INDI-integrated nanobody database for immunoinformatics

Nanobodies, a subclass of antibodies found in camelids, are versatile molecular binding scaffolds composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to >11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.

Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification

High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in these large datasets, in particular the identification of therapeutic antibodies (Abs) or those associated with disease exposure and protection. Here, we describe our efforts to use artificial intelligence (AI)-based image-analyses for prospective classification of Abs based solely on sequence information. We hypothesized that Abs recognizing the same part of an antigen share a limited set of features at the binding interface, and that the binding site regions of these Abs share share common structure and physicochemical property patterns that can serve as a "fingerprint" to recognize uncharacterized Abs. We combined large-scale sequence-based protein-structure predictions to generate ensembles of 3-D Ab models, reduced the Ab binding interface to a 2-D image (fingerprint), used pre-trained convolutional neural networks to extract features, and trained deep neural networks (DNNs) to classify Abs. We evaluated this approach using Ab sequences derived from human HIV and Ebola viral infections to differentiate between two Abs, Abs belonging to specific B-cell family lineages, and Abs with different epitope preferences. In addition, we explored a different type of DNN method to detect one class of Abs from a larger pool of Abs. Testing on Ab sets that had been kept aside during model training, we achieved average prediction accuracies ranging from 71-96% depending on the complexity of the classification task. The high level of accuracies reached during these classification tests suggests that the DNN models were able to learn a series of structural patterns shared by Abs belonging to the same class. The developed methodology provides a means to apply AI-based image recognition techniques to analyze high-throughput B-cell sequencing datasets (repertoires) for Ab classification.

Advancing computational biology and bioinformatics research through open innovation competitions

Open data science and algorithm development competitions offer a unique avenue for rapid discovery of better computational strategies. We highlight three examples in computational biology and bioinformatics research in which the use of competitions has yielded significant performance gains over established algorithms. These include algorithms for antibody clustering, imputing gene expression data, and querying the Connectivity Map (CMap). Performance gains are evaluated quantitatively using realistic, albeit sanitized, data sets. The solutions produced through these competitions are then examined with respect to their utility and the prospects for implementation in the field. We present the decision process and competition design considerations that lead to these successful outcomes as a model for researchers who want to use competitions and non-domain crowds as collaborators to further their research.

Antibodies against recombinant alpha-galactosidase A in Fabry disease: Subclass analysis and impact on response to treatment

BACKGROUND

Treatment of Fabry disease (FD) with recombinant alpha-galactosidase A (r-αGAL A) is complicated by the formation of anti-drug antibodies in the majority of male patients with the classical disease phenotype. Detailed information regarding antibody subtypes, onset and persistence of antibody development and their effect on treatment efficacy is sparse.

METHODS

A retrospective study was carried out in 39 male patients with classical FD, treated with either agalsidase-alfa or agalsidase-beta (mean follow up of 10 years). With six to twelve months intervals plasma-induced in vitro inhibition of enzyme activity, lysoglobotriaosylsphingosine (lysoGb3) levels and renal function were assessed. In a subset of 12 patients, additionally anti- r-αGAL A IgM, IgA and IgG1, 2, 3 and 4 levels were analyzed.

RESULTS

In 23 out of 39 patients, plasma-induced in vitro inhibition of r-αGAL A activity was observed (inhibition-positive). The inhibition titer was strongly negatively correlated to the decrease in lysoGb3: agalsidase-alfa (FE_{log10(inhibition)} = -10.3, P ≤.001), agalsidase-beta (FE_{log10(inhibition)} = -4.7, P ≤.001). Inhibition-positive patients had an accelerated decline in renal function (FE = 1.21, p = .042). During treatment IgG1 anti-r-αGAL A levels increased only in inhibition-positive patients (p = .0045). IgG4 anti-r-αGAL A antibodies developed in 7 out of 9 inhibition-positive patients. Other antibody subclasses were either not present or too low to quantify.

CONCLUSION

Development of inhibiting antibodies against r-αGAL A negatively affects the biochemical response to ERT and resulted in an accelerated decline in renal function. The presence of IgG1 and IgG4 anti-r-αGAL A antibodies is associated with in vitro αGAL A activity inhibition.

[Analysis of irregular antibody screening and antibody identification results in 31 858 cases of inpatients]

Objective To explore clinical significance of transfusion safety by analyzing the results of screening the irregular antibodies and antibody identification. Methods The micro-column gel test cards were used to screen and identify irregular antibodies of 31 858 inpatients. Results Among the 31 858 cases, 31 517 (98.92%) had positive results in RhD detection, and 341 (1.08%) had negative results in RhD detection. The number of patients who had positive results in screening the irregular antibodies was 92 cases and the positive rate was 0.3%. The highest detected rate of positive results in screening the irregular antibodies was obtained in the patients with hematologic diseases at a rate of 2.21% (11/497), closely followed by the pregnant women at a rate of 0.72% (31/4313). The 92 cases had positive results in antibody identification, including 45 cases of anti-E (48.91%), 11 cases of anti-D (11.96%), 10 cases of anti-c (10.87%), 6 cases of anti-Le^a (6.52%), 5 cases of anti-Ec (5.44%), 5 cases of anti-M (5.44%), and 10 cases of other antibodies. Conclusion Screening the irregular antibodies and antibody identification before blood transfusion can effectively avoid the adverse reactions of blood transfusion and improve the quality of blood transfusion.

The differential dynamics of antibody subpopulation expression during affinity maturation in a teleost

A compositional analysis of the antibody response in rainbow trout was conducted using an affinity-based immunopartitioning assay. Trout were immunized with TNP-keyhole limpet hemocyanin (TNP-KLH) and individual serum titers and their affinity distributions analyzed over a period of 27 weeks. The kinetics of antibody affinity subpopulation development revealed certain key features: 1) the lowest affinity subpopulation (log aK, 3.5-3.99) appears early, does not achieve high titer, and was more transient than the higher affinity subpopulations; 2) intermediate affinity subpopulations (log aK, 5.0-5.99) appear later (week 5), achieve relatively high titers and persist longer; and 3) the highest affinity subpopulations (log aK, 6.0-7.49) emerge much later (post week 15), and have comparable titers to the intermediate affinity group. We find that the affinity maturation of the serum antibody response can be resolved into each affinity subpopulation's contribution both in quantity and timing.

Glatiramer acetate immunization induces specific antibody and cytokine responses in ALS patients

We assessed humoral and cytokine responses in monthly plasma samples from ALS patients who received glatiramer acetate (GA) immunization every day or every other week, or remained untreated (control) from a six-month phase II trial. Samples were evaluated by GA-specific ELISA assays for detection of combined immunoglobulin (Ig) classes (IgM,A,G), IgG alone, and IgG subclasses (IgG1, IgG2, IgG3, and IgG4). T-helper (Th) type 1 and 2 (Th1 and Th2) cytokine levels were determined by flow cytometric cytokine bead arrays. Fourteen of 21 GA-immunized patients produced anti-GA Ig responses. Those treated every day produced anti-GA responses within one month, while those treated every other week exhibited responses by month two. All anti-GA IgG subclass concentrations were increased in excess of 4.2-fold in plasma from treated patients, and anti-GA IgG1 comprised the majority of the humoral response. Mean plasma cytokine levels were statistically indistinguishable between treatment regimens; however, stratification by patient and time on study showed more prevalent trends in changes of Th1 or Th2 cytokine levels following GA treatment every other week or every day, respectively. These data show significant humoral responses and cytokine trends following GA immunization in ALS patients.

The IgG subclass-specificities of anti-IFNβ antibodies change with time and differ between the IFNβ products in relapsing remitting multiple sclerosis patients

Anti-Interferon beta (IFNbeta) antibodies are frequently produced during treatment with IFNbeta in Multiple Sclerosis (MS) patients. In recent years, it has become clear that these antibodies cause a decrease in IFNbeta-induced biomarkers and in IFNbeta clinical efficacy. Anti-IFNbeta antibodies are mainly of the IgG isotype, which consists of 4 subclasses. In this study, we tested whether changes occurred in IgG subclasses over time. A series of sera from 21 IFNbeta-treated patients (11 IFNbeta-1a, 10 IFNbeta-1b) were analysed longitudinally using a capture ELISA. IFNbeta-1a treated patients had a restricted subclass distribution, whilst IFNbeta-1b-treated patients demonstrated a wider distribution. When compared to IFNbeta-1b-treated patients, IFNbeta-1a-treated patients had lower levels of total and subclass-specific IgGs against IFNbeta. In particular, antibody levels were markedly lower in the neutralizing antibody (NAb) negative (-) category of IFNbeta-1a-treated patients in comparison to the NAb-IFNbeta-1b-treated patients. The most striking observation of this study were the very low levels or complete absence of IgG3 subclass-specific antibodies to IFNbeta in IFNbeta-1a-treated patients. This difference in the levels of IgG3 may help to clarify the differences in the overall pattern of development of anti-IFNbeta antibodies in IFNbeta-1a-and IFNbeta-1b-treated patients.

Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme

The topography of antibody binding sites has been classified into five types that evoke familiar geomorphic features of the Earth. The 229 antibody crystal structures from the Protein Data Bank were analyzed and classified into these classes. Relationships to previous topography classifications by Rees et al., who defined three classes, and Thornton et al., who defined four classes, are identified. An algorithm was developed to identify the antibody binding site class automatically based on the definition and the shape of the binding site. A three-dimensional convex hull was formed around the complementarity determining regions (CDRs) of the antibody. The convex hull was then "trimmed" to fit the binding site by using distance criteria and morphological techniques. Once the program identified the binding site shape, a statistical and distance based analysis was performed to classify automatically the antibody into one of the five geomorphic classes. The five antibody topography classes are as follows: cave (mostly hapten binders), crater (mostly protein and peptide/carbohydrate/nucleic acid binders), canyon, valley, and plain (mostly protein binders). Comparisons of the binding sites of empty and of complexed antibody binding sites gave an indication of how the shape of the binding site is influenced by binding of the antigen.

Biosensor-based characterization of serum antibodies during development of an anti-IgE immunotherapeutic against allergy and asthma

Antibody responses, induced in Cynomolgus monkey by recombinant IgE-derived immunotherapeutic protein against atopic allergies and asthma, were characterized using label-free, real-time protein interaction analysis. The effects of two different immunotherapeutic proteins were compared. Active concentrations of specific anti-IgE antibodies formed were determined in sera sampled at multiple time points, using conditions of total mass transport limitation that were proved to exist on the sensor surface. These concentrations varied from about 0.4 to 35 microg/ml among the monkeys and throughout the immunization period. Based on these concentrations, the rate and affinity constants for the binding of antibody populations to the antigen could be determined. The apparent equilibrium dissociation constant decreased during the immunization period, for all the monkeys, by a factor between 6 and 50, ending at values from approximately 2 x 10(-9) to approximately 2 x 10(-11) M among the animals. This affinity maturation was attributable to the changes in both rate constants, although the magnitude of the contribution of each constant depended partly on specimen, but primarily on the immunotherapeutic used. The immunotherapeutic proteins examined showed excellent immunogenic properties, providing the basis for a new and effective treatment for allergy and asthma.

Structural and functional properties of antibodies to the superantigen TSST-1 and their relationship to menstrual toxic shock syndrome

Menstrual toxic shock syndrome (mTSS) is an acute febrile disease accompanied by hypotension and multiple organ involvement. Infection with Staphylococcus aureus producing the superantigen toxic shock syndrome toxin-1 (TSST-1) vaginally is necessary; however, only a small fraction of those infected with TSST-1 producing bacteria actually develop mTSS, suggesting that host factors modulate disease susceptibility. Serum antibodies to the toxin protect against development of the syndrome, but not all antibodies can neutralize the toxin. We set out to determine whether risk of developing the syndrome is related to the absence of neutralizing antibody and if antibody isotypes influence the neutralization capacity. In healthy subjects, TSST-1-binding serum antibodies were exclusively of the IgG and IgM classes; however, toxin-neutralizing capacity was correlated to the TSST-1-specific IgG1 and IgG4 antibodies (r (2)=0.88, p<0.0001 and 0.33, p<0.0086, respectively) but not with IgM antibodies. Specific IgA was not detectable. Compared to healthy matched controls who were colonized vaginally with S. aureus, IgG1 anti-TSST-1 antibodies and toxin neutralizing activity was lacking in all of the acute phases and in the majority of convalescent sera, suggesting that these patients may be incapable of generating TSST-1 neutralizing antibodies. These new findings support the hypothesis that host factors are important in the development of mTSS and that the anti-toxin isotype impacts antibody functionality.

Reactivity of human natural antibodies to endothelial cells from Galalpha(1,3)Gal-deficient pigs

BACKGROUND

Xenoreactive human natural antibodies (NAb) are predominantly directed against galactose-alpha(1,3)galactose (Gal). Binding of immunoglobulin (Ig) G and IgM NAb activates porcine endothelial cells (pEC) and triggers complement lysis responsible for hyperacute xenograft rejection. In vitro, IgG NAb induce human natural killer (NK) cell-mediated lysis of pEC by antibody-dependent cell-mediated cytotoxicity (ADCC). The present study examined the levels of anti-porcine NAb in a large number of individuals and addressed the functional role of non-Gal anti-porcine NAb.

METHODS

Sera from 120 healthy human blood donors were analyzed for the presence of anti-porcine NAb by flow cytometry using porcine red blood cells (pRBC), lymphoblastoid cells (pLCL), and pEC derived from control or Gal-deficient pigs. Xenogeneic complement lysis was measured by flow cytometry using human serum and rabbit complement. ADCC was analyzed by chromium-release assays using human serum and freshly isolated NK cells.

RESULTS

Human IgM binding to pRBC was found in 93% and IgG binding in 86% of all samples. Non-Gal NAb comprised 13% of total IgM and 36% of total IgG binding to pEC. NAb/complement-induced lysis and ADCC of Gal-deficient compared to Gal-positive pEC were 21% and 29%, respectively. The majority of anti-Gal and non-Gal IgG NAb were of the IgG2 subclass.

CONCLUSIONS

The generation of Gal-deficient pigs has overcome hyperacute anti-Gal-mediated xenograft rejection in nonhuman primates. Non-Gal anti-porcine NAb represent a potentially relevant immunological hurdle in a subgroup of individuals by inducing endothelial damage in xenografts.

Incidence and clinical significance of anti-PF4/heparin antibodies of the IgG, IgM, and IgA class in 755 consecutive patient samples referred for diagnostic testing for heparin-induced thrombocytopenia

BACKGROUND

Heparin-induced thrombocytopenia (HIT) is usually caused by anti-platelet factor 4 (PF4)/heparin antibodies, leading to intravascular platelet activation. These antibodies can be detected by PF4/polyanion antigen assays or platelet activation assays. While antigen assays are very sensitive and recognize immunoglobulin (Ig)G, IgA, and IgM antibodies, the role of IgM and IgA HIT-antibodies is debated. Platelet activation assays recognize IgG and are more specific for clinical HIT.

METHODS

We analyzed sera from 755 consecutive patients referred for diagnostic testing for HIT using a PF4/heparin enzyme-linked immunosorbent assay (ELISA) for IgG, IgA, and IgM and by the heparin-induced platelet activation (HIPA) test. Clinical information was provided by the treating physicians.

RESULTS

A total of 108 of 755 (14.3%) patients tested positive, 105 (13.9%) in the PF4/heparin IgG/A/M ELISA [28 (26.7%) only for IgM/A]; 53 (7.0%) sera were positive in the HIPA, of those 50 tested also positive in the ELISA. In 77 patients sufficient clinical information was provided. Available clinical information for 17 of the 28 patients who had only IgM and/or IgA detected showed plausible alternative (non-HIT) explanations in four of seven who had thromboembolic complications and in nine of 10 who had isolated HIT.

CONCLUSION

Detection of IgG, IgM and IgA class antibodies by PF4/heparin ELISA yields a positive test result about twice as often as does a platelet activation assay, with only a minority of the additional patients detected likely having HIT. Thus, there is a potential for considerable over-diagnosis of HIT by laboratories that utilize only an ELISA for diagnostic testing.

Optimization of antibodies for detection of the mismatch repair proteins MLH1, MSH2, MSH6, and PMS2 using a biotin-free visualization system

Testing for microsatellite instability (MSI) has become an important step in the planning of therapeutic and follow-up procedures for patients with colorectal cancer, both as a prognostic marker and as a screening tool for hereditary non-polyposis colorectal cancer. Today the gold standard for MSI testing is based on the polymerase chain reaction. Immunohistochemistry may represent an alternative or complement to molecular MSI testing. Antibodies against the protein products of the most commonly affected mismatch repair genes (hMLH1, hMSH2, hMSH6, and hPMS2) have been available for some time now. However, the quality of the primary antibody and optimization of the antigen retrieval methods are essential to get reproducible results. The aim of the present study was to test and optimize a panel of antibodies against the mismatch repair proteins MLH1, MSH2, MSH6, and PMS2 using biotin-free, polymer-based visualization systems. The antibodies were tested on multitissue blocks containing normal tissue and tumor tissue from patients with known microsatellite-stable and microsatellite-instable tumors. For all four antibody groups, the chosen clones gave specific and reproducible staining. Furthermore, with the PowerVision+ detection system, the influence of endogenous biotin was eliminated, the incubation time with the primary antibody was significantly reduced, and the primary antibody could be further diluted. The authors found that immunohistochemistry may provide a cost-effective and time-saving complement to the molecular MSI analysis, and using the PowerVision+ detection system has greatly decreased the turnaround time as well as reduced the cost of immunohistochemistry in the authors' laboratory.

HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies

The key requirement for successful immunochemical assay is the availability of antibodies with high specificity and desired affinity. Small molecules, when used as haptens, are not immunogenic. However, on conjugating with carrier molecule they elicit antibody response. The production of anti-hapten antibodies of desired specificity largely depends on the hapten design (preserving greatly the chemical structure and spatial conformation of target compound), selection of the appropriate carrier protein and the conjugation method. This manuscript describes a curated database HaptenDB, where information is collected from published literature and web resources. The current version of the database has 2021 entries for 1087 haptens and 25 carrier proteins, where each entry provides comprehensive details about (1) nature of the hapten, (2) 2D and 3D structures of haptens, (3) carrier proteins, (4) coupling method, (5) method of anti-hapten antibody production, (6) assay method (used for characterization) and (7) specificities of antibodies. The current version of HaptenDB covers a wide array of haptens including pesticides, herbicides, insecticides, drugs, vitamins, steroids, hormones, toxins, dyes, explosives, etc. It provides internal and external links to various databases/resources to obtain further information about the nature of haptens, carriers and respective antibodies. For structure similarity comparison of haptens, the database also integrates tools like JME Editor and JMOL for sketching, displaying and manipulating hapten 2D/3D structures online. So the database would be of great help in identifying functional group(s) in smaller molecules using antibodies as well as for the development of immunodiagnostics/therapeutics by providing data and procedures available so far for the generation of specific or cross-reactive antibodies.

AVAILABILITY

HaptenDB is available on http://www.imtech.res.in/raghava/haptendb/ and http://bioinformatics.uams.edu/raghava/haptendb/ (Mirror site).

Phage Display‐Derived Human Antibodies Against Specific Glycosaminoglycan Epitopes

Glycosaminoglycans (GAGs) are long unbranched polysaccharides, most of which are linked to a core protein to form proteoglycans. Depending on the nature of their backbone, one can discern galactosaminoglycans (chondroitin sulfate [CS] and dermatan sulfate [DS]) and glucosaminoglycans (heparan sulfate [HS], heparin, hyaluronic acid, and keratan sulfate). Modification of the backbone by sulfation, deacetylation, and epimerization results in unique sequences within GAG molecules, which are instrumental in the binding of a large number of proteins. Investigating the exact roles of GAGs has long been hampered by the lack of appropriate tools, but we have successfully implemented phage display technology to generate a large panel of antibodies against CS, DS, HS, and heparin epitopes. These antibodies provide unique and highly versatile tools to study the topography, structure, and function of specific GAG domains. In this chapter, we describe the selection, characterization, and application of antibodies against specific GAG epitopes.

The glycopeptide CSF114(Glc) detects serum antibodies in multiple sclerosis

Synthetic glycopeptides have the potential to detect antibodies in multiple sclerosis (MS). In the present study, we analyzed the antibodies (IgM class, IgG class and IgG subclasses) to the synthetic glycopeptide CSF114(Glc) in the serum of 186 MS patients, 166 blood donors (BDs), 25 patients affected by meningitis/encephalitis, 41 affected by systemic lupus erythematosus (SLE) and 49 affected by rheumatoid arthritis (RA). The IgM antibody level to CSF114(Glc) was significantly increased in MS patients versus BDs (p<0.001) or versus other autoimmune diseases (SLE or RA, p<0.001). The IgG response was restricted to the subclass IgG2. IgM antibodies to CSF114(Glc) were found in 30% of relapsing/remitting MS patients and, at lower levels, in subjects affected by meningitis/encephalitis. The study of antibodies to CSF114(Glc) is a new, potential immunological marker of MS.

Detecting antibodies with similar reactivity patterns in the HLDA8 blind panel of flow cytometry data

The blind panel collected for the 8th Human Leucocyte Differentiation Antigens Workshop (HLDA8; ) included 49 antibodies of known CD specificities and 76 antibodies of unknown specificity. We have identified groups of antibodies showing similar patterns of reactivity that need to be investigated by biochemical methods to evaluate whether the antibodies within these groups are reacting with the same molecule. Our approach to data analysis was based on the work of Salganik et al. (in press) [Salganik, M.P., Milford E.L., Hardie D.L., Shaw, S., Wand, M.P., in press. Classifying antibodies using flow cytometry data: class prediction and class discovery. Biometrical Journal].

Antibodies to peripheral nerve myelin proteins in chronic inflammatory demyelinating polyradiculoneuropathy

Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is an acquired disorder of the peripheral nervous system with a probable auto-immune pathogenesis. The nature of the responsible autoantigens is unclear in most patients. We used the Western immunoblot technique to seek antibodies to peripheral nerve protein antigens. Sera from eight of 32 (25%) CIDP patients, 12 of 37 (32%) Guillain-Barré syndrome (GBS) patients, zero of 30 (0%) chronic idiopathic axonal polyneuropathy patients and two of 39 (5%) healthy control subjects contained anti-peripheral nerve protein antibodies. The frequency of such antibodies was significantly greater in both CIDP (p = 0.04) and GBS (p = 0.003) patients than in normal control subjects. For CIDP patients, there were non-significant trends for antibodies to be more common in females and in those who responded to treatment with either intravenous immunoglobulin or plasma exchange. The commonest antibodies were directed against a band at 28 kDa, resembling that labelled by a monoclonal antibody against myelin protein zero (P0). Six CIDP and seven GBS patients' sera reacted with this band. These results support the view that antibodies to myelin proteins, and especially P0, are present in the serum of some patients with CIDP and GBS.

Lamprey neurofilaments contain a previously unreported 50-kDa protein

We have previously hypothesized that regeneration of axons after spinal cord injury in the lamprey may involve assembly and transport of neurofilaments (NFs) into the growing tip. A single NF, NF-180, has been cloned in this laboratory and until now was thought to be the only NF subunit in lamprey nervous system. However, homopolymerization of NF-180 has not been observed either in experiments on transfected cells or in self-assembly tests in vitro. Forty-three monoclonal antibodies designated as LCM series were generated previously against cytoskeletal proteins of the lamprey nervous system. Seven LCMs were NF specific, and five were keratin specific, as demonstrated by immunohistochemistry. In the present study, one antibody, LCM40, selectively labeled axons in immunohistochemical sections and recognized a single 50-kDa protein in Western blots. Other neuron-specific LCMs and anti-NF antibodies, e.g., LCM39, recognized a known NF subunit, NF-180. Two-dimensional (2-D) gel electrophoresis was employed to separate otherwise indistinguishable individual cytoskeletal proteins. Western blot analysis with an antibody (IFA) that selectively labels all known intermediate filaments indicated that this 50-kDa protein is an intermediate filament (IF). The new protein was incorporated into IF polymers in vitro. Immunoelectron microscopy confirmed that neuronal IFs contain this novel protein. These results suggest that the 50-kDa protein is a previously unrecognized neuronal IF subunit in the lamprey.

Celiac disease-related antibodies in an epilepsy cohort and matched reference population

Celiac disease (CD) is a common immunologically mediated enteropathic condition manifesting in genetically predisposed individuals after exposure to wheat gluten. CD may be associated with a number of neurological disorders, and the prevalence of epilepsy is reported to be increased in patients with CD. We studied the prevalence of CD-associated antibodies in a cohort of 968 patients with epilepsy and in a population-based reference group of 584 subjects. There was no difference in the prevalence of IgA and IgG class antigliadin antibodies (AGAbA and AGAbG, respectively), endomysial antibodies (EMA), and tissue transglutaminase antibodies (tTGAbA) between patients with epilepsy and the control population. This suggests the presence of CD to be the same in patients with epilepsy and the reference population. However, AGAbA was more prevalent in patients with primary generalized epilepsy (19.6%) than in the reference population (10.6%, relative risk 1.8, 95% confidence interval 1.1-3.0, P=0.012).

A multicolor fluorescence immunostaining technique for simultaneous antigen targeting

A general problem in immunocytochemistry is the development of a reliable multiple immunolabeling method with primary antibodies originating from the same host species. Here, we briefly outline different approaches intended to close this technological gap and focus on multiple immunolabeling with monoclonal primary antibodies. To this end, we generated a basic universal protocol for the use of secondary antibodies selectively recognizing different isotypes/subclasses of monoclonal primary antibodies. This approach is widely applicable and offers a simple procedure for simultaneously detecting two or more antigens.

VAP1, with cystatin C motif, an oocyte protein encoded by a novel ovarian-specific gene during oogenesis in the common brushtail possum (Trichosurus vulpecula)

In the brushtail possum oocyte, vesicles accumulate in a polarized fashion at the vegetal pole and cytoplasm rich in mitochondria and containing the germinal vesicle comprise the animal pole. During cleavage to early blastocyst stages, animal pole cytoplasm locates to the cells of the embryonic hemisphere (pluriblast) and vegetal pole vesicular cytoplasm to cells of the abembryonic hemisphere (trophoblast). Previously identified 16 amino acid residues, associated with the vesicle-rich cytoplasm were used for molecular cloning and characterization of a vesicle associated protein, VAP1. The degenerate primer was used in a 3'RACE for vap1 gene cloning. The cDNA encoding VAP1 was 516 bp in length with no significant homologies and coded for 172 amino acid residues for the mature protein. The N-terminal domain of VAP1 showed a structural homology to the cysteine protease inhibitor, Cystatin. Gene expression studies during oogenesis revealed that vap1 had an ovary-specific, possibly oocyte-specific expression, which occurs during follicle formation and growth and in adult ovaries. Recombinant VAP1 fusion protein generated polyclonal antibodies in the mouse and in the brushtail possum.

Motor nerve damage is associated with anti-ganglioside antibodies in diabetes

Few reports exist on the association between the humoral immune response to glycolipids and neuropathic findings in diabetes. To address this issue, we assayed serum anti-GM1, GD1b, GD1a, and sulfatides IgG and IgM in a group of 85 non-selected diabetic patients, and correlated these antibodies to clinical and electrophysiological findings. Diabetic patients had higher mean titers of anti-GM1 (IgM), GD1b, GD1a, and sulfatide (IgG) antibodies when compared to healthy controls. Patients with a positive titer of anti-ganglioside antibodies had significant alterations of motor conduction parameters. The statistical significance increased when considering those patients with both anti-ganglioside reactivity and a high value for glycosylated hemoglobin. Production of antibodies to ganglioside may follow the exposure of hidden motor nerve epitopes in damaged motor nerves and contribute to the neuropathy.

Immunological profile of patients awaiting a renal transplant

BACKGROUND

A renal transplant is the best possible treatment for patients with terminal renal failure. Advances in the development of techniques of screening of pre-formed antibodies have contributed to a notable improvement in the results obtained with allogenic transplants.

METHODS

The aim of the present work is to study the nature, class, isotype and specificity of antibodies detected in patients awaiting renal transplantation at Complejo Hospitalario Universitario Juan Canalejo, as well as their relation with the level of anti-human leucocyte antigen (HLA) sensitization.

RESULTS

In all patient groups, there was a predominance of IgG. The distribution of anti-HLA antibody class showed that the most frequent pattern corresponded to a mixture of class I and class II antibodies for all groups. The study of specificity of anti-HLA antibody showed that of the patients with at least one previous transplant, 72% developed specific anti-HLA antibodies against some of the incompatible antigens of the donor, 12% against HLA antigens not related with the phenotype of the donor and in 16% it was not possible to determine their specificity. Most patients developed antibodies against antigens of locus B, probably because of that the number of incompatibilities contributed by the donors is also greater for locus B.

CONCLUSIONS

The exhaustive study of sera of patients on a waiting list for transplantation with respect to the nature, isotype, class and specificity of the antibody is important since it is possible that different antibodies can bring about, in the transplant, events that will have different consequences for the survival of the graft.

Production and purification of monoclonal and polyclonal antibodies against cholera toxin

The aim of this study was to produce monoclonal and polyclonal antibodies against cholera toxin (CT). Hyperimmune ICR mice produced polyclonal antibodies (PAbs) after injection with 0.5 mL of pristane and were injected with NS-1 myeloma cells 2 weeks later. Hyperimmune Balb/c mice were used for the production of monoclonal antibodies (MAbs). After these mice were immunized four times and given a final boost, their spleen cells were collected and fused with NS-1 myeloma cells under the presence of PEG 1500. The fused cells were then selected in the hypoxanthine, aminopterin, and thymidine (HAT)-RPMIX medium. Anti-CT antibody-secreting hybridoma cell lines with high titer were cloned by enzyme-linked immunosorbent assay (ELISA) and then subcloned by limiting dilution in 15% fetal bovine serum (FBS) HT-RPMIX medium. Eleven murine hybridoma producing anti-CT MAbs were obtained and designated CT-A2, CT-B4, CT-B11, CT-C7, CT-D7, CT-E8, CT-F4, CT-F2, CT-F8, CT-E3, CT-E6. Isotypes of MAbs were identified as IgM heavy chain and all were lambda light chain. Hitrap rProtein A and Hitrap IgM purification columns were used for the purification of PAbs and MAbs, respectively.

SCOP database in 2004: refinements integrate structure and sequence family data

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

The Remarkable Flexibility of the Human Antibody Repertoire; Isolation of Over One Thousand Different Antibodies to a Single Protein, BLyS

It is well established that the humoral immune response can generate antibodies to many different antigens. The antibody diversity required to achieve this is believed to be substantial. However, the extent to which the immune repertoire can generate structural diversity against a single target antigen has never been addressed. Here, we have used phage display to demonstrate the extraordinary capacity of the human antibody repertoire. Over 1000 antibodies, all different in amino acid sequence, were generated to a single protein, B-lymphocyte stimulator (BLyS protein). This is a highly diverse panel of antibodies as exemplified by the extensive heavy and light chain germline usage: 42/49 functional heavy chain germlines and 19/33 V(lambda) and 13/35 V(kappa) light chain germlines were all represented in the panel of antibodies. Moreover, a high level of sequence diversity was observed in the V(H) CDR3 domains of these antibodies, with 568 different amino acid sequences identified. Thus we have demonstrated that specific recognition of a single antigen can be achieved from many different VDJ combinations, illustrating the remarkable problem-solving ability of the human immune repertoire. When studied in a biochemical assay, around 500 (40%) of these antibodies inhibited the binding of BLyS to its receptors on B-cell lines. The most potent antibodies inhibited BLyS binding with sub-nanomolar IC(50) values and with sub-nanomolar affinities. Such antibodies provide excellent choices as candidates for the treatment of BLyS-associated autoimmune diseases.

Effect of age on immunoglobulin A subclass distribution in human parotid saliva

Two subclasses of immunoglobulin A (IgA) antibodies are produced in humans, IgA1 and IgA2, IgA2 being more resistant to digestion by bacterial proteases than IgA1. The amount of IgA in saliva has been shown to vary with age; however, little is known about the correlation between IgA subclass distribution in saliva and age. The purpose of this study was to determine whether differences exist in the levels and ratio of IgA subclasses in parotid saliva of children and adults. Parotid saliva was obtained from healthy children (age range 6-12 years, n = 14) and adults (age range 22-51 years, n = 20) using Schaefer cups. Samples were analyzed for levels of total IgA, IgA1, and IgA2 by ELISA. IgA and IgA1 levels were significantly higher in adults than in children. However, no differences were seen in the ratio of IgA1 and IgA2 in the two groups of subjects. These findings indicate that levels of IgA increase with age, whereas the IgA subclass ratio is established early in life.

Three Forms of Immune Myasthenia

We propose a new classification for immune myasthenia based on antibody pattern. The types of immune myasthenia presently characterized by known antibody targets segregate into three groups: type 1, in which the muscle target is the acetylcholine receptor only; type 2, in which titin antibodies are present in addition to acetylcholine receptor antibodies; and type 3, in which muscle-specific kinase antibodies are present in the absence of acetylcholine receptor antibodies. The immune target is unknown in the patients with immune myasthenia not associated with these antibodies. This classification has advantages over the present classifications as regards homogeneity of groups, etiology, mechanism of disease, and prognosis.

Antibodies in Myasthenia Gravis and Related Disorders

Acetylcholine receptor (AChR) antibodies are present in around 85% of patients with myasthenia gravis (MG) as measured by the conventional radioimmunoprecipitation assay. Antibodies that block the fetal form of the AChR are occasionally present in mothers who develop MG after pregnancy, especially in those whose babies are born with arthrogryposis multiplex congenita. The antibodies cross the placenta and block neuromuscular transmission, leading to joint deformities and often stillbirth. In these mothers, antibodies made in the thymus are mainly specific for fetal AChR and show restricted germline origins, suggesting a highly mutated clonal response; subsequent spread to involve adult AChR could explain development of maternal MG in those cases who first present after pregnancy. In the 15% of "seronegative" MG patients without AChR antibodies (SNMG), there are serum factors that increase AChR phosphorylation and reduce AChR function, probably acting via a different membrane receptor. These factors are not IgG and could be IgM or even non-Ig serum proteins. In a proportion of SNMG patients, however, IgG antibodies to the muscle-specific kinase, MuSK, are present. These antibodies are not found in AChR antibody-positive MG and are predominantly IgG4. MuSK antibody positivity appears to be associated with more severe bulbar disease that can be difficult to treat effectively.

Structural modeling extends QSAR analysis of antibody-lysozyme interactions to 3D-QSAR

This work shows that quantitative multivariate modeling is an emerging possibility for unraveling protein-protein interactions using a combination of designed mutations with sequence and structure information. Using this approach, it is possible to stereochemically determine which residue properties contribute most to the interaction. This is illustrated by results from modeling of the interaction of the wild-type and 17 single and double mutants of a camel antibody specific for lysozyme. Linear multivariate models describing association and dissociation rates as well as affinity were developed. Sequence information in the form of amino acid property scales was combined with 3D structure information (obtained using molecular mechanics calculations) in the form of coordinates of the alpha-carbons and the center of the side chains. The results show that in addition to the amino acid properties of the mutated residues 101 and 105, the dissociation rate is controlled by the side-chain coordinate of residue 105, whereas the association is determined by the coordinates of residues 99, 100, 105 (side chain), 111, and 112. The great difference between the models for association and dissociation rates illustrates that the event of molecular recognition and the property of binding stability rely on different physical processes.

Distribution of Th1- and Th2-induced anti-factor VIII IgG subclasses in congenital and acquired hemophilia patients

Development of antibodies (Ab) that inhibit the procoagulant function of factor VIII (fVIII) seriously complicates the treatment of hemophilia A patients. It also causes acquired hemophilia, a rare yet serious autoimmune disease. The design of effective fVIII-specific tolerizing procedures will require lucidation of the role of the different CD4(+) T cell subsets that drive inhibitor synthesis. To examine the contribution of Th1 and Th2 cells in the anti-fVIII Ab response, we measured the concentration of Th1- and Th2-driven anti-fVIII IgG subclasses in 17 patients with severe hemophilia A and 18 patients with acquired hemophilia. We found that both congenital and acquired hemophilia patients had similar and comparable proportions of Th1- and Th2-induced anti-fVIII Ab, suggesting a more important role of Th1 cells in the immune response to fVIII than previously appreciated. The distribution of anti-fVIII IgG subclasses was stable for periods of up to six months. More intense anti-fVIII Ab responses and higher inhibitor titers correlated with a predominance of Th2-driven subclasses. In contrast, Th1-driven anti-fVIII Ab were predominant in patients who had low anti-fVIII Ab concentrations, even when this was the result of successful immune tolerance or immunosuppressive therapy, which had caused drastic reduction or disappearance of inhibitors. Thus, synthesis of Th2-driven inhibitors occurs when the anti-fVIII Ab response is intense, while Th1 cells may be involved in the long-term maintenance of anti-fVIII Ab synthesis.

Distinct epitopes on formiminotransferase cyclodeaminase induce autoimmune liver cytosol antibody type 1

Liver cytosol antibody type 1 (LC1) is regarded as a serologic marker of type 2 autoimmune hepatitis, in addition to liver kidney microsomal antibody type 1. Among 38 patients with type 2 autoimmune hepatitis, 23 were positive for LC1 antibodies. The antigen recognized by LC1 has been identified as a liver-specific 58-kd metabolic enzyme named formiminotransferase cyclodeaminase (FTCD). All 23 LC1-positive sera immunoprecipitated rat FTCD, and 22 gave an identity reaction with rat FTCD by immunodiffusion. No reaction was observed with sera from 10 patients with type 1 autoimmune hepatitis, 10 with primary biliary cirrhosis, 10 with chronic hepatitis C, and 10 healthy controls. By Western immunoblotting all 23 LC1-positive sera and all the controls tested negative, suggesting that all the antigenic epitopes were destroyed by denaturation. FTCD is a bifunctional protein composed of distinct globular FT and CD domains connected by a short linker. To identify epitopes that trigger the LC1 autoimmune response, we tested LC1 antibodies against FTCD constructs encoding the N-terminal FT domain (amino acids 1-339), or the C-terminal CD domain (amino acids 332-541). Of 20 sera positive against full-length FTCD, 8 (40%) recognized the FT domain and the CD domain, 7 (35%) recognized only the FT domain, and 5 (25%) did not recognize either construct. No sera reacted with only the CD domain. These data indicate that multiple regions of FTCD trigger the LC1 autoimmune response, and that LC1 reactivity is mainly directed to conformation-sensitive epitopes located in the FT region of FTCD.

Epitope mapping of 53 antibodies against prostate-specific antigen

A panel of 53 antibodies from the ISOBM TD-3 PSA Workshop were tested for reactivity with iodinated derivatives of free PSA or the alpha1-antichymotrypsin PSA complex using the BIAcore system. Two antibodies (#69 and #83) showed low binding (<8%) for both antigens. One group of antibodies (#25, #26, #33, #54, #68, #73, #77, #78 and #91) had a much lower affinity for the complex (<12%) than for the free antigen (>65%). According to the mapping study, it was possible to categorize the antibodies into 29 different groups. Four antibodies were not classified. The two-dimensional representation of all interactions between the antibodies showed a complex network on the PSA molecule. Antibodies with lower affinity for the complex than for the free PSA appeared to bind epitopes in a common region, and thus it was not possible to perform sandwich assays with antibodies specific for free PSA.

The association of CD18 alleles with anti-myeloperoxidase subtypes of ANCA-associated systemic vasculitides

Wegener granulomatosis (WG), microscopic polyangiitis (MP), and Churg Strauss syndrome (CSS) are rare systemic autoimmune disorders. Common features are anti-neutrophil cytoplasmic antibodies (ANCA) in patient sera. Whereas WG patients show mainly anti-proteinase 3 ANCA, MP and CSS patients typically present anti-myeloperoxidase (MPO) ANCA. ANCA play an important role in the pathogenesis in the vessel wall by activating polymorphonuclear cells (PMN) and increased adhesivity between PMN and endothelial cells via adhesion molecules. Here we investigated major adhesion molecules as predisposition factors via common polymorphisms in or in the vicinity of the candidate genes ICAM-1, e-selectin, PLAUR, CD11b, and CD18. A restriction fragment-length polymorphism in exon 11 of the CD18 gene was associated with MPO-ANCA(+) systemic vasculitis. Our data indicate that a common variant of the CD18 gene confers increased risk for CSS and MP, supporting that genetic factors are involved in the etiology and pathogenesis of ANCA-associated systemic vasculitides.

Induction of antibodies to methadone during methadone maintenance treatment of heroin addicts and its possible clinical implications

By means of two different types of enzyme-linked immunosorbent assay (ELISA) techniques, antibodies to methadone were detected in blood plasma of heroin addicts on methadone maintenance treatment. In 11-15% of cases immunoglobulin (Ig) M antibodies were detected, while IgG antibodies were observed in 33-40%. At least two types of antibodies to methadone were induced-antibodies with high affinity to methadone and low-affinity antibodies more specific for morphine than for methadone. The methadone antibody-positive group of patients had a significantly higher plasma methadone concentration--440 ng/ml, than the antibody-negative group--250 ng/ml (P < 0.005) despite almost the same mean therapeutic doses of methadone. Of patients with all types of antibodies to methadone 52% were human immunodeficiency virus (HIV)-positive, whereas in the group without antibodies, HIV-positive reactions were observed in 10.5% only (P < 0.002). Alternatively, 87.5% of HIV-positive patients had antibodies to methadone, a fact which should be taken into consideration during methadone dose adjustment.

Seasonal variation of IgG subclass antibodies to house dust mite in sera from mite-sensitive asthmatic patients

BACKGROUND

House dust mite is an important cause of bronchial asthma. Seasonal variation of environmental house dust mite allergen levels and the specific IgE antibody to house dust mite have been reported.

OBJECTIVE

We studied the changes in IgG subclass antibodies to house dust mite associated with seasonal variation of house dust mite allergen levels in houses of mite-sensitive asthmatic patients.

METHODS

In 14 mite-sensitive asthmatic patients, house dust mite allergen (Der f 1) contents in bedding were measured monthly, and IgG subclass antibodies to house dust mite, Dermatophagoides farinae (D. farinae), were determined by enzyme-linked immunosorbent assay (ELISA) every 3 months from July to December.

RESULTS

The concentration of Der f 1 in dust from bedding reached maximum levels in August and September, and significantly decreased in November and December compared with August and September (P < .05). Levels of D. farinae-specific IgG4 antibodies significantly decreased in December compared with September (P < .05) with no statistically significant change between September and June (P > .05). Levels of D. farinae-specific IgG2 antibodies decreased significantly in December compared with June (P < .05). The levels of IgG1 and IgG3 antibodies to D. farinae showed no significant differences during the study period.

CONCLUSION

These findings suggest that seasonal changes in natural exposure to house dust mite allergen might lead to concurrent changes in specific IgG4 antibodies to house dust mite in mite-sensitive asthmatic patients and each IgG subclass antibodies to house dust mite might have a different kinetics.

[A rapid polycationic method for typing erythrocyte antibodies in liquid blood and stains]

The new rapid polycationic method for typing erythrocytic antibodies in liquid blood and its smears permits a rapid (within 4-5 min) detection of antibodies of virtually all erythrocytic isoserological systems ABO, MNSs, Rh, P, Lewis, Duffy, and Kidd in liquid blood and the group isohemagglutinins and incomplete Rh antibodies in blood smears. The test is performed on plane surface at ambient temperature and requires no special equipment. The sensitivity of the proposed method is much superior to that of the most sensitive and routine tests: enzymatic, antiglobulin, and salt. The only exclusion were anti-K antibodies, the majority of which were not detected by modern polycationic (tube and plane) methods.

Humoral immune response against Campylobacter jejuni lipopolysaccharides in Guillain-Barré and Miller Fisher syndrome

In this study we characterized the IgG antibodies against lipopolysaccharides (LPS) of Campylobacter jejuni in serum from patients with Guillain-Barré syndrome (GBS), Miller Fisher syndrome (MFS), C. jejuni enteritis and normal controls. In patients with GBS and MFS long-lasting titers of IgG1 and IgG3 antibodies against LPS from GBS and MFS associated C. jejuni were found. The subclass and course of these antibodies were highly associated with those of antibodies against GM1 and GQ1b in GBS and MFS patients. However, in C. jejuni enteritis and normal controls anti-LPS antibodies were predominantly IgG2. Antibody binding with LPS was reduced after treatment with choleratoxin and sialidases, suggesting that the ganglioside-like epitopes in LPS are immunodominant. These results further indicate that antecedent C. jejuni infections determine the specificity and isotype of anti-ganglioside antibodies in GBS and MFS patients.

Maternal influence on IgG subclass antibodies to Bet v 1 during the first 18 months of life as detected with a sensitive ELISA

BACKGROUND

The initial encounters with allergens are crucial for sensitisation later in life. The IgG1 responses to house dust mite in infancy are later accompanied by an IgG4 response, with high levels seen particularly in atopic children. Little is known of the development of IgG subclass responses to other inhalant allergens. The aims of this study were to develop a sensitive method for the study of postnatal immune responses to the important seasonal inhalant allergen Bet v 1.

METHODS

Antibodies to rBet v 1 were analyzed in 96 children at birth, 6 and 18 months using a sensitive enzyme-amplified ELISA.

RESULTS

Immunoglobulin G responses to rBet v 1, mainly of the IgG1 subclass, were common in young children, and could at 6 months be demonstrated in several infants who had not yet experienced a postnatal birch pollen season. Atopic dermatitis was associated with high levels of IgG subclass antibodies to birch at 18 months. Maternal atopy was associated with high levels of all IgG subclass antibodies to rBet v 1 in cord blood. In postnatally birch-pollen-exposed infants with atopic mothers, the levels of IgG antibodies at birth correlated with the levels at 6 months. In contrast, high antibody levels to rBet v 1 at birth were associated with low IgG titres to rBet v 1 at 18 months.

CONCLUSIONS

IgG1 responses to birch are common during the first 18 months of life. High levels of maternally derived birch-specific IgG antibodies are associated with maternal atopy and may influence the development of the IgG antibody responses to birch in their child.

Glomerular basement membrane antibodies in hantavirus disease (hemorrhagic fever with renal syndrome)

The prevalence of antibodies against glomerular basement membrane (GBM) antigens in sera from 47 patients with serologically verified hantavirus (Puumala serotype) infection were investigated. Antibodies were measured by immunoassays using as antigen a crude human GBM preparation and the NC1 portion of type IV collagen (Goodpasture antigen), respectively. Seventy-seven percent of the patients had IgM antibodies against the non-Goodpasture glomerular basement membrane (non-GP GBM) in their acute phase serum samples as compared to only 4% seropositivity rate in convalescent phase samples. However, there was no correlation between the non-GP GBM IgM antibody levels and the decrease in GFR as measured by Cr EDTA clearance. None of the patients had antibodies against the Goodpasture antigen. In a control group of 10 patients with influenza and parainfluenza infections serum IgM against non-GP GBM could not be demonstrated, neither in acute phase nor in convalescent phase sera. The possible pathophysiological implications of these findings are discussed.

Antibody-antigen recognition: a canonical structure paradigm

The antibodies of known three-dimensional structure exhibit a definite number of conformations (canonical structures) for five of six hypervariable loops. In the present study it was found that approximately 85% of the immunoglobulin sequences analyzed fall into a small number of canonical structure combinations, representing only 3% of the total possible. These structures were classified into six distinct groups, depending on the type of antigen with which they interact. Within each loop, the positions responsible for maintaining these canonical structures show a use frequency of amino acids that fits an inverse power law, whereas the use frequency of the amino acids responsible for the detailed antigenic specificity follows an exponential distribution. We propose an evolutionary interpretation that connects these data, using the fact that the inverse power law is generated by statistical processes of the type that yield a wealth curve and the fact that exponential distribution is generated by processes that are not biased by past history.

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies

Loop regions of polypeptide in homologous proteins may be classified into structural families. A method is described by which this classification may be performed automatically and "key residue" templates, which may be responsible for the loop adopting a given conformation, are defined. The technique has been applied to the hypervariable loops of antibodies and the results are compared with the previous definition of canonical classes. We have extended these definitions and provide complete sets of structurally determining residues (SDRs) for the observed clusters including the first set of key residues for seven-residue CDR-H3 loops.