Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA

Cellobiohydrolase CbhA from Clostridium thermocellum cellulosome is a multi-modular protein composed starting from the N-terminus of a carbohydrate-binding module (CBM) of family 4, an immunoglobulin(Ig)-like module, a catalytic module of family 9 glycoside hydrolases (GH9), X1(1) and X1(2) modules, a CBM of family 3 and a dockerin module. Deletion of the Ig-like module from the Ig-GH9 construct results in complete inactivation of the GH9 module. The crystal structure of the Ig-GH9 module pair reveals the existence of an extensive module interface composed of over 40 amino acid residues of both modules and maintained through a large number of hydrophilic and hydrophobic interactions. To investigate the importance of these interactions between the two modules, we compared the secondary and tertiary structures and thermostabilities of the individual Ig-like and GH9 modules and the Ig-GH9 module pair using both circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC). Thr230, Asp262 and Asp264 of the Ig-like module are located in the module interface of the Ig-GH9 module pair and are suggested to be important in 'communication' between the modules. These residues were mutated to alanyl residues. The structure, stability and catalytic properties of the native Ig-GH9 and its D264A and T230A/D262A mutants were compared. The results indicate that despite being able to fold relatively independently, the Ig-like and GH9 modules interact and these interactions affect the final fold and stability of each module. Mutations of one or two amino acid residues lead to destabilization and change of the mechanism of thermal unfolding of the polypeptides. The enzymatic properties of native Ig-GH9, D264A and T230A/D262A mutants are similar. The results indicate that inactivation of the GH9 module occurs as a result of multiple structural disturbances finally affecting the topology of the catalytic center.     

Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure

A model of the lignin peroxidase LIII of Phlebia radiata wasconstructed on the basis of the structure of cytochrome c peroxidase(CCP). Because of the low percentage of amino acid identitybetween the CCP and the lignin peroxidase LIII of Phlebia radiata,alignment of the sequences was based on the generation of atemplate from a knowledge of the 3-D structure of CCP and consensussequences of lignin peroxidases. This approach gave an alignmentin which all the insertions in the lignin peroxidase were placedat loop regions of CCP, with a 21.1% identity for these twoproteins. The model was constructed using this alignment andthe computer program COMPOSER, which assembles the model asa series of rigid fragments derived from CCP and other proteins.Manual intervention was required for some of the longer loopregions. The -helices forming the structural framework, andespecially the haem environment of CCP, are conserved in theLIII model and the core is close packed without holes. A possiblesite of the substrate oxidation at the haem edge of LIII isdiscussed.     

A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation

A globular domain can be decomposed into compact modules consistingof contiguous 10–30 amino acid residues. The correlationbetween modules and exons observed in different proteins suggeststhat each module was encoded by an ancestral exon and that moduleswere combined into globular domains by exon fusion. Barnaseis a single domain RNase consisting of 110 amino acid residuesand was decomposed into six modules. We designed a mini-proteinby removing the second module, M2, from barnase in order togain an insight into the structural and functional roles ofthe module. In the molecular modeling of the mini-protein, weevaluated thermodynamic stability and aqueous solubility togetherwith mechanical stability of the model. We chemically synthesizeda mini-barnase with ¹⁵N-labeling at 10 residues, whose correspondingresidues in barnase are all found in the region around the hydrophobiccore. Circular dichroism and NMR measurements revealed thatmini-barnase takes a non-random specific conformation that hasa similar hydrophobic core structure to that of barnase. Thisresult, that a module could be deleted without altering thestructure of core region of barnase, supports the view thatmodules act as the building blocks of protein design.     

Molecular dynamics simulation of fungal cellulose-binding domains: differences in molecular rigidity but a preserved cellulose binding surface

A total of 23 fungal cellulose-binding domain (CBD) sequenceswere aligned. Structural models of the cellulosebinding domainof an exoglucanase (CBHII) and of three endoglucanases (EGI,EGII and EGV) from Trichoderma reesei cellulases were homologymodelled based on the NMR structure of the fungal cellobiohydrolaseCBHI, from the same organism. The completed models and the knownstructure of the CBHI cellulose-binding domain were refinedby molecular dynamics simulations in water. All four modelswere found to be very similar to the structure of the CBHI cellulose-bindingdomain and sequence comparison indicated that in general thethree-dimensional structures of fungal cellulose-binding domainsare very similar. In all the CBDs studied, two disulphide bridgesapparently stabilize the polypeptide fold. From the models,an additional disulphide bridge was predicted in EGI and CBHII,and in eight further CBDs from other organisms. Three highlyconserved aromatic residues on the hydrophilic side of the wedgemake this surface flat This surface is expected to make contactwith the substrate. Three invariant amino acids, Gln7, Asn29and Gln34, on this flat face are in suitable positions for hydrogenbonding with the cellulose surface. Analysis of the differencesin the protein surface properties indicated that the endoglucanasestend to be more hydrophilic than the exoglucanases. The largeststructural variation was found around positions 12-16. The fungalCBD sequences are discussed in relation to variations in functionand pH dependence. Comparison of the modelled structures withexperimental binding data for the CBHI and EGI allowed the formulationof a qualitative relationship to cellulose affinity. This relationshipwas used to predict the cellulose affinities for 21 CBDs.     

Detection of secondary structure elements in proteins by hydrophobic cluster analysis

Hydrophobic cluster analysis (HCA) is a protein sequence comparisonmethod based on -helical representations of the sequences wherethe size, shape and orientation of the clusters of hydrophobicresidues are primarily compared. The effectiveness of HCA hasbeen suggested to originate from its potential ability to focuson the residues forming the hydrophobic core of globular proteins.We have addressed the robustness of the bidimensional representationused for HCA in its ability to detect the regular secondarystructure elements of proteins. Various parameters have beenstudied such as those governing cluster size and limits, thehydrophobic residues constituting the clusters as well as thepotential shift of the cluster positions with respect to theposition of the regular secondary structure elements. The followingresults have been found to support the -helical bidimensionalrepresentation used in HCA: (i) there is a positive correlation(clearly above background noise) between the hydrophobic clustersand the regular secondary structure elements in proteins; (ii)the hydrophobic clusters are centred on the regular secondarystructure elements; (iii) the pitch of the helical representationwhich gives the best correspondence is that of an -helix. Thecorrespondence between hydrophobic clusters and regular secondarystructure elements suggests a way to implement variable gappenalties during the automatic alignment of protein sequences.     

Alternating charge clusters of side chains: new surface structural invariants observed in calf eye lens gamma-crystallins

A detailed stereochemical analysis of the oppositely chargedside chains of amino acid residues on the surface of calf eyelens protein gamma-crystallin B has been carried out. The refinedstructural data of very high quality obtained at 1.47 Åresolution have been used. Charge–charge interactionswere considered to be valuable for all the charged oxygen andnitrogen atoms situated at distances, d, between 2.4 and 7.0Å. This means we consider short contact ion pairs as thosewith interchange distances 2.4 < d 4.0 Å and distantcontact ion pairs as those with distances 4.0 < d 7.0 Å.Hydrogen bonding of the charged atomic groups with the structuralwater molecules also has been considered. We have not lookedat the side groups of histidines which are charged only partiallyat neutral pH. Five clusters of charged side chains which werelarge enough were observed. The clusters are comprised of fourto six residues which compose 543% of the total charged residuesin the protein. The clusters contain from eight to 12 chargedatoms and look like the bent chains of oppositely charged atoms.All clusters are of plane geometry and their maximal lineardimensions are from 11 to 18 Å. The root mean square deviationsof charged atoms from the cluster plane varied from 0.63 to0.86 Å for four clusters and was only 1.85 Å forthe largest cluster. All clusters include a number of watermolecules situated on the cluster boundary and grouped nearthe cluster plane. It was shown that the amino acid sequencepositions of charged residues are conservative for all the proteinsof the gamma-crystallin family of vertebrates including fish,frog, mouse, rat, calf and human. The cluster properties werediscussed both in their functional aspect for gamma-crystallinsand in other aspects common for globular proteins. As a result,the alternating charge clusters should be considered as newlyrecognized surface structural invariants. The importance ofthe charged side chain clusters is claimed for the updated conceptof the protein surface.     

Spatial sign-alternating charge clusters in globular proteins

Large sign-alternating charge clusters formed by the chargedside groups of amino acid residues and N- and C-terminal groupswere found in the majority of considered globular proteins,namely 235 in a total of 274 protein structures, i.e. 85.8%.The clusters were determined by the criteria proposed earlier:charged groups were included in the cluster if their chargedN and O atoms were located at distances between 2.4 and 7.0Å. The set of selected proteins consisted of known non-homologousprotein structures from the Protein Data Bank with a resolutionless than or equal to 2.5 Å and pair sequence similarityless than 25%. Molecular masses of the proteins were from 5.5to 91.5 kDa and protein chain length from 50 to 830 residues.The distribution of charged groups on the protein surface betweenisolated charged groups, small clusters with two and three groups,and large clusters with four or more groups were found to beapproximately similar making 33, 35 and 32% of the total amountof protein charged groups, respectively. The large sign-alternatingcharge clusters with four or more charged groups were studiedin greater detail. The amount of such clusters depends on theprotein chain length. The small proteins contain 1–3 clusterswhile the large proteins display 4–6 or more clusters.On average, 1.5 clusters per each 100 residues were observed.In contrast with this, the size of a cluster, i.e. the numberof charged groups inside a cluster, does not depend on the proteinmolecular mass, and large clusters are observed for proteinsfrom a range of molecular masses. Clusters consisting of fourto six charged groups occur most frequently, although extralarge clusters are also often revealed. We can conclude thatsign-alternating charge clusters are a common feature of theprotein surface of globular protein. They are suggested to playa general functional role as a local polar factor of proteinsurface.     

Improvement of nutritional value and functional properties of soybean glycinin by protein engineering

Glycinin is one of the predominant storage proteins of soybean.To improve its functional properties (heat-induced gelationand emulsification) and/or nutritional value, the A_1aB_1b proglycininsubunit was modified on the basis of genetically variable domainssuggested from the comparison of amino acid sequences of glycinin-typeglobulins from various legumes and nonlegumes and the relationshipsbetween the structure and the functional properties of glycinin.Thus, nucleotide sequences corresponding to each of the variabledomains were deleted from the cDN A encoding the A_1aB_1b proglycinin,and a synthetic DNA encoding four continuous methionines wasinserted into the cDNA region corresponding to each of the variabledomains. Expression plasmids carrying the modified cDNAs wereconstructed and expressed in Escherichia coli strain JM105.Some of the modified proteins were accumulated as soluble proteinsin the cells at a high level and self-assembled. They exhibitedfunctional properties superior to those of the native glycininfrom soybean, which establishes the possibility of creatingtheoretically designed novel glycinins with high food qualities.     

Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data

A general solution to the problem of directly incorporatingdata from multiple sequence alignments into the constructionof molecular models was approached through the calculation ofan estimated pairwise distance based on conserved hydrophobidty.A scaling method was developed that allowed the required bulkgeometric properties of the estimated pair-wise distances (meanand mean squared) to mimic those expected in a globular protein.These properties were maintained independently of the composition,length, number or degree of conservation of the original sequences.Despite being a poor estimate for individual distances, thescaled distances were found to be compatible with the nativestructure and could be weighted highly. While the estimateddistances provided a general drive towards hydrophobk packing,more specific structures (including secondary structures andmotifs) were induced by regularization towards an ideal form.These constraints were used to refine an outline starting structure(derived only from secondary structure axes) towards a compactform that was sufficiently protein-like for side chains to beadded with almost no further adjustment of the a-carbon positions.This process allows rough folds based on abstract representationsof protein architecture to be rapidly converted to a form wherethey can be analysed by the growing number of methods designedto assess molecular models.     

Retrovirus integrase: identification of a potential leucine zipper motif

The secondary structure of the retrovirus integration protein(IN) was predicted from seven inferred retrovirus IN sequences.The IN sequences were aligned by computer and the phylogeneticrelationships between them were determined. The secondary structureof the aligned IN sequences was predicted by two consensus predictionmethods. The predicted secondary structural patterns from thetwo consensus prediction schemes were compared with and superimposedon a composite structural profile of hydropathic/chain flexibility/amphipathicindexes with each index profile being calculated independentlyfor the aligned IN sequences. The use of this composite structuralprofile not only enhanced the prediction accuracy but also helpedin defining the surface loop regions which would be otherwiseunpredictable by the use of consensus prediction methods alone.An amphipathic helix was identified by these united structuralprediction-chain property profiles. Helical wheel analysis gavethe amphipathic helix a coiled-coil like pattern which was similarto the leucine zipper discovered for some eukaryotic gene regulatoryproteins. The proposed amphipathic helix may play an essentialrole in defining the biological properties of IN.     

Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface

Cellobiohydrolases are the most effective single component of fungal cellulase systems; however, their molecular mode of action on cellulose is not well understood. These enzymes act to detach and hydrolyze cellodextrin chains from crystalline cellulose in a processive manner, and the carbohydrate-binding module (CBM) is thought to play an important role in this process. Understanding the interactions between the CBM and cellulose at the molecular level can assist greatly in formulating selective mutagenesis experiments to confirm the function of the CBM. Computational molecular dynamics was used to investigate the interaction of the CBM from Trichoderma reesei cellobiohydrolase I with a model of the (1,0,0) cellulose surface modified to display a broken chain. Initially, the CBM was located in different positions relative to the reducing end of this break, and during the simulations it appeared to translate freely and randomly across the cellulose surface, which is consistent with its role in processivity. Another important finding is that the reducing end of a cellulose chain appears to induce a conformational change in the CBM. Simulations show that the tyrosine residues on the hydrophobic surface of the CBM, Y5, Y31 and Y32 align with the cellulose chain adjacent to the reducing end and, importantly, that the fourth tyrosine residue in the CBM (Y13) moves from its internal position to form van der Waals interactions with the cellulose surface. As a consequence of this induced change near the surface, the CBM straddles the reducing end of the broken chain. Interestingly, all four aromatic residues are highly conserved in Family I CBM, and thus this recognition mechanism may be universal to this family.     

Identification of sequence motifs from a set of porteins with related function

The automatic identification of motifs associated with a givenfunction is an important challenge for molecular sequence analysis.A method is presented for the extraction of such patterns fromlarge sets of unaligned sequences with related but general function,for example, a set of heat shock proteins. In such a set ofproteins there can often be several subfamilies each characterizedby one or more distinct motifs. The aim is to develop computationaltools to identify these motifs. The algorithm presented locateshigh frequency words of length k with a given number of positions,r, fixed. Statistics for a binomial distribution are used toassess the significance of the words. The high-frequency wordsare clustered and highly populated clusters retained. The compositionof the clusters is displayed graphically. A set of motifs associatedwith the sequence family can automatically be extracted. Themethod is benchmarked on a set of 106 heat shock sequences anda set of 257 toxin sequences. It is shown to recover previouslyidentified motifs.     

Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly

A quantitative structure–property relationship (QSPR)was used to design model protein sequences that fold repeatedlyand relatively rapidly to stable target structures. The specificmodel was a 125-residue heteropolymer chain subject to MonteCarlo dynamics on a simple cubic lattice. The QSPR was derivedfrom an analysis of a database of 200 sequences by a statisticalmethod that uses a genetic algorithm to select the sequenceattributes that are most important for folding and a neuralnetwork to determine the corresponding functional dependenceof folding ability on the chosen attributes. The QSPR dependson the number of anti-parallel sheet contacts, the energy gapbetween the native state and quasi-continuous part of the spectrumand the total energy of the contacts between surface residues.Two Monte Carlo procedures were used in series to optimize boththe target structures and the sequences. We generated 20 fullyoptimized sequences and 60 partially optimized control sequencesand tested each for its ability to fold in dynamic MC simulations.Although sequences in which either the number of anti-parallelsheet contacts or the energy of the surface residues is non-optimalare capable of folding almost as well as fully optimized ones,sequences in which only the energy gap is optimized fold markedlymore slowly. Implications of the results for the design of proteinsare discussed.     

Comparison of conservation within and between the Ser/Thr and Tyr protein kinase family: proposed model for the catalytic domain of the epidermal growth factor receptor

The protein kinase family can be subdivided into two main groupsbased on their ability to phosphorylate Ser/Thr or Tyr substrates.In order to understand the basis of this functional difference,we have carried out a comparative analysis of sequence conservationwithin and between the Ser/Thr and Tyr protein kinases. A multiplesequence alignment of 86 protein kinase sequences was generated.For each position in the alignment we have computed the conservationof residue type in the Ser/Thr, in the Tyr and in both of thekinase subfamilies. To understand the structural and/or functionalbasis for the conservation, we have mapped these conservationproperties onto the backbone of the recently determined structureof the cAMP–dependent Ser/Thr kinase. The results showthat the kinase structure can be roughly segregated, based uponconservation, into three zones. The inner zone contains residueshighly conserved in all the kinase family and describes thehydrophobic core of the enzyme together with residues essentialfor substrate and ATP binding and catalysis. The outer zonecontains residues highly variable in all kinases and representsthe solvent–exposed surface of the protein. The thirdzone is comprised of residues conserved in either the Ser/Thror Tyr kinases or in both, but which are not conserved betweenthem. These are sandwiched between the hydrophobic core andthe solvent-exposed surface. In addition to analyzing overallconservation hi the kinase family, we have also looked at conservationof its substrate and ATP binding sites. The ATP site is highlyconserved throughout the kinases, whereas the substrate bindingsite is more variable. The active site contains several positionswhich differ between the Ser/Thr and Tyr kinases and may beresponsible for discriminating between hydroxyl bearing sidechains. Using this information we propose a model for Tyr substratebinding to the catalytic domain of the epidermal growth factorreceptor (EGFR).     

PSIC: profile extraction from sequence alignments with position-specific counts of independent observations

Sequence weighting techniques are aimed at balancing redundantobserved information from subsets of similar sequences in multiplealignments. Traditional approaches apply the same weight toall positions of a given sequence, hence equal efficiency ofphylogenetic changes is assumed along the whole sequence. Thisrestrictive assumption is not required for the new method PSIC(position-specific independent counts) described in this paper.The number of independent observations (counts) of an aminoacid type at a given alignment position is calculated from theoverall similarity of the sequences that share the amino acidtype at this position with the help of statistical concepts.This approach allows the fast computation of position-specificsequence weights even for alignments containing hundreds ofsequences. The PSIC approach has been applied to profile extractionand to the fold family assignment of protein sequences withknown structures. Our method was shown to be very productivein finding distantly related sequences and more powerful thanHidden Markov Models or the profile methods in WiseTools andPSI-BLAST in many cases. The profile extraction routine is availableon the WWW (http://www.bork.embl-heidelberg.de/PSIC or http://www.imb.ac.ru/PSIC).     

Inhibition of cell growth by a fused protein of human ribonuclease 1 and human basic fibroblast growth factor

Pancreatic-type RNases are considered to have cytotoxic potentialdue to their ability to degrade RNA molecules when they enterthe cytosol. However, most of these RNases show little cytotoxicitybecause cells have no active uptake mechanism for these RNasesand because the ubiquitous cytoplasmic RNase inhibitor is consideredto play a protective role against the endocytotic leak of RNasesfrom the outside of cells. To study the cytotoxic potentialof RNase toward malignant cells targeting growth factor receptors,the C-terminus of human RNase 1 was fused to the N-terminusof human basic fibroblast growth factor (bFGF). This RNase–FGFfused protein effectively inhibited the growth of mouse melanomacell line B16/BL6 with high levels of cell surface FGF receptor.This effect appeared to result from prolongation of the overallcell cycle rather than the killing of cells or specific arrestin a particular phase of the cell cycle. Thus, human RNase 1fused to a ligand of cell surface molecules, such as the FGFreceptor, is shown to be an effective candidate for a selectivecell targeting agent with low toxic effects on normal cell types.     

Model structures and action of interleukin 1 and its antagonist

A comparison has been made between the homology and hydrophobkityprofiles of six interleukin amino add sequences and that ofthe human interleukin 1ß (IL-lß) for whicha crystal structure exists. The resulting sequence alignmentwas used to build model structures for the sequences for threeIL-l, two IL-1ß and an interleukin receptor antagonist.Analysis of these structures demonstrates that the interleukinmolecule has a strong electric dipole which is generated bythe topological position of the amino acids in the sequence.Electrostatic surface calculations implicate a particular residues(Lysl45) as being fundamental to interleukin activity and thissupports site-directed mutation evidence that this residue isrequired for activity.     

Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries

The directed evolution of proteins has benefited greatly from site-specific methods of diversification such as saturation mutagenesis. These techniques target diversity to a number of chosen positions that are usually non-contiguous in the protein's primary structure. However, the number of targeted positions can be large, thus leading to impractically large library size, wherein almost all library variants are inactive and the likelihood of selecting desirable properties is extremely small. We describe a versatile combinatorial method for the partial diversification of large sets of residues. Our library oligonucleotides comprise randomized codons that are flanked by wild-type sequences. Adding these oligonucleotides to an assembly PCR of wild-type gene fragments incorporates the randomized cassettes, at their target sites, into the reassembled gene. Varying the oligonucleotides concentration resulted in library variants that carry a different average number of mutated positions that comprise a random subset of the entire set of diversified codons. This method, dubbed Incorporating Synthetic Oligos via Gene Reassembly (ISOR), was used to create libraries of a cytosine-C5 methyltransferase wherein 45 individual positions were randomized. One library, containing an average of 5.6 mutated residues per gene, was selected, and mutants with wild-type-like activities isolated. We also created libraries of serum paraoxonase PON1 harboring insertions and deletions (indels) in various areas surrounding the active site. Screening these libraries yielded a range of mutants with altered substrate specificities and indicated that certain regions of this enzyme have a surprisingly high tolerance to indels.     

Prediction of the antigenic sites of the cystic fibrosis transmembrane conductance regulator protein by molecular modelling

Antibodies are powerful tools for studying the in situ localizationand physiology of proteins. The prediction of epitopes by molecularmodelling has been used successfully for the papilloma virus,and valuable antibodies have been raised [Muller et aL (1990)J. Gen. Virol, 71, 2709–2717]. We have improved the modellingapproach to allow us to predict epitopes from the primary sequencesof the cystic fibrosis transmembrane conductance regulator.The procedure involves searching for fragments of primary sequenceslikely to make amphipathic secondary structures, which are hydrophilicenough to be at the surface of the folded protein and thus accessibleto antibodies. Amphipathic helices were predicted using themethods of Berzofsky, Eisenberg and Jahnig. Their hydrophobichydrophilicinterface was calculated and drawn, and used to predict theorientation of the helices at the surface of the native protein.Amino acids involved in turns were selected using the algorithmof Eisenberg. Tertiary structures were calculated using ‘FOLDING’,a software developed by R.Brasseur for the prediction of smallprotein structures [Brasseur (1995) J. MoL Graphics, in press].We selected sequences that folded as turns with at least fiveprotruding polar residues. One important property of antibodiesis selectivity. To optimize the selectivity of the raised antibodies,each sequence was screened for similarity (FASTA) to the proteinsequences from several databanks. Ubiquitous sequences werediscarded. This approach led to the identification of 13 potentialepitopes in the cystic fibrosis transmembrane conductance regulator:seven helices and six loops.     

A library of organic landscapes on filamentous phage

A billion-clone library of filamentous phage with differentsurface structures (‘landscapes’) was generatedby fusing random octapeptides to the N-terminus of all 4000copies of the major coat protein. Such a ‘landscape library’might include clones exhibiting emergent properties that inherein the entire surface architecture, not in the peptides by themselves.Because the diverse surface landscapes are displayed on viablephage, they can be surveyed for exceedingly rare functions usingmicrobiological selection methods. Clones with several emergentproperties of the sort envisioned were successfully selected,suggesting that landscape libraries have promise as a novelsource of nanomaterials with exploitable surface properties.