system, pig kidney and several other tissues contained demonstrable catalytic activity against the cis to trans interconversion of the proline containing peptides. The active protein fraction was purified 38-fold from pig kidney cortex by ammonium sulfate precipitation and a series of column chromatographic techniques. Activity was detected against the cis to trans interconversion of Glt-Ala-Ala-Pro-Phe-4-nitroanilide to a different extent. No activity was found with Phe-Pro-4-nitroanilide. With respect to the substrate specificity, this enzyme must be classified as a peptidyl-prolyl cis-trans-isomerase. The enzyme was strongly inactivated by p-chloromercuribenzoate, sodium dodecylsulfate, Hg2+- and Cu2+-ions, but was not inhibited by metal chelators, diisopropylphosphorofluoridate and chlorotosylamidophenylbutane. The activity is abolished by incubation with trypsin. The enzyme is heat sensitive at 50 degrees C. The results presented in this paper suggest a new type of enzymes, characterized by catalytic activity against conformational interconversions. The possibility of the location of the enzyme on ribosomal particles is discussed.

Amino Acid Isomerases↗

PubMed2006

Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides.

MOTIVATION: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and hypersensitivity reactions. Sequence-based computational techniques for predicting HLA-DQ binding peptides have encountered limited success, with few prediction techniques developed using three-dimensional models. METHODS: We describe a structure-based prediction model for modeling peptide-DQ3.2beta complexes. We have developed a rapid and accurate protocol for docking candidate peptides into the DQ3.2beta receptor and a scoring function to discriminate binders from the background. The scoring function was rigorously trained, tested and validated using experimentally verified DQ3.2beta binding and non-binding peptides obtained from biochemical and functional studies. RESULTS: Our model predicts DQ3.2beta binding peptides with high accuracy [area under the receiver operating characteristic (ROC) curve A(ROC) > 0.90], compared with experimental data. We investigated the binding patterns of DQ3.2beta peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders.

Antibodies↗

PubMed2005

Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR.

Complexes of the HIV transactivation response element (TAR) RNA with the viral regulatory protein tat are of special interest due in particular to the plasticity of the RNA at this binding site and to the potential for therapeutic targeting of the interaction. We performed REDOR solid-state NMR experiments on lyophilized samples of a 29 nt HIV-1 TAR construct to measure conformational changes in the tat-binding site concomitant with binding of a short peptide comprising the residues of the tat basic binding domain. Peptide binding was observed to produce a nearly 4 A decrease in the separation between phosphorothioate and 2'F labels incorporated at A27 in the upper helix and U23 in the bulge, respectively, consistent with distance changes observed in previous solution NMR studies, and with models showing significant rearrangement in position of bulge residue U23 in the bound-form RNA. In addition to providing long-range constraints on free TAR and the TAR-tat complex, these results suggest that in RNAs known to undergo large deformations upon ligand binding, 31P-19F REDOR measurements can also serve as an assay for complex formation in solid-state samples. To our knowledge, these experiments provide the first example of a solid-state NMR distance measurement in an RNA-peptide complex.

Binding Sites↗

PubMed2004

Endolysosomal processing of exogenous antigen into major histocompatibility complex class I-binding peptides.

An alternative endolysosomal pathway has recently been suggested for the processing of MHC-I-binding peptides, and peptide/MHC-I complexes have been demonstrated in this compartment. However, it remains unclear where in the antigen-presenting cells such peptides are processed, in the endolysosomes themselves or in the proteasomal complex. Here, we have investigated this using monoclonal antibodies specific for the immunodominant SIINFEKL/Kb complex (25-D1) or for the carbohydrate part of Db- or Kb-binding glycopeptides in combination with inhibitors for classical and endolysosomal MHC-I-processing pathways. Alternative processing was detected in both wt and TAP1(-/-) immature DC (iDC) as the expression of SIINFEKL/Kb complexes on the surface of OVA-treated cells in the presence of Brefeldin A (BFA) or lactacystin and their absence in the presence of the lysosomotropic amines ammonium chloride, chloroquine and methylamine. Internalized Db- and Kb-binding glycopeptides, detected with high specificity using an anti-galabiose (Gal2) monoclonal antibody, were found to appear on the cell surface of BFA-treated cells after intracellular MHC-I-binding. Peptide exchange in Kb was demonstrated as the gradual appearance of SIINFEKL/Kb complexes on BFA-treated cells which earlier had been saturated with another Kb-binding peptide. Our data support the presence of a fully functional endolysosomal processing pathway in iDC guided by the chaperone function of MHC-I molecules.

Animals↗

PubMed1992

The peptide binding specificity of HLA class I molecules is largely allele-specific and non-overlapping.

To understand better the specificity of peptide binding by MHC class I molecules, we have evaluated the capacity of a panel of unrelated peptides to compete for the presentation of viral peptides presented by HLA-A3 and HLA-B27. The HIV-Nef7F peptide (74-82) was presented by HLA-A3 to Nef-specific HLA-A3-restricted CTL lines, and the influenza nucleoprotein peptide NP(380-393) was presented by HLA-B27 to NP(380-393)-specific HLA-B27-restricted CTL lines. In addition, we have extended studies from our group that have evaluated the capacity of a similar panel of peptides to inhibit presentation of an influenza nucleoprotein peptide NP (335-349) by HLA-B37 and a matrix peptide, M1 (57-68), by HLA-A2 to the appropriate peptide-specific CTL lines. Out of 41 peptides tested, only five bound to more than one of the MHC molecules analyzed. Pairwise comparisons of the peptide binding specificities among these four different class I molecules revealed no common competitor peptides in four of the six possible comparisons. Thus, each class I molecule appears to have a functionally distinct peptide binding site, as reflected by the ability to bind largely non-overlapping sets of peptides.

Adult↗

PubMed2005

1.15 A crystal structure of the X. tropicalis Spred1 EVH1 domain suggests a fourth distinct peptide-binding mechanism within the EVH1 family.

The recently described Spred protein family has been implicated in the modulation of receptor tyrosine kinase signalling. We report the crystal structure of the Enabled/vasodilator-stimulated phosphoprotein homology-1 (EVH1) domain from Xenopus tropicalis Spred1, solved to 1.15 A resolution. This structure confirms that the Spred EVH1 adopts the pleckstrin-homology fold, with a similar secondary structure to Enabled. A translation of one of the peptide-binding groove beta-strands narrows this groove, whilst one end of the groove shows structural flexibility. We propose that Spred1 will bind peptides that are less proline-rich than other EVH1 domains, with conformational changes indicating an induced fit.

Amino Acid Sequence↗

PubMedDate not supplied

Isolation of mercury-binding peptides in vegetative parts of Chromolaena odorata.

Mercury-binding peptides from roots, stems, and leaves of Hg-treated Chromolaena odorata plants were isolated and partially characterized using RP-HPLC and ESI-MS. Upon exposure of C. odorata plants to high concentrations of 1.0 and 2.0 microM Hg(NO3)2 treatments from 0-28 days, they accumulated as much as 125 mg/g (dry wt) Hg in the roots, 15.280 mg/g (dry wt) Hg in the stems, and 0.800 mg/g (dry wt) Hg in the leaves indicating that C. odorata has a high potential as a phytoremediation agent of inorganic mercury. The plant's ability to accumulate and sequester Hg ions was primarily attributed to the production of Hg-binding peptides, which were initially detected through the use of Ellman's reagent. Isolation techniques using RP-HPLC equipped with a C18 column manifested a single prominent peak consistently appearing at a retention time of 2.6-2.8 min in all the plant samples treated with different Hg concentrations at varying lengths of exposure. Further characterization of this prominent peak using electrospray ionization mass spectrometry revealed the presence of a peptide containing several cysteine residues with the highest peak concentration recorded at 91 mV and 89 mV in roots and stems of plants treated with 2.0 microM Hg(NO3)2 for 4 wk (P < 0.05) and 85 mV in leaves treated with 1.0 microM Hg(NO3)2 for 1 wk.

Biodegradation, Environmental↗

PubMed1992

Synthesis and characterization of a 29-amino acid residue DNA-binding peptide derived from alpha/beta-type small, acid-soluble spore proteins (SASP) of bacteria.

A 29-amino acid residue peptide (SASP-peptide) derived from the sequence of the putative DNA-contacting portion at the carboxyl terminus of an alpha/beta-type small, acid-soluble spore protein (SASP) of Bacillus subtilis has been synthesized by automated solid-phase methods and tested for its ability to interact with DNA. Circular dichroism (CD) spectroscopy reveals an interaction between this SASP-peptide and DNA, both by an increase in alpha-helix content of the peptide (which alone has a mostly random conformation) and by enhancement of the 275-nm CD band of the DNA. In contrast to results with intact alpha/beta-type SASP, however, the peptide does not induce a B----A conformational transition in the DNA. The SASP-peptide also binds to poly(dG).poly(dC) and protects this polynucleotide against DNase I digestion and UV light-induced cytosine dimer formation, parallel to findings made previously with native alpha/beta-type SASP. The results confirm the hypothesis that the carboxyl-terminal region of the alpha/beta-type SASP directly contacts DNA and possesses some, but not all, of the functional characteristics of the intact molecule.

Amino Acid Sequence↗

PubMed2002

Selection of RNA-binding peptides containing Arg-rich motif.

In order to search the RNA-binding peptides, selection from randomized peptides containing Arg-rich motif was carried out using rRNA-immobilized column. As a result of the selection for 16S- and 23S-rRNA from E. coli, six peptides were identified to be the rRNA-binding peptide by MALDI-TOF MS. These peptides contained R, N, Q, or G at three randomized positions. This result indicates that amino acids with a positive residue or an amide residue might be essential for peptides to recognize the RNA.

Amino Acid Motifs↗

PubMedDate not supplied

Identification of CD21-binding peptides with phage display and investigation of binding properties of HPMA copolymer-peptide conjugates.

Cancer targeting with peptides has become promising with the emergence of combinatorial peptide techniques such as phage display. Using phage display under stringent screening conditions, we selected five distinct peptides that specifically recognized the CD21 receptor, a cell surface marker of malignant B cell lymphoma. Two highly hydrophobic sequences were excluded (RLAYWCFSGLFLLVC and PVAAVSFVPYLVKTY). The binding affinity toward CD21 of the other three selected peptides (RMWPSSTVNLSAGRR, PNLDFSPTCSFRFGC, and GRVPSMFGGHFFFSR) was analyzed with fluorescence quenching. Their dissociation constants were determined to be within the micromolar range. On the basis of the results of phage ELISA, competitive phage ELISA, and fluorescence quenching, the binding sites of the three selected peptides were found to reside within the first four short consensus repeats of CD21 (SCR1-4). The peptide RMWPSSTVNLSAGRR (P1) was bound to the N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer, a potential drug carrier for chemotherapeutic agents, and the surface binding properties of HPMA copolymer-P1 conjugates were investigated. Specific interactions were observed between HPMA copolymer-P1 conjugates and surface-bound receptor. Binding of HPMA copolymer-P1 conjugates was directly related to the amount of surface (MaxiSorp plate) bound receptor, and the binding of the conjugates could be inhibited by the application of a 3-4 orders-of-magnitude excess of free peptide over the peptide concentration in conjugates. The enhanced binding of polymer-bound peptide was ascribed to multivalent interactions between the HPMA copolymer-P1 conjugate and the surface-bound CD21 receptor.

Amino Acid Sequence↗

PubMed1993

Real-time measurement of antigenic peptide binding to empty and preloaded single-chain major histocompatibility complex class I molecules.

Cytotoxic T lymphocytes (CTL) recognize peptides in association with major histocompatibility complex (MHC) class I proteins, but how peptides bind to class I is not well understood. We used a fluorescence technique to measure antigenic peptide binding to a soluble, single-chain Kd (SC-Kd) molecule in which the Kd heavy chain was connected by a 15-residue link to beta 2-microglobulin. Peptides were covalently labeled at their N terminus with dansyl, and binding of dansylated Kd-restricted peptides to SC-Kd resulted in significant fluorescence enhancement, which could be inhibited by unmodified Kd-restricted peptides. Real-time binding of a dansylated peptide could be followed by monitoring the fluorescence at 530 nm. The dansylated Plasmodium berghei circumsporozoite (PbCS) 263-260 peptide bound to "empty" SC-Kd with an association rate constant of 1140 M-1s-1, and the subsequent spontaneous dissociation of the SC-Kd-peptide complex was slow. The dissociation increased dramatically after addition of excess unlabeled PbCS 253-260 peptide, but with a slower association constant for unlabeled peptide, 77 M-1s-1. Thus, the Kd-peptide complex on the surface of antigen-presenting cells should be stable, but high concentrations of peptides in the endoplasmic reticulum (ER) lumen would allow for peptide exchange on Kd before export to the surface. The apparent activation energy for PbCS 253-260 peptide binding to SC-Kd was 6.78 +/- 0.64 kcal/mole, similar to values previously reported for antigen-antibody interactions.

Amino Acid Sequence↗

PubMed1998

On the kinetics of peptide binding to MHC proteins.

An experimental study of kinetics of peptide binding to MHC proteins [S. Witt, H. McConnell, Acc. Chem. Res. 26 (1993) 442 (and references therein)] showed an unusual phenomenon of the so-called 'negative' t1/2 plots (where t1/2 is half time of reaching equilibrium concentration of peptide-protein complexes), which is the shorter t1/2 at lower added peptide concentrations. The bell-shaped curve for t1/2 as a function of peptide concentration is a seemingly peculiar effect, because in general, binding reactions go faster with an increase of reagent concentrations. It is shown that the suggested explanation of this phenomenon [S. Witt, H. McConnell, Acc. Chem. Res. 26 (1993) 442 (and references therein)] is misleading (and the numerical simulation used to support this explanation is inconsistent with the experimental data), so that the existence of 'negative' t1/2 is in no way to be considered as an experimental indication of the two-step reaction of peptide binding to protein. This article gives a consistent explanation of the bell-shaped t1/2 plots for peptide-protein association and obtains the criteria for its existence, based exclusively on the formal chemical kinetics analysis of the accepted peptide-protein binding model and briefly discusses the experimental data, which really confirm the existence of the two-step mechanism of binding. The analysis of the maximum location of the half-time curves indicates a controversy between the prediction of the two-step binding model and the experimental data [S. Witt, H. McConnell, Acc. Chem. Res. 26 (1993) 442 (and references therein)]: either more complicated mechanism is involved in peptide-MHC binding or experimental data [S. Witt, H. McConnell, Acc. Chem. Res. 26 (1993) 442 (and references therein)] are not quite accurate.

Algorithms↗