Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “PAPAIN”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources
PubMed2005

Connecting traditional QSAR and molecular simulations of papain hydrolysis--importance of charge transfer.

Molecular dynamics and full structure LocalSCF semi-empirical quantum mechanics calculations of receptor-ligand complexes were carried out to investigate structure-activity relationship for the papain hydrolysis of a series of N-benzoylglycine esters and reinterpret traditional QSAR descriptors using detailed structural information. A correlation of r(2)=0.694 was obtained and it was shown that the pattern of charge distribution on the ester group is different if charges of free or complex ligands or are analyzed. The results can help to understand how traditional QSAR descriptors, such as F or sigma, interacts with other electronic effects during complex formation.

Computer Simulation↗
PubMed2006

Dipeptide vinyl sultams: synthesis via the Wittig-Horner reaction and activity against papain, falcipain-2 and Plasmodium falciparum.

The synthesis of phosphonate derivatives of N-phenyl- and N-benzyl-gamma- and delta-sultams, and their application in the Wittig-Horner reaction with N-Boc-L-phenylalanine aldehyde to afford E- and Z-isomers, are described. These compounds were further processed to provide five dipeptide vinyl sultams, which were found to be inactive against papain at concentrations up to 50 microM. In contrast, vinyl sultams demonstrated weak activity against recombinant falcipain-2 and Plasmodium falciparum W2.

Animals↗
PubMed2006

Bicyclic carbamates as inhibitors of papain-like cathepsin proteases.

A 6-oxa-1-aza-bicyclo[3.2.1]octan-7-one system inhibits the proteolytic activity of several cysteine proteases belonging to the papain family. In vitro mechanistic studies and in silico calculations suggest that the minimal pi-overlap between the bridgehead nitrogen and the carbonyl leads to a considerable weakening of the urethane system, making it susceptible to nucleophilic attack from the active site thiol group. The resulting covalent adduct is slowly hydrolyzed, releasing the hydroxypiperidine product of the inhibitor. Synthesis and testing of a set of analogs led to variable protease subtype selectivities ranging from micromolar to nanomolar potencies.

Binding Sites↗
PubMed2006

Inhibitory activity against papain, a CA1 cysteine peptidase, in Saccharomycetaceae.

A search for new biological sources of cysteine peptidase inhibitors has not only an academic aspect but is of great importance in medicine and biotechnology. The activity of CA1 peptidases can be inhibited by proteins of nine structurally different families. Although these inhibitors are widespread in nature, there is little information on them in yeast and in the kingdom of fungi overall. To gain insight into the endogenous inhibitors of CA1 cysteine peptidases in unicellular fungi, we initiated a study of the extra- and intracellular antipapain activity in yeast. We report here, for the first time, an analysis of the inhibitory activity against papain in the culture medium and the cell-free extract of 16 yeast strains belonging to the Saccharomycetaceae family. The existence of the antipapain activity, likely from protein inhibitors, in all the tested yeast strains has been demonstrated.

Culture Media↗
PubMed2002

A 40-kDa polypeptide from papain digestion of the rabbit intestinal Na+/phosphate cotransporter retains Na+ and phosphate cotransport.

The rabbit intestinal brush border membrane Na+/phosphate cotransporter was digested with a variety of proteolytic enzymes. Limited papain digestion generated a 40-kDa polypeptide (P40) which retained putative substrate site markers, fluorescein isothiocyanatophenyl glyoxal and eosin n-acetyl imidazole. P40 retained Na+- and phosphate-selective tryptophan fluorescence quenching, pH sensitivity of ion-induced conformational changes, and tight Na+ and H(2)PO(4)(-) binding. Reconstituted into proteoliposomes, P40 catalyzed Na+-dependent phosphate uptake. The N-terminus of P40 was blocked. An internal sequence of P40 demonstrated that it was derived from NaPi II b. These results suggest that P40 may be a useful model system for studies of the molecular mechanism of Na+-dependent phosphate cotransport and a starting point for structural studies.

Amino Acid Sequence↗
PubMed2000

Molecular dynamics of hinge-bending motion of IgG vanishing with hydrolysis by papain.

We have performed dielectric relaxation measurements via a time domain reflectometry (TDR) method to study dynamic behaviors of the segmental flexibility of immunoglobulin G (IgG) in aqueous solution without antigen binding. In general, an intermediate relaxation process due to bound water is observed around 100 MHz at 25 degrees C for common proteins between two relaxation processes due to overall rotation and reorientation of free water. However, the intermediate process observed around 6 MHz for IgG was due to both bound water and hinge-bending motion. The apparent activation energy of 33 kJ/mol was larger than 27 kJ/mol for only bound water, and the relaxation strength was about five times as large as expected for bound water. The shape of the relaxation curve was very broad and asymmetric. These characteristic differences arising from the hinge-bending motion of IgG disappeared for fragments decomposed from IgG hydrolyzed by papain, since the hinge-bending motion did not exist in this case. We have separated the relaxation processes due to hinge-bending motion and bound water for IgG and obtained the Fab-Fab angle of IgG as about 130 degrees by Kirkwood's correlation parameter and the activation energy of 34 kJ/mol for hinge-bending motion.

Animals↗
PubMed1976

Thin-layer chromatography for detection of peptide cleavage or integrity during reactions of the Z-alanylglycines with aniline or phenylhydrazine under papain catalysis.

Z-l-Ala-gly and Z-dl-ala-gly can yield anilides and phenylhydrazides through peptide cleavage or peptide integrity during papain-catalyzed reactions with aniline (NH2Ph) or phenylhydrazine (NH2NHPh). Since Z-d-ala-gly yielded only uncleaved Z-d-ala-gly-NHPh or Z-d-ala-gly-NHNHPh, these were used as standards in thinlayer chromatography (TLC) for detecting integrity. Known Z-l-ala-NHPh and Z-l-ala-NHNHPh were the standards for cleavage. Depending on the time of incubation, cleaved or unsplit products, or both, were readily detected. The solvent systems that were used for TLC were also effectively employed for separations of reasonable amounts of mixtures of cleaved and uncleaved products through thick-layer chromatography on Chrom AR. This was followed by isolation of the separated components.

Alanine↗
PubMed1998

Dual effect of actin on the accessibility of myosin essential light chain A1 to papain cleavage.

The influence of various amounts of actin on the proteolytic susceptibility of myosin essential light chain (ELC) A1, the binding of isolated A1 light chain and the N-peptide spanning N-terminal sequence of A1 to actin is studied to obtain more information on the role of the N-terminus of A1 light chain in the myosin-actin interaction. Low ratios of actin to myosin (1:1) lead to stimulate cleavage, whereas higher ratios (4:1) lead to protection of A1. Exposure of A1 by actin is especially seen in heavy meromyosin (HMM) and monomeric myosin and this is probably related to the full saturation of actin protomers with myosin heads. The protecting action of actin on A1 cleavage is more pronounced in myosin filaments. Conditions favoring the saturation of myosin regulatory light chain (RLC) with calcium ions instead of magnesium ions promotes the protection of A1. Cross-linking of HMM and actin results in higher yields of A1-actin product at high actin to myosin heads ratios. Isolated A1 light chain is pelleted by actin. A synthetic peptide spanning the N-terminal sequence of A1 can be cross-linked to actin. It is postulated that the protective action of actin on A1 papain cleavage is caused by the binding of the A1 N-terminus to actin. Changes in the RLC phosphorylation level and magnesium-for-calcium exchange in RLC may affect the probability of this interaction.

Actins↗
PubMed2001

The H1 double-stranded RNA genome of Ustilago maydis virus-H1 encodes a polyprotein that contains structural motifs for capsid polypeptide, papain-like protease, and RNA-dependent RNA polymerase.

The Ustilago maydis viral (UmV) genome consists of three distinct size groups of double-stranded RNA (dsRNA) segments: H (heavy), M (medium), and L (light). The H segments have been suggested to encode all essential viral proteins, but without any molecular evidences. As a preliminary step to understand viral genomic organization and the molecular mechanism governing gene expression in UmV, we determined the complete nucleotide sequence of the H1 dsRNA genome in P1 viral killer subtype. The H1 dsRNA genome (designated UmV-H1) contained a single open reading frame that encodes a polyprotein of 1820 residues, which is predicted to be autocatalytically processed by a viral papain-like protease to generate viral proteins. The amino-terminal region is the capsid polypeptide with a predicted molecular mass of 79.9 kDa. The carboxy-terminal region is the RNA-dependent RNA polymerase (RDRP) that has a high sequence homology to those of the totiviruses. The H2 dsRNA also encodes a distinct RDRP, suggesting that UmV is a complex virus system like the Saccharomyces cerevisiae viruses ScV-L1 and -La.

Amino Acid Sequence↗
PubMed1997

Proregion structure of members of the papain superfamily. Mode of inhibition of enzymatic activity.

Papain-like cysteine proteases have been divided into two subfamilies represented by mammalian enzymes cathepsin L and cathepsin B, respectively. The recent determination of the three-dimensional structures of four cysteine protease proenzymes showed that the mechanism of inhibition of the activity by the proregions is the same in both subfamilies despite significant differences in the proregion lengths. Here we describe the structures of the proregions, their binding to cognate enzymes and analyze similarities and differences between them.

Amino Acid Sequence↗
PubMed1997

Cysteine proteases such as papain are not inhibited by substrate analogue peptidyl boronic acids.

Peptidyl boronic acids that are close structural analogues of good substrates have been prepared and evaluated as potential transition state analogue inhibitors of the representative cysteine protease, papain. However, no inhibition could be detected at concentrations up to 10 mM. The reasons for the lack of inhibition were sought from molecular modeling. Molecular mechanics and semi-empirical quantum mechanics calculations indicated that the absence of inhibition was due to boronic acid-cysteine protease tetrahedral complexes being 0.79 kcal mol-1 less stable than their preceding noncovalent EI-complexes. In contrast, an analogous boronic acid-serine protease tetrahedral complex was calculated to be 2.74 kcal mol-1 more stable than its precursor Michaelis EI-complex. It thus appears that boronic acids are ineffective inhibitors of cysteine proteases due to the thermodynamic favoring of a weak EI-complex preceding tetrahedral intermediate formation, and that any oxyanion hole stabilization of the subsequent tetrahedral intermediate cannot overcome this energy handicap.

Boronic Acids↗
PubMed1991

Cooperativity of papain-substrate interaction energies in the S2 to S2' subsites.

Enzyme-substrate contacts in the hydrolysis of ester substrates by the cysteine protease papain were investigated by systematically altering backbone hydrogen-bonding and side-chain hydrophobic contacts in the substrate and determining each substrate's kinetic constants. The observed specificity energies [defined as delta delta G obs = -RT ln [(kcat/KM)first/(kcat/KM)second)]] of the substrate backbone hydrogen bonds were -2.7 kcal/mol for the P2 NH and -2.6 kcal/mol for the P1 NH when compared against substrates containing esters at those sites. The observed binding energies were -4.0 kcal/mol for the P2 Phe side chain, -1.0 kcal/mol for the P1' C=O, and -2.3 kcal/mol for the P2' NH. The latter three values probably all significantly underestimate the incremental binding energies. The P2 NH, P2 Phe side-chain, and P1 NH contacts display a strong interdependence, or cooperativity, of interaction energies that is characteristic of enzyme-substrate interactions. This interdependence arises largely from the entropic cost of forming the enzyme-substrate transition state. As favorable contacts are added successively to a substrate, the entropic penalty associated with each decreases and the free energy expressed approaches the incremental interaction energy. This is the first report of a graded cooperative effect. Elucidation of favorable enzyme-substrate contacts remote from the catalytic site will assist in the design of highly specific cysteine protease inhibitors.

Allosteric Regulation↗
PubMed1983

Primary structure of papain-solubilized human histocompatibility antigen HLA-B40 (-Bw60). An outline of alloantigenic determinants.

The primary structure of papain-solubilized human histocompatibility antigen HLA-B40 (-Bw60) has been determined. Its comparison with that of the cross-reactive HLA-B7 antigen allows for the first time a direct sequence comparison between two HLA-B locus products and an outline of the location of their alloantigenic sites. Overall sequence homology between HLA-B40 and HLA-B7 is 93%. Of 19 detected differences, 18 are located in the two amino-terminal domains (residues 1-182). Half of them are clustered in two short segments spanning residues 63-74 and 147-156, respectively, which suggests that they may encompass major sites of their alloantigenic determinants. The first of these segments is highly polymorphic in HLA and H-2 molecules. It is proposed that it may belong to a hypervariable region of class I histocompatibility antigens. The remaining substitutions are scattered through the N-terminal portions of the two external domains. Thus, in addition to the above-mentioned segments, other positions may contribute significantly to the antigenic polymorphism of these molecules.

Amino Acid Sequence↗
PubMed1985

Primary structure of papain-solubilized human histocompatibility antigen HLA-B27.

The complete amino acid sequence of papain-solubilized HLA-B27, an antigen that presents a very strong association to the development of ankylosing spondylitis, has been determined. The overall sequence homology with the cross-reactive allelic products HLA-B7 and HLA-B40 (Bw60) is 93% and 92%, respectively. Half of the differences between HLA-B27 and -B7 are located in segments 63-83 and 113-116. Most of the known HLA class I antigens are different in these segments, and it is suggested that the corresponding residues may be involved in the alloantigenic determinants of HLA-B27. A free cysteine residue is present at position 67, and it is at least partially exposed to solvent. In addition, other differences are found in various areas of the two N-terminal domains. The comparison with available HLA class I sequences allows an evaluation of their contribution to the antigenic polymorphism of these molecules. The relevance of these data is discussed in connection with the mapping of functional sites of HLA class I antigens and with the association between HLA-B27 and ankylosing spondylitis.

Amino Acid Sequence↗
PubMed1979

Chemical, physical-chemical, and immunological properties of papain-solubilized human transplatation antigens.

Papain-solubilized HLA-A, -B, and -C antigens have been isolated from cadaveric spleens. The isolated material was homogeneous and comprised subunits with the apparent molecular weights 33,000 and 12,000. Amino acid analyses of a mixture of HLA antigen heavy chains obtained from a great number of spleens with different HLA antigen phenotypes revealed a composition that is very similar to that of individual HLA-A and -B antigens. Likewise, the NH2-terminal 30 residues of the HLA-antigen heavy chain mixture were virtually identical with that recorded for individual specificities. The circular dichroism spectra for the isolated HLA antigens and for free beta2-microglobulin revealed similarities with spectra recorded for immunoglobulin chains and domains. The HLA-antigen heavy chain may contain an appreciable amount of beta structure. Antibodies raised against free beta2-microglobulin react better with beta2-microglobulin in free form than when bound to the HLA-A, -B, and -C antigen heavy chains. This is due to the fact that free beta2-microglobulin can bind a maximum of four Fab fragments simultaneously, whereas the HLA-antigen-associated beta2-microglobulin can bind only two Fab fragments without dissociating from the heavy HLA-antigen subunit.

Amino Acid Sequence↗
PubMed1979

Complete amino acid sequence of a papain-solubilized human histocompatibility antigen HLA-B7. 1. Isolation and amino acid composition of fragments and of tryptic and chymotryptic peptides.

As a part of the overall strategy for determining the complete covalent structure of the papain-solubilized portion of the heavy chain of the human histocompatibility antigen HLA-B7, the protein was dissected into various fragments by a combination of partial acid hydrolysis and cyanogen bromide cleavage. After purification by chromatographic procedures, these fragments have been used as a source for tryptic and chymotryptic peptides. Thirty-three major tryptic and twenty-two major chymotryptic peptides were purified in nanomole amounts and their amino acid compositions determined. These peptides account for the whole extent of the polypeptide chain with the exception of the amino-terminal CNBr pentapeptide. They provide the basis for the formal alignment of the acid cleavage and cyanogen bromide fragments of the molecule as well as the source material for the elucidation of the primary structure of the HLA-B7 heavy chain.

Amino Acid Sequence↗
PubMed1979

Complete amino acid sequence of a papain-solubilized human histocompatibility antigen, HLA-B7. 2. Sequence determination and search for homologies.

The complete amino acid sequence of the papain-solubilized heavy chain of a human histocompatibility antigen (HLA-B7) has been elucidated. It consists of a polypeptide of 271 residues (31 333 daltons). A single glycan moiety is attached to an asparagine residue at position 86 by an N-glycosidic bond. Two intrachain disulfide bonds, arranged linearly, involve half-cystine residues at positions 101 and 164 and at positions 203 and 259. They form two loops of 62 and 55 residues, respectively, separated by 38 residues. Computer analysis of the sequence suggests the existence of internal homology between the amino-terminal portion (residues 1--90) and the region of the first disulfide loop (residues 91--180). There is a significant homology between the second disulfide loop region of the chain (residues 182-271) and immunoglobulin (Ig) constant domains and beta 2-microglobulin [Orr, H. T., Lancet, D., Robb, R. J., López de Castro, J. A., & Strominger, J. L. (1979A) Nature (London) (in press)]. However, no such homology to Ig is apparent in the amino-terminal or in the first disulfide loop regions.

Amino Acid Sequence↗
PubMed1977

Thiohemiacetal formation by inhibitory aldehydes at the active site of papain.

Papain is strongly inhibited by aldehydes resembling carboxylic acids, released by hydrolysis of specific substrates (Westerik, J. O'C., and Wolfenden, R. (1972), J. Biol. Chem. 247, 8195-8197). Inhibitory complexes might involve binding of the aldehyde intact or as a covalent hydrate, or the aldehyde might undergo covalent addition of an active site sulfhydryl group to form a thiohemiacetal derivative. In an attempt to distinguish between these possibilities, benzamidoacetaldehyde-1-d has been synthesized, and its properties compared with those of the undeuterated inhibitor. After correction for differences in hydration, the observed effect on inhibition is found to be compatible with formation of a thiohemiacetal. In keeping with this conclusion, benzamidoethanol (a partial analogue of the covalent hydrate) and benzamide, N-methylbenzamide and N-ethylbenzamide (somewhat similar to the free aldehyde in size and hydrophobic character) are found to exhibit negligible affinity for the active site.

Acetaldehyde↗