Graph-theoretical comparison of protein surfaces reveals potential determinants of cross-reactivity and the molecular mimicry.


:Different proteins, even without sequence similarity, still can contain similar surface regions involved in protein-protein interactions with common target. These regions can serve as structural determinants of cross-reactivity and molecular mimicry. Molecular mimicry, defined as the process in which structural properties of one molecule are simulated by the dissimilar molecules, is implicated in several biologically important processes, including autoimmune and allergic reactions, binding of some ligands to common receptor, and interactions in cell signaling. The problem of identification of the determinants of molecular mimicry is not completely solved at this time. We hypothesize that identification of structurally and chemically similar surface regions of two protein molecules capable of binding to the same target will allow us to identify sites involved in cross-reactivity including determinants of the molecular mimicry. We used a graph-theoretical approach in order to determine highly similar surface regions of two proteins with known three-dimensional structures. This approach uses a variation of Maximal Common Subgraph (MCS) isomorphism, where an association graph is constructed based on the surface-exposed residues of the two molecules and the matching regions are found based on the maximum cliques in the association graph. Testing the proposed method on the targets of autoantibody involved in antiphopholipid syndrome (APS)--beta2-GPI, PC, thrombin, factor IX, factor X, and plasmin allowed identifying potential epitopes for antibody that can inhibit coagulation proteases. Application of this method to the Activated Protein C and factor VII Gla-domains revealed surface regions involved in EPCR and plasma membrane binding, consistent with known experimental results. Analysis of major pollen allergen that can cause food allergies through cross-reactivity found known epitopes involved in cross-reactivity and also revealed additional surface regions that can complement the list of epitopes. Taken together, our results suggest that the proposed graph-theoretical approach can identify determinants of cross-reactivity and molecular mimicry.


Mol Immunol


Molecular immunology


Iakhiaev MA,Iakhiaev AV




Has Abstract


2010-01-01 00:00:00














  • Strategies for targeting complement inhibitors in ischaemia/reperfusion injury.

    abstract::A transplanted organ suffers inherently from an ischaemic insult and subsequent reperfusion injury. The severity of such early events is thought to influence the success of the transplant procedure, not only in the immediate post-transplant period, but also to predispose the graft to both acute and chronic rejection. ...

    journal_title:Molecular immunology

    pub_type: 杂志文章,评审


    authors: Dong J,Pratt JR,Smith RA,Dodd I,Sacks SH

    更新日期:1999-09-01 00:00:00

  • Genomic organisation of 34 kb of the human immunoglobulin lambda locus (IGLV): restriction map and sequences of new V lambda III genes.

    abstract::In order to improve our knowledge of the human immunoglobulin variable lambda locus (IGLV), we mapped one cosmid clone (designated as C40.2) isolated by screening a Colo320HSR genomic library. The 34 kb insert of the C40.2 clone was shown to contain six genes. One gene, IGLV2S1, belongs to the V lambda II subgroup. Fo...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Frippiat JP,Lefranc MP

    更新日期:1994-06-01 00:00:00

  • Maleimide conjugation markedly enhances the immunogenicity of both human and murine idiotype-KLH vaccines.

    abstract::The collection of epitopes present within the variable regions of the tumor-specific clonal immunoglobulin expressed by B cell lymphomas (idiotype, Id) can serve as a target for active immunotherapy. Traditionally, tumor-derived Id protein is chemically conjugated to the immunogenic foreign carrier protein keyhole lim...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Kafi K,Betting DJ,Yamada RE,Bacica M,Steward KK,Timmerman JM

    更新日期:2009-01-01 00:00:00

  • Analysis of immunoglobulin heavy chain delta transcription termination in the production of delta S or delta M mRNA.

    abstract::mRNA encoding secreted immunoglobulin is synthesized either by termination of transcription 3' to secreted terminus sequences and 5' to the membrane terminus sequences or by cleavage of a pre-mRNA transcript containing both secreted and membrane sequences at the appropriate polyadenylation site 5' to the membrane sequ...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Weiss EA,Tucker PW,Finkelman FD,Yuan D

    更新日期:1991-07-01 00:00:00

  • C-mip interacts physically with RelA and inhibits nuclear factor kappa B activity.

    abstract::The fine regulation of NF-kappaB activity is crucial for both resting and stimulated cells and relies on complex balance between multiple activators and inhibitors. We report here that c-mip, a recently identified pleckstrin homology (PH) and leucine-rich repeat (LRR)-domain-containing protein, inactivates GSKbeta and...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Kamal M,Valanciute A,Dahan K,Ory V,Pawlak A,Lang P,Guellaen G,Sahali D

    更新日期:2009-02-01 00:00:00

  • PAX2 oncogene negatively regulates the expression of the host defense peptide human beta defensin-1 in prostate cancer.

    abstract::Human beta defensin-1 (hBD1) is a component of the immune system which links the innate and adaptive immune responses. We have demonstrated that hBD1 induces rapid cytolysis of prostate cancer cells and that it may also possess tumor suppressive abilities. In addition, there is a high frequency of cancer-specific loss...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Bose SK,Gibson W,Bullard RS,Donald CD

    更新日期:2009-03-01 00:00:00

  • The role of poly(ADP-ribose) polymerase-1 inhibitor in carrageenan-induced lung inflammation in mice.

    abstract::Increasing indication is unveiling a role for poly(ADP-ribose) polymerase (PARP)-1 in the regulation of inflammatory/immune responses. The aim of the present study was to determine the potential anti-inflammatory effects of PARP-1 inhibitor 5-aminoisoquinolinone (5-AIQ) to explore the role of PARP-1 inhibitor in a mou...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Ahmad SF,Zoheir KM,Ansari MA,Korashy HM,Bakheet SA,Ashour AE,Al-Shabanah OA,Al-harbi MM,Attia SM

    更新日期:2015-02-01 00:00:00

  • HPLC purification of the main allergen of Parietaria judaica pollen.

    abstract::A two-step purification procedure of Par j I from the whole Parietaria judaica pollen extract is described. The first step consisted of gel filtration HPLC using a TSKG 3000 SW column, and 0.1% trifluoroacetic acid as the eluant. By this method, proteins were separated from the highly colored material present in the e...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Polo F,Ayuso R,Carreira J

    更新日期:1990-02-01 00:00:00

  • IL-12 and IL-23 modulate plasticity of FoxP3+ regulatory T cells in human Leprosy.

    abstract::Leprosy is a bacterial disease caused by M. leprae. Its clinical spectrum reflects the host's immune response to the M. leprae and provide an ideal model to investigate the host pathogen interaction and immunological dysregulation. Tregs are high in leprosy patients and responsible for immune suppression of the host b...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Tarique M,Saini C,Naqvi RA,Khanna N,Sharma A,Rao DN

    更新日期:2017-03-01 00:00:00

  • Atypical combined immunodeficiency due to Artemis defect: a case presenting as hyperimmunoglobulin M syndrome and with LGLL.

    abstract::SCID can be caused by various genetic mutations leading to distinctive phenotypes according to the presence of T, B and NK cells. Artemis is a gene encoded on chromosome 10p. The deficiency of this molecule causes an inability to repair DNA double strand breaks and is one of the causes of radiosensitive T-B-NK+ SCID. ...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Bajin İY,Ayvaz DÇ,Ünal S,Özgür TT,Çetin M,Gümrük F,Tezcan İ,de Villartay JP,Sanal Ö

    更新日期:2013-12-01 00:00:00

  • Cloning of a cDNA for a T cell produced molecule with a putative immune regulatory role.

    abstract::An expression cDNA library was constructed from the helper T cell hybridoma, A.1.1, which has been shown to produce constitutively proteins involved in the down regulation of the immune response. From this library we identified and characterized a cDNA clone, J6B7, by screening with a polyclonal antibody specific for ...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Lee C,Ghoshal K,Beaman KD

    更新日期:1990-11-01 00:00:00

  • Increased PD-1+CD154+ Tfh cells are possibly the most important functional subset of PD-1+ T follicular helper cells in adult patients with minimal change disease.

    abstract::T follicular helper (Tfh) cells, especially programmed cell death protein 1 (PD-1)+ Tfh cells, exert important functions in the normal immune response. The purpose of this study was to determine the frequency of different subsets of PD-1+ Tfh cells and their functional effects in adult patients with minimal change dis...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Li T,Shi Y,Sun W,Wang H,Wang Q,Jiang Y

    更新日期:2018-02-01 00:00:00

  • Maintaining dendritic cell viability in culture.

    abstract::When mouse dendritic cells (DCs) are isolated from tissues, purified and placed in a nutritive culture they die more rapidly than would be expected from their normal turnover in vivo. This can distort culture assays of DC function. We therefore tested several approaches to prolonging DC survival in culture. Of several...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Vremec D,Hansen J,Strasser A,Acha-Orbea H,Zhan Y,O'Keeffe M,Shortman K

    更新日期:2015-02-01 00:00:00

  • MicroRNA regulation of natural killer cell development and function in leukemia.

    abstract::MicroRNAs (miRNAs) are now recognized as important regulators of all cellular processes, including immune function and cancer survival. These evolutionary preserved, single-stranded, non-coding RNA molecules mediate important functional effects primarily through post-transcriptional regulation of protein expression. M...

    journal_title:Molecular immunology

    pub_type: 杂志文章,评审


    authors: Saultz JN,Freud AG,Mundy-Bosse BL

    更新日期:2019-11-01 00:00:00

  • Interleukin-1 receptor associated kinase 1 is a potential therapeutic target of anti-inflammatory therapy for systemic lupus erythematosus.

    abstract::Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease and currently has no effective therapy. The genome-wide analyses indicate that interleukin-1 receptor associated kinase 1 (IRAK1) is associated with the susceptibility of SLE in humans. In the present study, we identified that IRAK1 was ov...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Li M,Yu D,Ni B,Hao F

    更新日期:2017-07-01 00:00:00

  • Unique biochemical properties of a mutant MHC class I molecule, H-2Ksm1.

    abstract::This study describes serological and biochemical properties of a novel MHC class I molecule. The mutant H-2Ksm1 molecule was discovered in a mouse because of loss of reactivity of its peripheral blood lymphocytes to monoclonal antibodies. This mutation in the H-2Ks molecule is the first in vivo mutation described that...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Hasenkrug KJ,Kesari KV,Nathenson SG

    更新日期:1992-12-01 00:00:00

  • Studies of the antigenic structure of two cross-reacting proteins, pertussis and cholera toxins, using synthetic peptides.

    abstract::Peptide fragments of pertussis toxin subunit 1 (PT-S1) have been synthesized in order to investigate their antigenic and immunogenic activity, and to evaluate their possible use as components of a new vaccine. Two peptides (sequence 73-82, EAERAGRGTG and sequence 107-116, YVDTYGDNAG) were selected for their predictabl...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Presentini R,Perin F,Ancilli G,Nucci D,Bartoloni A,Rappuoli R,Antoni G

    更新日期:1989-01-01 00:00:00

  • RIP2-beta: a novel alternative mRNA splice variant of the receptor interacting protein kinase RIP2.

    abstract::RIP2/RICK/CARDIAK is a member of the receptor interacting protein kinase (RIP) family. RIP2 promotes NF-kappaB activation as well as activation of the MAPKs JNK, ERK1/2 and p38 MAPK, thereby playing an emergent role in the innate immune response and NOD signaling. Moreover, RIP2 has been shown to interact with the CAR...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Krieg A,Le Negrate G,Reed JC

    更新日期:2009-03-01 00:00:00

  • Molecular characterization of woodchuck CD4 (wCD4) and production of a depletion monoclonal antibody against wCD4.

    abstract::CD4 T cells play an important role in the immune response against hepatitis B virus (HBV) infection. Woodchucks represent an excellent animal model to study HBV infection. In this study, we characterized the cDNA sequence of woodchuck CD4 (wCD4). The deduced wCD4 protein has four extracellular immunoglobulin-like doma...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Yang Y,Zhang X,Zhang C,Tao Y,Fan W,Wang Z,Wang H,Lu M,Yang D,Fiedler M,Wang B

    更新日期:2013-11-01 00:00:00

  • Mucosal innate immune response to intragastric infection by Salmonella enterica serovar Choleraesuis.

    abstract::The innate immune response is critical to enteric disease resistance and the induction of mucosal adaptive immunity. In mucosae of the small intestine, Peyer's patches play a central role in immune surveillance and sampling of bacteria by specialized M cells. The innate immune response to Salmonella enterica serovar C...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Hyland KA,Kohrt L,Vulchanova L,Murtaugh MP

    更新日期:2006-04-01 00:00:00

  • Viral and bacterial minigene products are presented by MHC class I molecules with similar efficiencies.

    abstract::MHC class I molecules present short peptides, usually 8-10 amino acids in length, to CD8(+) T cells. These peptides are typically generated from full-length endogenously synthesized proteins degraded by the antigen processing machinery of the target cell. However, exogenous proteins, whether originating from intracell...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Wolf BJ,Princiotta MF

    更新日期:2011-01-01 00:00:00

  • H-2K molecules have two different C-termini, one of which is K-region specific.

    abstract::Amino acid sequences encoded by exon 8 of the H-2K and H-2D/L genes appear to be locus specific. The majority of H-2Kb molecules contain 10 amino acids that are derived from exon 8. In contrast, the H-2Db, -Dd and -Ld molecules contain only one amino acid which is encoded by exon 8, even though the genetic information...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Maloy WL,Lew AM,Anderson RW,Coligan JE

    更新日期:1988-05-01 00:00:00

  • Lupus-derived monoclonal autoantibodies against apoptotic chromatin recognize acetylated conformational epitopes.

    abstract:OBJECTIVE:Nuclear components targeted by autoantibodies are a characteristic feature of the autoimmune disease systemic lupus erythematosus (SLE). The nucleosome, a major autoantigen, is released in patients with SLE as a result of a disturbed apoptosis and/or an insufficient clearance of apoptotic debris. During apopt...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: van Bavel CC,Dieker JW,Tamboer WP,van der Vlag J,Berden JH

    更新日期:2010-11-01 00:00:00

  • The emerging role of nanomaterials in immunological sensing - a brief review.

    abstract::Nanomaterials are beginning to play an important role in the next generation of immunological assays and biosensors, with potential impacts both in research and clinical practice. In this brief review, we highlight two areas in which nanomaterials are already making new and important contributions in the past 5-10 yea...

    journal_title:Molecular immunology

    pub_type: 杂志文章,评审


    authors: Corrie SR,Plebanski M

    更新日期:2018-06-01 00:00:00

  • Cloning, expression and characterization of mugwort pollen allergen Art v 2, a pathogenesis-related protein from family group 1.

    abstract::Mugwort (Artemisia vulgaris) belongs to the Compositae family, and is one of the main causes of allergy in late summer and autumn. The aim of the study was to characterize the allergen Art v 2 from mugwort pollen. Skin prick tests, performed in 19 patients allergic to mugwort and 10 control patients, showed an Art v 2...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Arilla MC,Ibarrola I,Puente Y,Daza JC,Martínez A,Asturias JA

    更新日期:2007-07-01 00:00:00

  • The rabbit B cell antigen receptor is non-covalently associated with unique heteromeric protein complexes: possible insights into the membrane IgM/IgD coexpression paradox.

    abstract::We describe several proteins that are components of the rabbit B cell receptor complex. Two proteins (37 kDa and 42 kDa) were found in non-covalent association with IgM expressed on B cells from peripheral blood. These proteins were also immunoprecipitated by anti-B29 (Ig-beta) and anti-mb1 (Ig-alpha) monoclonal antib...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Fitts MG,Metzger DW,Hendershot LM,Mage RG

    更新日期:1995-07-01 00:00:00

  • CD4 regulation in human lymphoid non-T-cells: a role for the silencer element.

    abstract::In humans, the CD4 molecule is expressed on a subset of T-cells and at various levels on myeloid and lymphoid cells. The mechanisms regulating human CD4 gene expression are yet poorly understood. We speculated that the CD4 silencer, which operates in CD8+ T-cells to repress CD4 expression, could be responsible for CD4...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Mouly E,Dorival C,Pflumio F,Baillou C,Coulombel L,Levy Y,Lemoine FM,Klatzmann D,Marodon G

    更新日期:2007-01-01 00:00:00

  • Antigen degradation or presentation by MHC class I molecules via classical and non-classical pathways.

    abstract::Major histocompatibility complex (MHC) class I molecules usually present endogenous peptides at the cell surface. This is the result of a cascade of events involving various dedicated proteins like the peptide transporter associated with antigen processing (TAP) and the ER chaperone tapasin. However, alternative ways ...

    journal_title:Molecular immunology

    pub_type: 杂志文章,评审


    authors: Grommé M,Neefjes J

    更新日期:2002-10-01 00:00:00

  • Variation in the ordered structure of complexes between CD154 and anti-CD154 monoclonal antibodies.

    abstract::The cell surface co-stimulatory protein CD154 (CD40L) is a target for monoclonal antibody (mAb) inhibitors of T-cell mediated immune diseases. This protein, like most other members of the TNF ligand family, forms homotrimeric complexes on the cell surface and in solution, with a three-fold axis of symmetry. We find th...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Ferrant JL,Wilson CA,Benjamin CD,Hess DM,Hsu YM,Karpusas M,Roux KH,Taylor FR

    更新日期:2002-09-01 00:00:00

  • The dual specificity phosphatase transcriptome of the murine thymus.

    abstract::Properly regulated mitogen-activated protein (MAP) kinase activity is critical for normal thymocyte development. MAP kinases are activated by phosphorylation of tyrosine and threonine, and dual specificity phosphatases (DUSPs) can inactivate MAP kinases by dephosphorylating both tyrosine and threonine. However, a role...

    journal_title:Molecular immunology

    pub_type: 杂志文章


    authors: Tanzola MB,Kersh GJ

    更新日期:2006-02-01 00:00:00