SEARCH · PubMed Health

Results for “cryptic proteins”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 145 records · Page 8Linked to original sources

PubMedDate not supplied

Characterization of two novel pre-B-cell lines (LK63 and LiLa-1): potential models of pre-B-cell differentiation.

In this report we describe two newly isolated pre-B acute lymphoblastic leukaemia cell lines. Both cell lines lack EBV as detected by the EBNA-1 gene probed Southern-blots. Neither cell line expressed the B-cell-specific CD20 antigen on the cell membrane. However surface expression of CD20 was induced by phorbol ester (TPA) on both LiLa-1 and LK63 cell lines. Other pre-B and B-cell lines, such as Reh, Nalm-1, and BALL-1 did not exhibit these changes in phenotype. Previous immunoprecipitation studies have noted that a broad 50-55 kD band co-precipitates with the characteristic 33-37 kD CD20 protein. We demonstrate that, while the 33-37 kD CD20 species was undetectable on resting LiLa-1 and LK63 cells, in each case a 50-55 kD protein was immunoprecipitated by the CD20 antibody. However, the failure to detect any cell surface CD20-associated antigen on the control cells by immunophenotyping indicated that the CD20 epitope of the 50-55 kD molecule was not expressed on the cell surface. Following exposure to TPA the 50-55 kD species was reduced over 48-72 h while the level of the p33-37 CD20 protein was increased. Northern-blot analysis showed that the 50-55 kD protein was not a cryptic form of CD20 as the uninduced cells contained no detectable CD20 mRNA. The decrease of the 50-55 kD protein and the acquisition of the mature CD20 molecule were paralleled by a decline in proliferative activity in both cell lines. As expression of CD20 by normal pre-B cells also coincides with the cessation of cell division and maturation towards a mature B-cell phenotype, these cell lines appear to represent models for a discrete stage of B-cell differentiation which may be valuable in defining the signals regulating pre-B-cell proliferation.

Antigens, CD↗

PubMed2004

Cryptic endotoxic nature of Bacillus thuringiensis Cry1Ab insecticidal crystal protein.

Cry1Ab is one of the most studied insecticidal proteins produced by Bacillus thuringiensis during sporulation. Structurally, this protoxin has been divided in two domains: the N-terminal toxin core and the C-terminal portion. Although many studies have addressed the biochemical characteristics of the active toxin that corresponds to the N-terminal portion, there are just few reports studying the importance of the C-terminal part of the protoxin. Herein, we show that Cry1Ab protoxin has a unique natural cryptic endotoxic property that is evident when their halves are expressed individually. This toxic effect of the separate protoxin domains was found against its original host B. thuringiensis, as well as to two other bacteria, Escherichia coli and Agrobacterium tumefaciens. Interestingly, either the fusion of the C-terminal portion with the insecticidal domain-III or the whole N-terminal region reduced or neutralized such a toxic effect, while a non-Cry1A peptide such as maltose binding protein did not neutralize the toxic effect. Furthermore, the C-terminal domain, in addition to being essential for crystal formation and solubility, plays a crucial role in neutralizing the toxicity caused by a separate expression of the insecticidal domain much like a dot/anti-dot system.

Agrobacterium tumefaciens↗

PubMed2004

Angiostatin.

The quiescent vascular system in the adult body represents the imbalanced net outcome of overproduction of endogenous angiogenesis inhibitors and reduced levels of angiogenic factors. While some endogenous inhibitors are expressed under physiological conditions, they can also be generated in association with tumor growth. Angiostatin is such a specific angiogenesis inhibitor produced by tumors. It inhibits primary and metastatic tumor growth by blocking tumor angiogenesis. Having demonstrated potent antitumor activity in animal studies, angiostatin is now in clinical trials for human cancer therapy. Angiostatin is not a novel protein molecule coded by novel DNA sequences. Instead, it is an internal proteolytic fragment of a known protein, plasminogen. Surprisingly, most kringle domains of plasminogen only inhibit angiogenesis when cleaved as fragments from their parent protein that lacks antiangiogenic activity. These findings suggest that they are cryptic fragments hidden in large protein molecules. Thus, proteolytic processing plays a critical role in down-regulation of angiogenesis. Despite proteolytic processing, the antiangiogenic mechanism of angiostatin remains an enigma. Without knowing the mechanisms, it is difficult to predict the ultimate outcome of ongoing clinical trials. In this article, we discuss what is known about angiostatin and how this molecule specifically inhibits angiogenesis. We hope that the information will be useful for further development of angiostatin and its related inhibitors as therapeutic agents.

Angiogenesis Inhibitors↗

PubMed2002

Kringle structures and antiangiogenesis.

The quiescent vascular system in the adult body represents the balanced net outcome of overproduction of endogenous angiogenesis inhibitors and reduced levels of angiogenic factors. While these inhibitors are expressed under physiological conditions, they are also generated in association with tumor growth. Angiostatin is such a specific angiogenesis inhibitor produced by tumors. It inhibits primary and metastatic tumor growth by blocking tumor angiogenesis. Encouraged by its potent anti-tumor activity, angiostatin is in clinical trials for cancer therapy. Angiostatin contains the first four triple loop structures, known as kringle domains, of plasminogen. The disulfide bond-linked kringle architectures are essential for the antiangiogenic activity of angiostatin. Based on this initial finding, recent work shows that kringle fragments of several other proteins also inhibit angiogenesis. Thus, kringle domains may provide a structural basis for identification of novel angiogenesis inhibitors. Surprisingly, most kringles only inhibit angiogenesis when cleaved as fragments from their parental proteins that lack antiangiogenic activity. These findings suggest that they are cryptic fragments hidden in large protein molecules. Thus, proteolytic processing plays a critical role in down regulation of angiogenesis. The kringle structure may provide the first example of a conserved architecture that specifically inhibits blood vessel growth. This review will focus on the structural and functional relationships of kringle domains in regulation of angiogenesis and tumor growth.

Angiogenesis Inhibitors↗

PubMed1996

Regulation of vinculin binding to talin and actin by phosphatidyl-inositol-4-5-bisphosphate.

Vinculin, a prominent cytoskeletal protein at cell-substrate adhesions (focal adhesions) and cell-cell adhesions (adherens junctions), interacts with other cytoskeletal proteins, including talin and actin. An intramolecular interaction between the head and tail domains of vinculin masks the binding sites for both proteins. The exposure of cryptic binding sites may be important for promoting focal adhesion assembly. Several agents that induce the formation of focal adhesions act through the GTP-binding protein Rho, which elevates phosphatidylinositol-4,5-bisphosphate (PtdInsP2) levels by activating phosphatidyl-inositol-4-phosphate-5-OH kinase (PtdIns-5-OH kinase). PtdInsP2 regulates several actin-binding proteins, including profilin, gelsolin and alpha-actinin, and interacts with vinculin. Here we report that PtdInsP2 dissociates vinculin's head-tail interaction, unmasking its talin- and actin-binding sites. Microinjection of antibodies against PtdInsP2 inhibit assembly of stress fibres and focal adhesions.

3T3 Cells↗

PubMed1997

Wild-type Escherichia coli grows on the chitin disaccharide, N,N'-diacetylchitobiose, by expressing the cel operon.

We report here that wild-type Escherichia coli can grow on the chitin disaccharide, N,N'-diacetylchitobiose (GlcNAc)2, as the sole source of carbon. Transposon mutants were isolated that were unable to ferment (GlcNAc)2 but grew normally on the monosaccharide GlcNAc. One such mutant was used to screen a wild-type E. coli genomic cosmid library for restoration of (GlcNAc)2 fermentation. A partial sequence analysis of the isolated fragment mapped the clone to the (previously sequenced) E. coli genome between 39.0 and 39.2 min. The nucleotide ORFs at this region had been previously assigned to code for a "cryptic" cellobiose utilization (cel) operon. We report here, however, that functional analysis of the operon, including growth and chemotaxis, reveal that it encodes a set of proteins that are not cryptic, but are induced by (GlcNAc)2 and catabolize the disaccharide. We therefore propose to rename the cel operon as the chb (N,N'-diacetylchitobiose) operon, with the letter designation of the genes of the operon to be reassigned consistent with the nomenclature based on functional characterization of the gene products as follows: celA to chbB, celB to chbC, celC to chbA, celD to chbR, and celF to chbF. Furthermore, sequencing evidence indicates that the operon contains an additional gene of unknown function to be designated as chbG. Thus, the overall gene sequence is to be named chbBCARFG.

Cellulase↗

PubMed2005

A cryptic Rab1-binding site in the p115 tethering protein.

Small GTPases and coiled-coil proteins of the golgin family help to tether COPI vesicles to Golgi membranes. At the cis-side of the Golgi, the Rab1 GTPase binds directly to each of three coiled-coil proteins: p115, GM130, and as now shown, Giantin. Rab1 binds to a coiled-coil region within the tail domain of p115 and this binding is inhibited by the C-terminal, acidic domain of p115. Furthermore, GM130 and Giantin bind to the acidic domain of p115 and stimulate p115 binding to Rab1, suggesting that p115 binding to Rab1 is regulated. Regulation of this interaction by proteins such as GM130 and Giantin may control the membrane recruitment of p115 by Rab1.

Animals↗

PubMed1992

Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa.

The nucleotide sequence of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa, was determined. The termini of the 7-kb plasmid are 349-bp inverted repeats (TIRs). Each DNA strand contains a long open reading frame (ORF) which begins within the TIR and extends toward the centre of the plasmid. ORF-1 codes for a single-subunit RNA polymerase that is not closely related to that encoded by another Neurospora plasmid, kalilo. The ORF-2 product may be a B-type DNA polymerase resembling those encoded by terminal protein-linked linear genetic elements, including linear mitochondrial plasmids and linear bacteriophages. A separate coding sequence for the terminal protein could not be identified; however, the DNA polymerase of maranhar has an amino-terminal extension with features that are also present in the terminal proteins of linear bacteriophages. The N-terminal extensions of the DNA polymerases of other linear mitochondrial plasmids contain similar features, suggesting that the terminal proteins of linear plasmids may be comprised, at least in part, of these cryptic domains. The terminal protein-DNA bond of maranhar is resistant to mild alkaline hydrolysis, indicating that it might involve a tyrosine or a lysine residue. Although maranhar and the senescence-inducing kalilo plasmid of N. intermedia are structurally similar, and integrate into mitochondrial DNA by a mechanism thus far unique to these two plasmids, they are not closely related to each other and they do not have any nucleotide sequence features, or ORFs, that distinguish them clearly from mitochondrial plasmids which are not associated with senescence and most of which are apparently non-integrative.

Amino Acid Sequence↗

PubMed1996

Harnessing self-reactivity in cancer immunotherapy.

Recent years have witnessed a significant advance in our understanding of the immune response to cancer through the identification of human tumor antigens at the molecular level. The growing list of normal self proteins recognized on tumors by T cells of cancer patients is consistent with the existence in humans of a self-reactive T-cell repertoire analogous to that described in murine models of autoimmune disease. The presence of these cells in normal individuals reveals the benign self-reactivity which lies dormant in the T-cell repertoire of humans. These autoreactive T cells, although pathogenic when activated in autoimmune disease, could be directed towards a beneficial effect in tumor immunotherapy. Potential targets for such a limited anti-self/anti-tumor immune response include overexpressed proteins, tissue-specific differentiation antigens and developmental proteins expressed aberrantly in tumor cells. Depending on the determinant chosen, recruitment of these self-directed T cells may require overcoming some degree of non-deletional peripheral tolerance. By specifically targeting immune responses to subdominant and cryptic determinants from these proteins, it may be possible to maximize the anti-tumor effect resulting from self-directed immunity while minimizing unwanted damage to normal tissue.

Animals↗

PubMed1989

Anaphylaxis to infusion of autologous bone marrow: an apparent reaction to self, mediated by IgE antibody to bovine serum albumin.

A case of anaphylaxis during autologous bone marrow infusion is reported. The patient was demonstrated to be skin test positive to fetal calf serum used in the cryopreservation of his bone marrow cells. The patient's serum was demonstrated to contain IgE antibody directed against bovine serum albumin. A second aliquot of the patient's bone marrow preparation was depleted of contaminating bovine proteins, and the patient successfully received a transplant and was engrafted. Clinicians need to be aware that the increasing use of biologic response modifiers, both as whole cells and effector molecules manipulated or produced in vitro, may lead to cryptic reactions to xenogeneic proteins.

Adult↗

PubMed1998

Exposure of the cryptic Arg-Gly-Asp sequence in thrombospondin-1 by protein disulfide isomerase.

Thrombospondin-1 is a matrix protein that inhibits proliferation, motility and sprouting of endothelial cells in vitro and angiogenesis in vivo. One mechanism by which thrombospondin-1 may influence endothelial cell biology is through interaction with the endothelial cell alphav beta3 integrin receptor. This interaction is mediated via a cryptic Arg-Gly-Asp sequence in the C-terminal Ca2+-binding region of thrombospondin-1. Exposure of the Arg-Gly-Asp sequence is controlled by disulfide interchange events in the Ca2+-binding loops and C-globular domain. Limited reduction of thrombospondin-1 by dithiothreitol exposes the Arg-Gly-Asp sequence which can bind to the alphav beta3 integrin receptor and support endothelial cell spreading (X. Sun, K. Skorstengaard, D.F. Mosher, J. Cell Biol. 118 (1992) 693-701). Our aim was to identify possible physiological reductants that can mediate Arg-Gly-Asp exposure. We now report that protein disulfide isomerase, which is known to catalyze disulfide interchange in thrombospondin-1 and change its enzyme inhibitory properties and its binding to monoclonal antibodies, was secreted by bovine aortic endothelial cells and deposited on the cell surface. There was an average of approximately 2.2 fg of protein disulfide isomerase on the surface of a bovine aortic endothelial cell. Treatment of thrombospondin-1 with purified protein disulfide isomerase enhanced adhesion of endothelial cells to thrombospondin-1 in an Arg-Gly-Asp-dependent manner through the alphav beta3 integrin receptor and supported cell spreading. Both Ca2+-depleted and Ca2+-replete thrombospondin-1 were substrates for protein disulfide isomerase. These results suggest that endothelial cell derived protein disulfide isomerase may regulate Arg-Gly-Asp-dependent binding of thrombospondin-1.

Animals↗

PubMed2001

Cryptic MCAT enhancer regulation in fibroblasts and smooth muscle cells. Suppression of TEF-1 mediated activation by the single-stranded DNA-binding proteins, Pur alpha, Pur beta, and MSY1.

An asymmetric polypurine-polypyrimidine cis-element located in the 5' region of the mouse vascular smooth muscle alpha-actin gene serves as a binding site for multiple proteins with specific affinity for either single- or double-stranded DNA. Here, we test the hypothesis that single-stranded DNA-binding proteins are responsible for preventing a cryptic MCAT enhancer centered within this element from cooperating with a nearby serum response factor-interacting CArG motif to trans-activate the minimal promoter in fibroblasts and smooth muscle cells. DNA binding studies revealed that the core MCAT sequence mediates binding of transcription enhancer factor-1 to the double-stranded polypurine-polypyrimidine element while flanking nucleotides account for interaction of Pur alpha and Pur beta with the purine-rich strand and MSY1 with the complementary pyrimidine-rich strand. Mutations that selectively impaired high affinity single-stranded DNA binding by fibroblast or smooth muscle cell-derived Pur alpha, Pur beta, and MSY1 in vitro, released the cryptic MCAT enhancer from repression in transfected cells. Additional experiments indicated that Pur alpha, Pur beta, and MSY1 also interact specifically, albeit weakly, with double-stranded DNA and with transcription enhancer factor-1. These results are consistent with two plausible models of cryptic MCAT enhancer regulation by Pur alpha, Pur beta, and MSY1 involving either competitive single-stranded DNA binding or masking of MCAT-bound transcription enhancer factor-1.

Amino Acid Motifs↗

PubMed2001

A population of autoantibodies against a centromere-associated protein A major epitope motif cross-reacts with related cryptic epitopes on other nuclear autoantigens and on the Epstein-Barr nuclear antigen 1.

Autoimmune diseases arise from a host's immune response against self-antigens. The triggering events ultimately resulting in such a break of tolerance are largely unknown. It is also not known why certain molecular structures become autoantigenic. The hypothesis has long been proposed that autoimmune diseases arise from molecular mimicry followed by an epitope spreading mechanism. Recently we have shown that the anti-centromere-associated protein A (CENP-A) immune response is directed against an autoantigenic motif, G/A-P-R/S-R-R, that occurs three times in the N-terminal amino acids of CENP-A. In the present study we used mutational analyses with immobilized oligopeptide arrays to identify the amino acids in this motif that are responsible for antibody binding. In particular, we found that surprisingly mimotopes of this motif are present in a vast number of autoantigens and in the Epstein-Barr nuclear antigen 1. With affinity-purified antibodies we show that the antibodies against this motif are polyclonal and cross-react with several autoantigens. However, in these autoantigens this motif often represents a cryptic epitope explaining the obvious conflict between our results and the known high specificity of autoantibodies. The presence of such an ubiquitous structure on autoantigens suggests a novel peptide-driven mechanism for the evolution of autoantibodies.

Amino Acid Motifs↗

PubMed1989

The PSA-2 glycoprotein complex of Leishmania major is a glycosylphosphatidylinositol-linked promastigote surface antigen.

Polyclonal rabbit antiserum to the Triton X-114 phase material of Leishmania major, which comprises the surface and internal integral membrane proteins of the parasite, was used to screen a lambda gt11 genomic expression library. A recombinant clone producing a Mr 123,000 beta-galactosidase fusion protein was isolated. Antibodies affinity-purified on this fusion protein recognized a complex of three surface-oriented proteins of promastigotes of L. major of Mr 94,000, 90,000, and 80,000 that we have termed the promastigote surface Ag 2 (PSA-2) complex. The DNA sequence of the insert in this clone predicted the 3' end of an open reading frame encoding a hydrophobic C-terminus. The inferred C-terminal sequence was suggestive of a glycosylphosphatidyl-inositol membrane anchoring mechanism. Phosphatidylinositol-specific phospholipase C treatment of the native PSA-2 proteins caused a shift in their electrophoretic mobility with an apparent reduction in the molecular weight of the PSA-2 complex. After phospholipase C treatment these proteins also displayed the cryptic cross-reacting determinant recognized by antibodies to the Trypanosoma brucei variant surface Ag. Moreover, PSA-2, which previously partitioned in the detergent phase after Triton X-114 phase separation, became water-soluble after phospholipase C treatment. Immunoprecipitation of the PSA-2 proteins with sera directed to lectin-binding proteins indicated that these polypeptides may be differentially glycosylated. Finally, these PSA-2 proteins were recognized by sera from some patients with cutaneous leishmaniasis.

Amino Acid Sequence↗

PubMed2003

Follicular lymphoma lacking the t(14;18)(q32;q21): identification of two disease subtypes.

The clinical and pathological features, including karyotype data and BCL2 protein expression pattern, of follicular lymphoma without a t(14;18)(q32;q21) have not been well defined. We have identified and conducted a detailed analysis of 50 cases with follicular lymphoma who lack the t(14;18). Fluorescent in situ hybridization (FISH) analysis was used to exclude cases with a cryptic IGH/BCL2 rearrangement. BCL2 protein expression level was assessed by immunohistochemistry. The karyotypes were assessed for recurrent sites of structural rearrangement, duplications and deletions on a band-by-band basis, and compared with a large cohort of cases with t(14;18). A distinct pattern of chromosomal alterations was identified in the cases without t(14;18). BCL2 protein overexpression was detected in 33% of 49 tested cases. In this minority, the karyotypes frequently showed increased copies of chromosome 18. The majority of cases (67%) did not show BCL2 overexpression and were characterized prominently by the presence of t(3;14)(q27;q32), implying a role for BCL6. Follicular lymphomas that lack a t(14;18) were segregated into two subgroups with distinct cytogenetic, phenotypic and possibly clinical features: one with BCL2 protein overexpression not related to an IGH/BCL2 rearrangement and a second without BCL2 overexpression. Objective identification of BCL2 expression level as well as BCL2 and BCL6 status by cytogenetic or FISH analysis has potential clinical utility and may yield insights into alternative genetic mechanisms associated with B-cell lymphomas with a follicular growth pattern.

Adult↗

PubMed1990

A site in the T4 bacteriophage major head protein gene that can promote the inhibition of all translation in Escherichia coli.

The cryptic DNA element, e14, synthesizes a protein, Lit, which can inhibit gene expression late in T4 bacteriophage development. This inhibition is due to the interaction between the Lit protein and a short region, the gol region, within gene 23, the major head protein gene of phage T4. We have constructed plasmids in which the gol region is transcribed from the lac promoter and fused translationally and transcriptionally to lacZ and cat (chloramphenicol acetyltransferase). These fusion plasmids were used to demonstrate that, in the presence of Lit protein, the gol region inhibits the expression of genes downstream in the same transcription unit. This local inhibition does not require the gene 23 polypeptide from the gol region. In addition, inducing the transcription and translation of the gol region in the presence of Lit protein causes an immediate global inhibition of all translation in Escherichia coli. This global inhibition does require the gene 23 polypeptide. No more than 75 base-pairs of DNA from the gol region are required for both the local and global inhibitions. The gol region sequence contains a short dyad symmetry. However, it is the sequence of bases in the region of dyad symmetry and not the ability to form a hairpin in the RNA that is required for gol region activity.

Amino Acid Sequence↗

PubMed1998

Disruption of PML subnuclear domains by the acidic IE1 protein of human cytomegalovirus is mediated through interaction with PML and may modulate a RING finger-dependent cryptic transactivator function of PML.

Both of the major immediate-early (IE) proteins IE1 and IE2 of human cytomegalovirus (HCMV) as well as input viral DNA and sites of viral IE transcription colocalize with or adjacent to punctate PML domains (PML oncogenic domains [PODs] or nuclear domain 10) in the nucleus within the first few hours after infection of permissive human fibroblasts. However, colocalization of IE1 and PML in PODs is only transient, with both proteins subsequently redistributing into a nuclear diffuse form. These processes are believed to promote efficient viral IE transcription and initiation of DNA synthesis especially at low multiplicities of infection. To examine the mechanism of PML displacement by IE1, we carried out indirect immunofluorescence assay experiments with plasmids expressing intact or deleted forms of PML and IE1 in DNA-transfected cells. The results demonstrated that deletion of the C-terminal acidic region of IE1 uncouples the requirements for displacement of both endogenous and coexpressed PML from those needed to target to the PODs. Mutant PML proteins containing either a Cys point mutation within the N-terminal RING finger domain or a small deletion (of positions 281 to 304) within the coiled-coil region did not localize to the PODs but instead gave a nuclear diffuse distribution, similar to that produced by intact PML in the presence of IE1. Endogenous PML also colocalized with IE1 in metaphase chromosomes in HCMV or recombinant adenovirus type 5-IE1-infected HF cells undergoing mitosis, implying that there may be a direct physical interaction between IE1 and PML. Indeed, a specific interaction between IE1 and PML was observed in a yeast two-hybrid assay, and the strength of this interaction was comparable to that of IE2 with the retinoblastoma protein. The RING finger mutant form of PML showed a threefold-lower interaction with IE1 in the yeast system, and deletion of the N-terminal RING finger domain of PML abolished the interaction. Consistent with the IFA results, a mutant IE1 protein that lacks the C-terminal acidic region was sufficient for interaction with PML in the yeast system. The two-hybrid interaction assay also showed that both the N-terminal RING finger domain and the intact coiled-coil region of PML are required cooperatively for efficient self-interactions involving dimerization or oligomerization. Furthermore, truncated or deleted GAL4/PML fusion proteins that retained the RING finger domain but lacked the intact coiled-coil region displayed an unmasked cryptic transactivator function in both yeast and mammalian cells, and the RING finger mutation abolished this transactivation property of PML. Therefore, we suggest that a direct interaction between IE1 and the N-terminal RING finger domain of PML may inhibit oligomerization and protein-protein complex formation by PML, leading to displacement of PML and IE1 from the PODs, and that this interaction may also modulate a putative conditional transactivator function of PML.

Animals↗

PubMed1995

Predicting ligand binding to proteins by affinity fingerprinting.

BACKGROUND: There are many ways to represent a molecule's properties, including atomic-connectivity drawings, NMR spectra, and molecular orbital models. Prior methods for predicting the biological activity of compounds have largely depended on these physical representations. Measuring a compound's binding potency against a small reference panel of diverse proteins defines a very different representation of the molecule, which we call an affinity fingerprint. Statistical analysis of such fingerprints provides new insights into aspects of binding interactions that are shared among a wide variety of proteins. These analyses facilitate prediction of the binding properties of these compounds assayed against new proteins. RESULTS: Affinity fingerprints are reported for 122 structurally-diverse compounds using a reference panel of eight proteins that collectively are able to generate unique fingerprints for about 75% of the small organic compounds tested. Application of multivariate regression techniques to this database enables the creation of computational surrogates to represent new proteins that are surprisingly effective at predicting binding potencies. We illustrate this for two enzymes with no previously recognizable similarity to each other or to any of the reference proteins. Fitting of analogous computational surrogates to four other proteins confirms the generality of the method; when applied to a fingerprinted library of 5000 compounds, several sub-micromolar hits were correctly predicted. CONCLUSIONS: An affinity fingerprint database, which provides a rich source of data defining operational similarities among proteins, can be used to test theories of cryptic homology unexpected from current understanding of protein structure. Practical applications to drug design include efficient pre-screening of large numbers of compounds against target proteins using fingerprint similarities, supplemented by a small number of empirical measurements, to select promising compounds for further study.

Chromatography, Affinity↗