Molecular modeling of antibody-antigen complexes between the Brucella abortus O-chain polysaccharide and a specific monoclonal antibody

A molecular model of the binding site of an anti-carbohydrateantibody (YsT9.1) has been developed using computer-assistedmodeling techniques and molecular dynamics calculations. Sequencehomologies among YsT9.1 and the Fv regions of McPC603, J539and human Bence-Jones protein REI, all of which have solvedcrystal structures, provided the basis for the modeling. Thegroove-type combining site model had a topography which wascomplementary to low energy confonners of the polysaccharide,a Brucella O-antigen, and the site could be almost completelyfilled by a pentasaccharide epitope in either of two dockingmodes. Putative interactions between this epitope and the antibodyare consistent with the known structural requirements for bindingand lead to the design of oligosaccharide inhibitors that probethe veracity of the modeled docked complex. Ultimately boththe Fv model and the docked complex will be compared with independentcrystal structures of YsT9.1 Fab with and without pentasaccharideinhibitor, currently at the stage of refinement.     

Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways

Proteins with similar structures may have different functions. Here, using a non-redundant two-chain protein-protein interface dataset containing 103 clusters, we show that this paradigm extends to interfaces. Whereas usually similar interfaces are obtained from globally similar chains, this is not always the case. Remarkably, in some interface clusters, although the interfaces are similar, the overall structures and functions of the chains are different. Hence, our work suggests that different folds may combinatorially assemble to yield similar local interface motifs. The preference of different folds to associate in similar ways illustrates that the paradigm is universal, whether for single chains in folding or for protein-protein association in binding. We analyze and compare the two types of clusters. Type I, with similar interfaces, similar global structures and similar functions, is better packed, less planar, has larger total and non-polar buried surface areas, better complementarity and more backbone-backbone hydrogen bonds than Type II (similar interfaces, different global structures and different functions). The dataset clusters may provide rich data for protein-protein recognition, cellular networks and drug design. In particular, they should be useful in addressing the difficult question of what the favorable ways for proteins to interact are.     

Modeling the uncleaved serpin antichymotrypsin and its chymotrypsin complex

In order to provide a structural reference for protein engineeringexperiments involving the serpin ₁-antichymotrypsin (ACT) andits complexes with chymotrypsin and DNA, a homology model ofACT has been constructed based on the 3-D structure of the relatedprotein ovalbumin [29% identical and 44% similar; see Stein,P., Leslie, A., Finch, J., Turnell, W., McLaughlin, P. and Carrell,R. (1990) Nature, 347, 99–102]. After mapping the aminoacid sequence of ACT onto the peptide backbone of ovalbumin,the resulting model was subjected to simulated annealing andenergy minimization. Overall, the final ACT model is structurallysimilar to ovalbumin, although the 2.4 Å root mean squaredeviation of corresponding C atoms reflects the presence ofregions exhibiting notable structural differences. The hydrogenbond stereochemistry of the ACT model is consistent with patternsfound in high resolution protein structures and 92% of its backboneatoms have acceptable conformations when evaluated in a Ramachandrananalysis. Significantly, the homology model serves as a structuralreference for protein engineering experiments aimed at redesigningthe functional properties of ACT, particularly with regard toits protease-bound conformation. Additionally, the homologymodel may be useful as a probe for solving the crystal structuresof certain ACT variants (e.g. Thr345 Arg) by molecular replacementmethods. Ultimately, the homology approach may be applied towardthe construction of other serpin models starting with an experimentallydetermined structure of uncleaved ACT as a template.     

Molecular modelling and site-directed mutagenesis on a bovine anti-testosterone monoclonal antibody

A three-dimensional (3D) molecular model of the antigen-combiningsite of a bovine anti-testosterone monoclonal antibody has beenconstructed. In the model, the CDRs, and a single heavy chainframework region residue (Trp47), associate to form a hydrophobiccavity large enough to accommodate a single molecule of testosterone.Tyr97 of CDR-H3 lies at the bottom of the cavity with its hydroxylgroup exposed to solvent. Using the model and data from bindingstudies, we predicted that the cavity forms the antibody's paratopeand on binding testosterone a hydrogen bond is formed betweenTyr97 of CDR-H3 and the hydroxyl group on the D-ring of testosterone.This prediction has subsequently been tested by site-directedmutagenesis. An antibody with phenylalanine in place of tyrosineat position 97 in CDR-H3 has its affinity reduced by {smalltilde}800 fold. The reduction in binding energy associated withthe reduced affinity has been calculated to be 3.9 kcal/molwhich is within the range (0.5–4.0 kcal/mol) expectedfor the loss of a single hydrogen bond. The model has been usedto suggest ways of increasing the antibody's affinity for testosterone.     

A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen

A predicted three-dimensional structure of the two N-terminalextracellular domains of human CD4 antigen, a cell surface glycoprotein,is reported. This region of CD4, particularly the first domain,has been identified as containing the binding region for theenvelope gp120 protein of the human immuno-deficiency virus.The model was predicted based on the sequence homology of eachdomain with the variable light chain of immunoglobulins. Theframework ß-sheet regions were taken from the crystalcoordinates of REI. For one region in the first domain of CD4there was an ambiguity in the alignment with REI and two alternatemodels are presented. Loops connecting the framework were modeledfrom fragments selected from a database of main chain coordinatesfrom all known protein structures. Residues identified as involvedin binding gp120 have been located in several other studieswithin the first domain of CD4. Epitopes from eight monoclonalantibodies have been mapped onto residues in both domains. Competitionof these antibodies with each other and with gp120 can be interpretedfrom the structural model.     

Engineering of protein epitopes: a single deletion in a snake toxin generates full binding capacity to a previously unrecognized antibody

Structural features associated with the ability of a monoclonalantibody (mAb) to discriminate between protein variants areidentified and engineered. The variants are the curaremimetictoxin from Naja nigricollis and erabutoxin a or b from Laticaudasemifasciata which differ from each other by 16 substitutionsand one insertion. The neutralizing mAb M1 recognizes with highaffinity a topographical epitope on the surface of toxin , butfails to recognize the erabutoxins although they possess mostof the residues forming the presumed epitope. Examinations ofthe toxin and erabutoxin 3-D structures and molecular dynamicssimulations reveal several differences between the variants.In particular, the region involving the ß-turn 17–24is organized differently. Analysis of the differences foundin this region suggests that the insertion (or deletion) atposition 18 of the variant amino add sequences is particularlyimportant in determining the differential cross-reactivity.To test this proposal, residue 18 was deleted in one erabutoxinusing sitedirected mutagenesis, and the biological propertiesof the resulting mutant were examined. We found that full antigenicitywas restored in the previously unrecognized variant. The implicationsof this finding are discussed.     

Genetically engineered brain drug delivery vectors: cloning, expression and in vivo application of an anti-transferrin receptor single chain antibodystreptavidin fusion gene and protein

A single chain Fv antibody–streptavidin fusion proteinwas expressed and purified from bacterial inclusion bodies followingcloning of the genes encoding the variable region of the heavychain and light chain of the murine OX26 monoclonal antibodyto the rat transferrin receptor. The latter undergoes receptormediated transcytosis through the brain capillary endothelialwall in vivo, which makes up the blood–brain barrier (BBB);therefore, the OX26 monoclonal antibody and its single chainFv analog may act as brain drug delivery vectors in vivo. Attachmentof biotinylated drugs to the antibody vector is facilitatedby production of the streptavidin fusion protein. The bi-functionalityof the OX26 single chain Fv antibody–streptavidin fusionprotein was retained, as the product both bound biotin and therat transferrin receptor in vitro and in vivo, based on pharmacokineticand brain uptake analyses in anesthetized rats. The attachmentof biotin–polyethyleneglycol–fluorescein to theOX26 single chain Fv antibody–streptavidin fusion proteinresulted in illumination of isolated rat brain capillaries inconfocal fluorescent microscopy. In conclusion, these studiesdemonstrate that genetically engineered single chain Fv antibody–streptavidinfusion proteins may be used for non-invasive neurotherapeuticdelivery to the brain using endogenous BBB transport systemssuch as the transferrin receptor.     

The influence of Glu44 and Glu56 of cytochrome b5 on the protein structure and interaction with cytochrome c

The gene encoding trypsin-solubilized bovine liver microsomalcytochrome b₅ (82 residues in length) has been mutated, in whichthe codons of Glu44 and Glu56 were changed to those of Ala.The mutated genes were expressed in Escherichia coli successfullyand three mutant proteins (E44A, E56A and E44/56A) were obtained.The UV-visible, CD and ¹H NMR spectra of proteins have beenstudied. The results show that the mutagenesis at surface residuesdoes not alter the secondary and tertiary structures of cytochromeb₅ significantly. The interactions between recombinant cytochromeb₅ and its mutants with cytochrome c were studied by using opticaldifference spectra. The results demonstrated that both Glu44and Glu56 of cytochrome b₅ participate in the formation of acomplex between cytochrome b₅ and cytochrome c.     

Sequence and structure of VH domain from naturally occurring camel heavy chain immunoglobulins lacking light chains

We cloned 17 different PCR fragments encoding V_H genes of camel(Camelus dromedarius). These clones were derived from the camelheavy chain immunoglobulins lacking the light chain counterpartof normal immunoglobulins. Insight into the camel V_H sequencesand structure may help the development of single domain antibodies.The most remarkable difference in the camel V_H, consistent withthe absence of the V_L interaction, is the substitution of theconserved Leu45 by an Arg or Cys. Another noteworthy substitutionis the Leu11 to Ser. This amino acid normally interacts withthe C_H1 domain, a domain missing in the camel heavy chain immunoglobulins.The nature of these substitutions agrees with the increasedsolubility behavior of an isolated camel V_H domain. The V_H domainsof the camels are also characterized by a long CDR3, possiblycompensating for the absence of the V_L contacts with the antigen.The CDR3 lacks the salt bridge between Arg94 and Asp101. However,the frequent occurrence of additional Cys residues in both theCDR1 and CDR3 might lead to the formation of a second internaldisulfide bridge, thereby stabilizing the CDR structure as inthe DAW antibody. Within CDRs of the camel V_H domains we observea broad size distribution and a different amino acid patterncompared with the mouse or human V_H. Therefore the camel hypervariableregions might adopt structures which differ substantially fromthe known canonical structures, thereby increasing the repertoireof the camel antigen binding sites within a V_H.     

Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 x 10(11) possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 A r.m.s. deviation of Calpha atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes.     

Design, synthesis and structure of an amphipathic peptide with pH-inducible haemolytic activity

A synthetic, 26–residue peptide having a strong helixforming potential in the protonated state was designed to interactwith lipid bilayers in a pH–dependent way. On the basisof this concept a cluster of four glutamk acid residues wasinserted in the central region of the amphipathic peptide topromote helix destabilization by mutual charge repulsion atneutral pH. Protonation of these residues might then bring aboutboth a pH-mediated change in hydrophobteity and conformationforming a membrane–active amphiphilk helix. The sequenceGLGTLLTLLEFLLEELLEFLKRKRQQamide produced by the design strategyinduced pH–triggered lysis of human erythrocytes. A molecularmodel correlating the lytic activity to the formation of transmembranepores which were detected by electron microscopy in erythrocytemembranes is discussed. Circular dichroism studies indicateda selfassociation of the monomeric random coil form with increasingpeptide concentration leading to the apparent induction of stronga-helix formation ({small tilde} 100% helkity) in the fullyaggregated state. However, no pH–dependent helixrandomcoil transition was observed, implying that interhelical hydrophobkand ionic interactions not only govern the self–associationbut also decisively influence the conformational stability ofthe peptide.     

Protein sequence entropy is closely related to packing density and hydrophobicity

We investigated the correlation between the Shannon information entropy, 'sequence entropy', with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of C(alpha) packing densities from 12 to 25 amino acids within a sphere of 9 angstrom radius. Three different hydrophobicity scales all mimic the behavior of the sequence entropies. This confirms the idea that the ability to accommodate mutations is strongly dependent on the available space and on the propensity for each amino acid type to be buried. Future applications of these types of methods may prove useful in identifying both core and flexible residues within a protein.     

Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power

Amino acid sequence patterns suggested to characterize specificrecurrent turn conformations in proteins are tested as to theirpredictive power in a database containing 75 proteins of knownstructure. Many of these patterns are found to be associatedwith local structures that differ from the motifs originallyused to derive them. It is therefore concluded that, while theycould be useful for improving predictions made by other methods,their stand-alone predictive power is poor. The issue of derivingand validating consensus sequence patterns for use in proteinstructure prediction is raised.     

The sequence and X-ray structure of the trypsin from Fusarium oxysporum

The trypsin from Fusarium oxysporum is equally homologous totrypsins from Streptomyces griseus, Streptomyces erythraeusand to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibitedform of the enzyme has been crystallized from 1.4 M Na₂SO₄,buffered with citrate at pH 5.0–5.5. The crystals belongto space group P2₁ with cell parameters a=33.43 Å, b=67.65Å, c=39.85 Å and ß=107.6°. There isone protein molecule in the asymmetric unit. X-ray diffractiondata to a resolution of 1.8 Å were collected on film usingsynchrotron radiation. The structure was solved by molecularreplacement using models of bovine and S.griseus trypsins andrefined to an R-factor of 0.141. The overall fold is similarto other trypsins, with some insertions and deletions. Thereis no evidence of the divalent cation binding sites seen inother trypsins. The covalently bound inhibitor molecule is clearlyvisible.     

Apomyoglobin as a molecular recognition surface: expression, reconstitution and crystallization of recombinant porcine myoglobin in Escherichia coli

Recombinant porcine myoglobin has been produced in Escherichiacoli using the cII fusion expression system of Nagai and Th?gersen[Nature, 309, 810–812 (1984)]. After processing and reconstitutionwith haem, the protein is gel-electrophoretically and spectrophotometricallyindistinguishable from native pig myoglobin. Large crystalsof both native and recombinant porcine myoglobin were grownfrom 50 mM sodium phosphate, pH 7.1, 80% ammonium sulphate.The crystals belong to space group C2 (a = 156.9 ?, b = 42.0?, c = 92.2 ?, ß = 127.9?) and diffract to a nominal2.5 ? resolution. We plan to explore apomyoglobin as a bindingsurface in studies combining site-directed mutagenesis and X-rayanalysis. These experiments will be extended by studying thebinding of haem analogues to the mutant apoproteins.     

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins

An amino acid index is a set of 20 numerical values representingany of the different physicochemical and biochemical propertiesof amino adds. As a follow-up to the previous study, we haveincreased the size of the database, which currently contains402 published indices, and re-performed the single-linkage clusteranalysis. The results basically confirmed the previous findings.Another important feature of amino acids that can be representednumerically is the similarity between them. Thus, a similaritymatrix, also called a mutation matrix, is a set of 20x20 numericalvalues used for protein sequence alignments and similarity searches.We have collected 42 published matrices, performed hierarchicalcluster analyses and identified several clusters correspondingto the nature of the data set and the method used for constructingthe mutation matrix. Further, we have tried to reproduce eachmutation matrix by the combination of amino acid indices inorder to understand which properties of amino acids are reflectedmost. There was a relationship between the PAM units of Dayhoff'smutation matrix and the volume and hydrophobicity of amino adds.The database of 402 amino acid indices and 42 amino acid mutationmatrices is made publicly available on the Internet.     

Spectroscopic investigation of structure in octarellin (a de novo protein designed to adopt the {alpha}/{beta}-barred packing)

We present here a spectroscopic structural characterizationof octarellin, a recently reported de novo protein modelledon /ß-barrel proteins [K. Go raj, A.Renard and J.A.Martial(1990) Protein Engng, 3, 259–266]. Infrared and Ramanspectra analyses of octarellin‘s secondary structure revealthe expected percentage of -helices (30%) and a higher ß-sheetcontent (40%) than predicted from the design. When the Ramanspectra obtained with octarellin and native triosephosphateisomerase (a natural /ß-barrel) are compared, similarpercentages of secondary structures are found. Thermal denaturationof octarellin monitored by CD confirms that its secondary structuresare quite stable, whereas its native-like tertiary fold is not.Tyrosine residues, predicted to be partially hidden from solvent,are actually exposed as revealed by Raman and UV absorptionspectra. We conclude that the attempted /ß-barrelconformation in octarellin may be loosely packed. The criteriaused to design octarellin are discussed and improvements suggested.     

Secretion and in vivo folding of the Fab fragment of the antibody McPC603 in Escherichia coli: influence of disulphides and cis-prolines

Using the well-characterized antibody McPC603 as a model, wehad found that the F_v fragment can be isolated from Escherichiacoli as a functional protein in good yields, whereas the amountof the correctly folded F_ab fragment of the same antibody producedunder identical conditions is significantly lower. In this paper,we analyse the reasons for this difference. We found that avariety of signal sequences function in the secretion of theisolated chains of the F_ab fragment or in the co-secretion ofboth chains in E.coli. The low yield of functional F_ab fragmentis not caused by inefficient expression or secretion in E.coli,but by inefficient folding and/or assembly in the periplasm.We compared the folding yields for the F_v and the F_ab fragmentin the periplasm under various conditions. Several diagnosticframework variants were constructed and their folding yieldsmeasured. The results show that substitutions affecting cis-prolineresidues and those affecting various disulphide bonds in theprotein are by themselves insufficient to dramatically changethe partitioning of the folding pathway to the native structure,and the cause must lie in a facile aggregation of folding intermediatescommon to all structural variants. However, all structural variantscould be obtained in native form, demonstrating the generalutility of the secretory expression strategy.     

Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase

We have performed molecular dynamics simulation of Rhizomucormiehei lipase (Rml) with explicit water molecules present. Thesimulation was carried out in periodic boundary conditions andconducted for 1.2 ns in order to determine the concerted proteindynamics and to examine how well the essential motions are preservedalong the trajectory. Protein motions are extracted by meansof the essential dynamics analysis method for different lengthsof the trajectory. Motions described by eigenvector 1 convergeafter approximately 200 ps and only small changes are observedwith increasing simulation time. Protein dynamics along eigenvectorswith larger indices, however, change with simulation time andgenerally, with increasing eigenvector index, longer simulationtimes are required for observing similar protein motions (alonga particular eigenvector). Several regions in the protein showrelatively large fluctuations and in particular motions in theactive site lid and the segments Thr57–Asn63 and the activesite hinge region Pro101–Gly104 are seen along severaleigenvectors. These motions are generally associated with glycineresidues, while no direct correlations are observed betweenthese fluctuations and the positioning of prolines in the proteinstructure. The partial opening/closing of the lid is an exampleof induced fit mechanisms seen in other enzymes and could bea general mechanism for the activation of Rml.