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PubMed2002

Fragmentation of short single DNA strands by 1-30 eV electrons: dependence on base identity and sequence.

PURPOSE: To investigate the dependence of base identity and sequence on the damage induced by low-energy (1-30 eV) electron impact on a short single strand of DNA. MATERIALS AND METHODS: Monolayers of homogeneous nonamers of deoxycytidine and thymidine (dCy9 and T9) and heterogeneous nonamers of thymidine substituted with 33 and 66% of deoxycytidine (dCy3-T6 and dCy6-T3) were chemisorbed onto a gold substrate. They were bombarded under ultrahigh vacuum conditions by a 1-30 eV electron beam. Neutral fragments desorbed from the films were detected by a mass spectrometer. From partial pressure measurements, the effective cross-section (ECS) per base for desorption of various fragments was estimated. RESULTS: CN, OCN and/or H2NCN were the major neutral species observed to desorb in the present experiments. A small contribution of 55 amu neutral species, tentatively attributed to CH3CCO, were only detected from fragmentation of oligonucleotides containing thymine. The total ECS per base estimated for the CN, OCN and CH3CCO species production from fragmentation of dCy9, dCy6-T3, dCy3-T6 and T9 at 12 eV incident electron energy were (3.4, 2.0, 2.9 and 2.3) x 10(-17) cm(2), respectively. The incident electron energy dependence of ECS for desorption of these fragments exhibited structures <20 eV, which are characteristic of transient anion formation. CONCLUSIONS: At incident electron energies <20 eV, neutral fragment desorption arise from dissociation of the DNA bases, principally via dissociative electron attachment and/or decay of the transient anion into a dissociative electronic excited state of the base. Non-resonant mechanisms (e.g. direct dipolar dissociation) mostly control the fragmentation processes >20 eV. From comparison of the electron energy dependence of the ECS for base fragmentation in the homo- and heteronucleotides, it is concluded that damage to a short DNA strand is dependent on base identity, sequence and electron energy.

Anions↗
PubMed1988

Mapping of the microvillar 110K-calmodulin complex: calmodulin-associated or -free fragments of the 110-kD polypeptide bind F-actin and retain ATPase activity.

The 110K-calmodulin complex isolated from intestinal microvilli is an ATPase consisting of one polypeptide chain of 110 kD in association with three to four calmodulin molecules. This complex is presumably the link between the actin filaments in the microvillar core and the surrounding cell membrane. To study its structural regions, we have partially cleaved the 110K-calmodulin complex with alpha-chymotrypsin; calmodulin remains essentially intact under the conditions used. As determined by 125I-calmodulin overlays, ion exchange chromatography, and actin-binding assays, a 90-kD digest fragment generated in EGTA remains associated with calmodulin. The 90K-calmodulin complex binds actin in an ATP-reversible manner and decorates actin filaments with an arrow-head appearance similar to that found after incubation of F-actin with the parent complex; binding occurs in either calcium- or EGTA-containing buffers. ATPase activity of the 90-kD digest closely resembles the parent complex. In calcium a digest mixture containing fragments of 78 kD, a group of three at approximately 40 kD, and a 32-kD fragment (78-kD digest mixture) is generated with alpha-chymotrypsin at a longer incubation time; no association of these fragments with calmodulin is observed. Time courses of digestions and cyanogen bromide cleavage indicate that the 78-kD fragment derives from the 90-kD peptide. The 78-kD mixture can also hydrolyze ATP. Furthermore, removal of the calmodulin by ion exchange chromatography from this 78-kD mixture had no effect on the ATPase activity of the digest, indicating that the ATPase activity resides on the 110-kD polypeptide. The 78 kD, two of the three fragments at approximately 40 kD, and the 32-kD fragments associate with F-actin in an ATP-reversible manner. Electron microscopy of actin filaments after incubation with the 78-kD digest mixture reveals coated filaments, although the prominent arrowhead appearance characteristic of the parent complex is not observed. These data indicate that calmodulin is not required either for the ATPase activity or the ATP-reversible binding of the 110K-calmodulin complex to F-actin. In addition, since all the fragments that bind F-actin do so in an ATP-reversible manner, the sites required for F-actin binding and ATP reversibility likely reside nearby.

Actins↗
PubMed1997

Fibronectin-derived fragments as inducers of adhesion and chemotaxis of Entamoeba histolytica trophozoites.

Active migration of Entamoeba histolytica trophozoites through extracellular matrixes might play a role in host tissue destruction. Trophozoites degrade soluble fibronectin (FN) bound to their surface and adhere to substrate-bound FN, producing local degradation. FN proteolytic fragments were used to determine the nature of adhesion and motility-promoting domains within the protein. The 70-kDa fragment (amino-terminal end) promoted the highest adhesion, followed by the 120-kDa fragment, which contains the cell-binding domain. The 25-kDa fragment (carboxy-terminal end of the A chain) promoted half the adhesion, while two Hep II-binding fragments had no effect. The 70- and 120-kDa fragments also stimulated directed migration and chemokinesis. Intact FN and the 25-kDa fragment showed lower stimulation. The Hep II-binding fragments had no activity. Results support previous evidence for distinct cell-surface components as mediators of adhesion to FN and trophozoite motility and the potential importance of cell matrix recognition and degradation in their invasive behavior.

Animals↗
PubMed2006

The fragments of bovine high molecular weight kininogen promote osteoblast proliferation in vitro.

High molecular weight (HMW) kininogen is known to be a large plasma protein and cleaved by plasma proteinase kallikrein, then it generates four fragments in the blood coagulation cascade: heavy chain, bradykinin, fragment 1.2, and light chain. The fragment 1.2 has also been found in the basic protein fraction of bovine milk as a bioactive protein which promotes osteoblast proliferation. The milk basic protein has been shown to be a multi functional edible protein which promotes bone formation and inhibits bone resorption. In the present study, we purified the fragment 1.2 from bovine plasma and assessed it could promote osteoblast proliferation and posses the activity after pepsin digestion. Purified plasma HMW kininogen did not promote the proliferation, however, the kallikrein-cleaved HMW kininogen promoted the proliferation. The fragment 1.2, purified from the proteolysate, also promoted the proliferation. The pepsin digestion was performed according to the method of the assessment of allergenesity of genetically modified crops. After pepsin digestion, the fragment 1.2 generated resistant fragments and showed the promoting activity of osteoblast proliferation. These results suggest that the enzymatically-digested fragments of bovine HMW kininogen are able to be a naturally occurred active protein that promotes the bone formation by oral administration.

3T3 Cells↗
PubMed1988

Radiolabeled monoclonal antibody 15 and its fragments for localization and imaging of xenografts of human lung cancer.

Monoclonal antibody (MAb) 15 and its F(ab')2 and Fab fragments were radioiodinated, and their biodistribution and imaging were compared in BALB/c nude mice bearing a xenograft of a human lung cancer (TKB-2). Association constants for 125I-labeled MAb 15 IgG, F(ab')2, and Fab were 1.9 X 10(9), 1.8 X 10(9), and 3.7 X 10(8) M-1, respectively. Immunoreactive fractions ranged from 0.59 to 0.50. Cultured TKB-2 cells expressed 1.1 X 10(4) binding sites/cell for MAb 15 IgG in vitro. The binding of a control antibody and the binding of its fragments to TKB-2 cells were less than 3% of the input doses. The mice with the TKB-2 tumors were given simultaneous injections of 10 microCi of 131I-labeled MAb 15 or its fragments and 10 microCi of 125I-labeled control IgG or its fragments. With MAb 15 IgG, the percentage of the injected dose bound per gram of tissue (ID/g) of the tumor was 3.68% at day 7, when the localization index (LI) was 4.38. At day 2 after MAb 15 F(ab')2 injection, 1.12% of the ID/g was localized in the tumor and the LI was 3.04. After MAb 15 Fab injection, the percentage of the ID/g of the tumor was 0.31% and the LI was 2.58 at day 1. MAb 15 IgG, F(ab')2, and Fab cleared from the blood early, with a half-life of 33, 16, and 9 hours, respectively. The distributions of MAb 15 and its fragments in the normal organs did not differ from those of the control. Radioimaging with 100 microCi of 131I-labeled MAb 15 and its fragments showed that 42%, 44%, and 32% of the total-body count were localized in the tumor with IgG at day 7, F(ab')2 at day 2, or Fab at day 1, respectively. Because the radioactivity remaining in the tumor with Fab was low, the image was insufficient. Throughout the period, less than 10% of the control IgG and its fragments remained in the tumor. Microautoradiography confirmed the binding of MAb 15 and its fragments to the tumor cells. In this study the F(ab')2 was the best compromise between the slowly cleared IgG and the poorly localized Fab in tumor imaging.

Animals↗
PubMed1999

Role of DNAS1L3 in Ca2+- and Mg2+-dependent cleavage of DNA into oligonucleosomal and high molecular mass fragments.

Ca2+- and Mg2+-dependent endonucleases have been implicated in DNA fragmentation during apoptosis. We have demonstrated that particular nucleases of this type are inhibited by poly(ADP-ribosyl)ation and suggested that subsequent cleavage of PARP by caspase-3 might release these nucleases from poly(ADP-ribosyl)ation-induced inhibition. Hence, we purified and partially sequenced such a nuclease isolated from bovine seminal plasma and identified human, rat and mouse homologs of this enzyme. The extent of sequence homology among these nucleases indicates that these four proteins are orthologous members of the family of DNase I-related enzymes. We demonstrate that the activation of the human homolog previously specified as DNAS1L3 can induce Ca2+- and Mg2+-dependent DNA fragmentation in vitro and in vivo. RT-PCR analysis failed to detect DNAS1L3 mRNA in HeLa cells and nuclei isolated from these cells did not exhibit internucleosomal DNA fragmentation when incubated in the presence of Ca2+and Mg2+. However, nuclei isolated from HeLa cells that had been stably transfected with DNAS1L3 cDNA underwent such DNA fragmentation in the presence of both ions. The Ca2+ionophore ionomycin also induced internucleosomal DNA degradation in transfected but not in control HeLa cells. Transverse alternating field electrophoresis revealed that in nuclei from transfected HeLa cells, but not in those from control cells, DNA was cleaved into fragments of >1000 kb in the presence of Mg2+; addition of Ca2+in the presence of Mg2+resulted in processing of the >1000 kb fragments into 50 kb and oligonucleosomal fragments. These results demonstrate that DNAS1L3 is necessary for Ca2+- and Mg2+-dependent cleavage of DNA into both oligonucleosomal and high molecular mass fragments in specific cell types.

Amino Acid Sequence↗
PubMed2005

Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution.

DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. Demonstrated here is the amplification of a gene library by PCR using uridine triphosphate (dUTP) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. The incorporated uracil bases were excised using uracil-DNA-glycosylase and the DNA backbone subsequently cleaved with piperidine. These end-point reactions required no adjustments. Polyacrylamide urea gels demonstrated adjustable fragmentation size over a wide range. The oligonucleotide pool was reassembled by internal primer extension to full length with a proofreading polymerase to improve yield over Taq. We present a computer program that accurately predicts the fragmentation pattern and yields all possible fragment sequences with their respective likelihood of occurrence, taking the guesswork out of the fragmentation. The technique has been demonstrated by shuffling chloramphenicol acetyltransferase gene libraries. A 33% dUTP PCR resulted in shuffled clones with an average parental fragment size of 86 bases even without employment of a fragment size separation, and revealed a low mutation rate (0.1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs.

Chloramphenicol O-Acetyltransferase↗
PubMed1976

Primary structure of bovine plasma high-molecular-weight kininogen. The amino acid sequence of a glycopeptide portion (fragment 1) following the C-terminus ot the bradykinin moiety.

On incubation of bovine plasma high-molecular-weight (HMW) kininogen with purified plasma kallikrein [EC 3.4.21.8], a large glycopeptide fragment and the vasoactive peptide, bradykinin, were initially liberated; the former, named fragment 1-2, was subsequently cleaved into fragment 1 (glycopeptide) and the previously established fragment 2 (histidine-rich peptide). The isolated fragment 1-2 contained a total of 108 to 110 amino acid residues and carbohydrates, and the amino-terminal sequence Ser-Val-Gln was established. The other fragment, fragment 1, consisted of a total of 69 amino acid residues with serine and arginine (and lysine) at the amino and carboxyl termini, respectively. It contained eleven residues each of histidine and glycine, together with an oligosaccharide chain consisting of galactosamine, hexose and sialic acid. The complete amino acid sequence of fragment 1 was determined by Edman degradation and standard enzymatic and chemical techniques. These results established the following sequence: H-Ser-Val-Gln-Val-Met-Lys-Thr-Glu-Gly-Ser-Thr-Pro/Thr-Val-Ser(CHO)-Val/Leu-Pro-His-Ser-Ala-Met-Ser-Pro-Val-Gln-Asp-Glu-Glu-Arg-Asp-Ser-Gly-Lys-Glu-Gln-Gly-Pro-Thr-His-Gly-His-Gly-Trp-Asp-His-Gly-Lys-Gln-Ile-Lys-Leu-His-Gly-Leu-Gly-Leu-Gly-His-Lys-His-Lys-His-Asp-Gln-Gly-His-Gly-His-His-Lys/ArgOH.

Amino Acid Sequence↗
PubMed1982

Primary structure of the polypeptide chain elongation factor Tu from E. coli. I. Amino acid sequence of fragment B.

The complete amino acid sequence of Fragment B obtained by the limited tryptic digestion of E. coli polypeptide chain elongation factor Tu (EF-Tu) was determined. Seven peptides formed from Fragment B by cleavage with cyanogen bromide (designated as CB1 to CB7 according to their order of alignment from N- to C-termini of Fragment B) were purified, and six of them were completely sequenced by the manual method of sequential Edman degradation with direct identification of the phenylthiohydantoin-amino acids. The remaining one cyanogen bromide peptide (CB6) containing 109 amino acid residues was further digested with trypsin. Twelve tryptic peptides (designated as T1 to T12 according to their order of alignment from N- to C-termini of CB6) were isolated, and their amino acid sequences were analyzed. The alignment of CB peptides was based on the results of the automated sequence analysis of Fragment B from its N-terminal, and the sequence analysis of the overlapping peptides containing sulfhydryl groups obtained by the complete tryptic digestion of Fragment B. The alignment of peptides T1 to T12 on CB6 was based on the result of the automated sequence analysis of CB6, and the sequence of the overlapping peptide obtained by the chemical cleavage of CB6 at the tryptophan residue using cyanogen bromide in heptafluorobutyric acid. The nucleotide sequence of the tuf A gene was also utilized for the alignment of these peptides. Fragment B comprises amino acid residues 59 to 263 of E. coli EF-Tu, which consists of 393 amino acids. It contains two functional (SH1 and SH2) and one non-functional (SH3) sulfhydryl groups of EF-Tu. All of the five histidine residues in Fragment B were distributed within the first N-terminal quarter, and three of them were found to be clustered around SH2. Although E. coli EF-Tu consists of two gene products (tuf A and tuf B), no microheterogeneity was found in the amino acid sequence of Fragment B.

Amino Acid Sequence↗
PubMed1990

Monoclonal antibody A7 tumor localization enhancement by its F(ab')2 fragments to colon carcinoma xenografts in nude mice.

The monoclonal antibody A7 (MoAb A7), which belongs to IgG1, was digested with pepsin to yield F(ab')2 fragments. The maximum binding to the human colon cancer cell line, SW1116, was 27% with 125-I labeled whole MoAb A7 and 24% with 125-I labeled F(ab')2 fragments using an in vitro binding assay. The results showed that the binding activity of F(ab')2 to SW1116 was practically the same as that of whole MoAb A7. The preferred localization of the fragments to tumor tissue, compared with normal mouse tissue, was demonstrated in mice carrying SW1116 xenografts. The tumor:blood ratio three days after injection was 2.64:18.5 for whole MoAb A7:F(ab')2, respectively. The tissue:blood ratios for the F(ab')2 fragments showed a value of 18.5 in tumors, whereas its was a value less than 1.0 in normal organs. The tumor accumulation of F(ab')2 fragments was also dependent on the antigenic expression of each tumor among xenografts of colon carcinoma SW1116 and WiDr, and squamous cell carcinoma KB. In kinetic experiments with whole MoAb A7 and its F(ab')2 fragments, whole MoAb A7 was lost, with a half-life of 4 days, in both blood and tumors, whereas F(ab')2 fragments were rapidly lost with a half-life of 1.5 days. These results suggested that the F(ab')2 fragments were cleared from the blood faster than was whole MoAb A7.

Animals↗
PubMed1997

Significance of alpha-fragment of metallothionein in cadmium binding.

In order to evaluate the significance of alpha- and beta-fragments of metallothionein with regard to Cd binding in biosynthetic processes, the Cd-binding ability of four mutant metallothioneins was examined using the Escherichia coli expression system. The features of the mutant metallothioneins were proteins in which cysteine residues in the alpha- or beta-fragment were replaced with alanine residues, or that the sequential order of the fragments was altered. The expressed mutant metallothioneins having an intact alpha-fragment showed the constructive abilities of the Cd-thiolate cluster. On the other hand, mutant metallothionein having an alpha-fragment lacking metal-binding sites exhibited no Cd-binding ability. The condition for maintaining the Cd-binding capability of metallothionein was that the alpha-fragment remains intact irrespective of the sequential order of the two fragments. The alpha-fragment is an indispensable component in metal-binding processes of Cd-metallothionein.

Amino Acid Sequence↗
PubMed1997

Detection of deoxyribonucleic acid fragmentation in human sperm: correlation with fertilization in vitro.

The objective of this study was to determine the incidence of DNA fragmentation in human sperm, and to correlate any detected DNA damage with semen analysis parameters and fertilization rates in in vitro fertilization (IVF). A total of 298 semen samples were collected from men in the infertility program at The Toronto Hospital. For each sample, the percentage of sperm with DNA fragmentation was determined using the method of terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling (TUNEL) and fluorescence-activated cell sorting. The percentage of sperm with fragmented DNA was less than 4% in the majority of samples but ranged from 5% to 40% in approximately 27% of the samples. A negative correlation was found between the percentage of DNA fragmentation and the motility, morphology, and concentration of the ejaculated sperm. In 143 IVF samples, a significant negative association was also found between the percentage of sperm with DNA fragmentation and fertilization rate (p = 0.008) and embryo cleavage rate (p = 0.01). In addition, 35 men who smoked demonstrated an increased percentage of sperm with fragmented DNA (4.7 +/- 1.2%) as compared to 78 nonsmokers (1.1 +/- 0.2%; p = 0.01). These results demonstrate a negative association between semen analysis parameters and sperm with fragmented DNA. Since extremely poor semen samples are the indication for intracytoplasmic sperm injection, there is a high likelihood that sperm with fragmented DNA may be selected by chance and used for oocyte injection, resulting in poor fertilization and/or cleavage rates.

Adult↗
PubMed2001

Hyperglycemia enhances DNA fragmentation after transient cerebral ischemia.

Previous histopathologic results have suggested that one mechanism whereby hyperglycemia (HG) leads to exaggerated ischemic damage involves fragmentation of DNA. DNA fragmentation in normoglycemia (NG) and HG rats subjected to 30 minutes of forebrain ischemia was studied by terminal deoxynucleotidyl transferase mediated DNA nick-labeling (TUNEL) staining, by pulse-field gel electrophoresis (PFGE), and by ligation-mediated polymerase chain reaction (LM-PCR). High molecular weight DNA fragments were detected by PFGE, whereas low molecular weight DNA fragments were detected using LM-PCR techniques. The LM-PCR procedure was performed on DNA from test samples with blunt (without Klenow polymerase) and 3'-recessed ends (with Klenow polymerase). In addition, cytochrome c release and caspase-3 activation were studied by immunocytochemistry. Results show that HG causes cytochrome c release, activates caspase-3, and exacerbates DNA fragments induced by ischemia. Thus, in HG rats, but not in control or NGs, TUNEL-stained cells were found in the cingulate cortex, neocortex, thalamus, and dorsolateral crest of the striatum, where neuronal death was observed by conventional histopathology, and where both cytosolic cytochrome c and active caspase-3 were detected by confocal microscopy. In the neocortex, both blunt-ended and stagger-ended fragments were detected in HG, but not in NG rats. Electron microscopy (EM) analysis was performed in the cingulate cortex, where numerous TUNEL-positive neurons were observed. Although DNA fragmentation was detected by TUNEL staining and electrophoresis techniques, EM analysis failed to indicate apoptotic cell death. It is concluded that HG triggers a cell death pathway and exacerbates DNA fragmentation induced by ischemia.

Animals↗
PubMed1995

Radiolocalization of pancreatic carcinoma xenografts in nude mice with radiolabeled chimeric Fab fragments of anti-carcinoembryonic antigen monoclonal antibody A10.

Recombinant mouse-human chimeric Fab fragments of anti-carcinoembryonic antigen monoclonal antibody (MAb) A10 react with various GI carcinomas. We tested radiolocalization of pancreatic carcinoma xenografts in nude mice using radiolabeled chimeric A10 Fab fragments, comparing them with murine Fab fragments and parental MAb. For mice injected with chimeric A10 Fab fragments, we obtained significantly higher uptake in tumors than in normal tissues at 24 and 48 h after injection. In addition, tumor/normal tissues labeling ratios for chimeric A10 Fab fragment were significantly greater than those for murine MAb at 24 h postinfusion. However, no significant difference in biodistribution was observed between chimeric and murine Fab fragments. In autoradiography imaging studies, we obtained clearer tumor detection without visible uptake in normal organs for chimeric Fab fragments than for murine MAb. These results suggest that chimeric Fab fragments of A10 could be a potentially useful candidate for radioimmunodetection of pancreatic carcinomas.

Animals↗
PubMed1991

OKT3 F(ab')2 fragments--retention of the immunosuppressive properties of whole antibody with marked reduction in T cell activation and lymphokine release.

Recent studies in mouse and man indicate that the first dose response to anti-CD3 mAbs likely results from in vivo T cell activation and concomitant lymphokine release. One approach toward amelioration of these effects involves the use of nonactivating digest fragment preparations of anti-CD3 mAbs. In the present study whole and F(ab')2 fragments of OKT3 were prepared and assayed for their immune-activating and -suppressing effects on human peripheral blood mononuclear cells. Immunosuppressive effects were evaluated by quantitation of TCR modulation and coating, and by inhibition of CTL activity. Whole mAb and F(ab')2 fragments both effectively coated the TCR complex. However, whole mAb was more efficient at modulating the TCR complex, suggesting that modulation is enhanced by FcR interactions. Whole and F(ab')2 fragments of OKT3 were equally efficacious in suppressing CTL activity. Immune activation was evaluated by quantitation of proliferation, activation marker expression (IL-2R and Leu-23), and lymphokine release (TNF-alpha, gamma-IFN, and GM-CSF). Rigorously purified F(ab')2 preparations demonstrated minimal T cell activation, suggesting TCR and macrophage FcR crosslinking as necessary. Whole OKT3 mAb induced expression of IL-2R and Leu-23 activation markers on the majority of CD4+ and CD8+ cells at mAb concentrations as low as 1 ng/ml, whereas F(ab')2 fragments induced detectable, but markedly reduced expression of these markers only at mAb concentrations greater than or equal to 100 ng/ml. Similarly, whole mAb induced release of TNF-alpha, gamma-IFN, and GM-CSF at low mAb concentrations, whereas F(ab')2 fragments induced detectable (though markedly reduced) levels of TNF-alpha only. However, increasing degrees of contamination with whole antibody resulted in increasing mitogenic potency of the F(ab')2 preparation, which in some cases, was actually enhanced compared with that observed with whole mAb alone. In conclusion, these studies indicate that OKT3 F(ab')2 digest fragments are markedly less potent than whole mAb in inducing T cell activation, yet they retain significant immunosuppressive effects. However, meticulous purification of F(ab')2 digest fragment preparations will likely be required to avoid T cell and macrophage activation following in vivo administration.

Antibodies, Monoclonal↗
PubMed2006

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.

The major aim of tertiary structure prediction is to obtain protein models with the highest possible accuracy. Fold recognition, homology modeling, and de novo prediction methods typically use predicted secondary structures as input, and all of these methods may significantly benefit from more accurate secondary structure predictions. Although there are many different secondary structure prediction methods available in the literature, their cross-validated prediction accuracy is generally <80%. In order to increase the prediction accuracy, we developed a novel hybrid algorithm called Consensus Data Mining (CDM) that combines our two previous successful methods: (1) Fragment Database Mining (FDM), which exploits the Protein Data Bank structures, and (2) GOR V, which is based on information theory, Bayesian statistics, and multiple sequence alignments (MSA). In CDM, the target sequence is dissected into smaller fragments that are compared with fragments obtained from related sequences in the PDB. For fragments with a sequence identity above a certain sequence identity threshold, the FDM method is applied for the prediction. The remainder of the fragments are predicted by GOR V. The results of the CDM are provided as a function of the upper sequence identities of aligned fragments and the sequence identity threshold. We observe that the value 50% is the optimum sequence identity threshold, and that the accuracy of the CDM method measured by Q(3) ranges from 67.5% to 93.2%, depending on the availability of known structural fragments with sufficiently high sequence identity. As the Protein Data Bank grows, it is anticipated that this consensus method will improve because it will rely more upon the structural fragments.

Algorithms↗
PubMed2001

Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR.

The N-terminal SH2 domain from the p85alpha subunit of phosphatidylinositol 3' kinase is cleaved specifically into 9- and 5-kD fragments by limited proteolytic digestion with trypsin. The noncovalent SH2 domain complex and its constituent tryptic peptides have been investigated using high-resolution heteronuclear magnetic resonance (NMR). These studies have established the viability of the SH2 domain as a fragment complementation system. The individual peptide fragments are predominantly unstructured in solution. In contrast, the noncovalent 9-kD + 5-kD complex shows a native-like (1)H-(15)N HSQC spectrum, demonstrating that the two fragments fold into a native-like structure on binding. Chemical shift analysis of the noncovalent complex compared to the native SH2 domain reveals that the highest degree of perturbation in the structure occurs at the cleavage site within a flexible loop and along the hydrophobic interface between the two peptide fragments. Mapping of these chemical shift changes on the structure of the domain reveals changes consistent with the reduction in affinity for the target peptide ligand observed in the noncovalent complex relative to the intact protein. The 5-kD fragment of the homologous Src protein is incapable of structurally complementing the p85 9-kD fragment, either in complex formation or in the context of the full-length protein. These high-resolution structural studies of the SH2 domain fragment complementation features establish the suitability of the system for further protein-folding and design studies.

Magnetic Resonance Spectroscopy↗
PubMed1980

The molar combining ratio of anti-albumin Fab' fragments to homologous and heterologous serum albumins.

The number of antibody combining sites on bovine (BSA), goat (GSA) and sheep (SSA) serum albumins was studied using rabbit and chicken antibodies. In homologous reactions, the profiles of quantitative precipitations with chicken antibody were similar to those with rabbit antibody reported previously (12), and the antigenic valence in the extreme antibody excess zone was found to be 6-7 for each albumin. The univalent Fab' fragments of rabbit and chicken antibodies were prepared. The stoichiometry of the soluble complex formed with the Fab' fragment and fluorescence labeled albumin was analyzed by gel filtration, and the number of Fab' fragment molecules capable of binding to an albumin molecule was estimated. In a homologous reaction with both rabbit and chicken Fab' fragments, the Fab' to albumin combining ratio revealed from the molecular weight of the soluble complex was 14:1. In the heterologous reactions, the combining ratio was 5:1 for rabbit Fab' fragments to BSA, and 9:1 for chicken Fab' fragment to BSA. From the heterologous reactions between GSA and SSA, it was demonstrated that the combining ratios were 10-11:1 with rabbit Fab' fragment and 11-13:1 with chicken Fab' fragment.

Antibodies, Anti-Idiotypic↗