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PubMed1990

[A study of protein engineering for human cardionatrin. I. Synthesis, cloning and expression of a gene analog of human atrial natriuretic polypeptide in E. coli].

An analog of the alpha-human atrial natriuretic polypeptide (alpha-hANP) gene, articulated with a peptidase inhibitor SQ20881 at its N-terminal and two prolines at the C-terminal was expressed in E. coli by cloning the reconstituted plasmid pRHL-1 in vivo. This gene analog, RH-1, comprising 154 base pairs in total, was designed to contain an equivalent of the alpha-hANP gene, capping the peptidase inhibitor SQ20881 at its 5' end with a glutamic acid codon GAA to facilitate enzymatic cleavage of the expressed end product by endoproteinase Glu-C, wedging in two proline codons CCG & CCG before the double terminal codons TGA TAG at the 3' end to retard hydrolysis of the expressed product by exopeptidase, and adding 3 restriction sites to both ends. Synthesis of the RH-1 gene was effected enzymatically by joining in predicted order the ten segments of oligodeoxynucleotides which had been chemically synthesized by the solid-phase phosphite-triester method. The synthetic gene was cloned into vector M13mp18. Phage bearing the gene analog was identified by dot blotting and restriction endonuclease mapping. Nucleotide sequence of the gene was determined by the dideoxynucleotide chain termination method.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1991

Use of 2D NMR, protein engineering, and molecular modeling to study the hapten-binding site of an antibody Fv fragment against 2-phenyloxazolone.

Two-dimensional (2D) 1H NMR spectroscopy was used to study the hapten-binding site of a recombinant antibody Fv fragment expressed in Escherichia coli. Point mutations of residues in the CDR loops of the Fv fragment were designed in order to investigate their influence on hapten binding and to make site-specific assignments of aromatic NMR proton signals. Two tyrosines giving NOEs to the ligand 2-phenyloxazolone were identified, residue 33 in CDR1 of the heavy chain and residue 32 in CDR1 of the light chain. The benzyl portion of 2-phenyloxazolone is located between these two residues. The binding site is close to the surface of the Fv fragment. Comparison with a different anti-2-phenyloxazolone antibody, the crystal structure of which has recently been solved, shows that the general location of the hapten-binding site in both antibodies is similar. However, in the crystallographically solved antibody, the hapten is bound farther from the surface in a pocket created by a short CDR3 loop of the heavy chain. In the binding site identified in the Fv fragment studied in this report, this space is probably filled by the extra seven residues of the CDR3.

Amino Acid Sequence↗
PubMed2001

Protein engineering of Bacillus megaterium CYP102. The oxidation of polycyclic aromatic hydrocarbons.

Cytochrome P450 (CYP) enzymes are involved in activating the carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) in mammals, but they are also utilized by microorganisms for the degradation of these hazardous environmental contaminants. Wild-type CYP102 (P450(BM-3)) from Bacillus megaterium has low activity for the oxidation of the PAHs phenanthrene, fluoranthene and pyrene. The double hydrophobic substitution R47L/Y51F at the entrance of the substrate access channel increased the PAH oxidation activity by up to 40-fold. Combining these mutations with the active site mutations F87A and A264G lead to order of magnitude increases in activity. Both these mutations increased the NADPH turnover rate, but the A264G mutation increased the coupling efficiency while the F87A mutation had dominant effects in product selectivity. Fast NADPH oxidation rates were observed (2250 min-1 for the R47L/Y51F/F87A mutant with phenanthrene) but the coupling efficiencies were relatively low (< 13%), resulting in a highest substrate oxidation rate of 110 min-1 for fluoranthene oxidation by the R47L/Y51F/A264G mutant. Mutation of M354 and L437 inside the substrate access channel reduced PAH oxidation activity. The PAHs were oxidized to a mixture of phenols and quinones. Notably mutants containing the A264G mutation showed some similarity to mammalian CYP enzymes in that some 9,10-phenanthrenequinone, the K-region oxidation product from phenanthrene, was formed. The results suggest that CYP102 mutants could be useful models for PAH oxidation by mammalian CYP enzymes, and also potentially for the preparation of novel PAH bioremediation systems.

Animals↗
PubMedDate not supplied

Protein engineering strategies for designing more stable hemoglobin-based blood substitutes.

Over the past five years our laboratory has been using rational, comparative, and random combinatorial mutagenesis strategies to optimize the alpha and beta subunits of recombinant human hemoglobin (Hb) for efficient O2 transport, greater stability, and minimum interference with vascular activity. In each approach, mammalian myoglobin (Mb) has been used as a prototype to develop experimental methodologies and to study the stereochemical mechanisms that govern O2 affinity, discrimination against CO, rates of ligand binding, auto- and chemically induced oxidation, resistance to hemin loss, and stability to globin denaturation. Multiple replacements in the distal portion of the heme pocket have been designed rationally to lower oxygen affinity and at the same time inhibit oxidative side reactions. The P50 values are adjusted by altering electrostatic and steric interactions between the bound ligand and residues at the Leu(B10), His(E7), and Va(E11) positions. Large apolar residues (Leu, Phe, Trp) at the B10 and E11 positions inhibit NO-induced and autooxidation in both myoglobin and hemoglobin by excluding oxidants and proton donors from the immediate vicinity of the bound ligand. Similar strategies appear to have evolved in a number of animal myoglobins and hemoglobins which have unusual amino acids at the E7, B10, and E11 positions. Random combinatorial mutagenesis techniques have been developed to insert new amino acid combinations near the bound ligand in sperm whale Mb. The objective is to obtain "unnatural" distal pocket structures that enhance O2 transport and resistance to oxidation by alternative mechanisms.

Blood Substitutes↗
PubMed1993

Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering.

Barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens, forms a very tight complex with its intracellular polypeptide inhibitor barstar. At pH 8, the values for the rate constants k1 (association) and k-1 (dissociation) are 6.0 x 10(8) s-1 M-1 and 8.0 x 10(-6) s-1, respectively. The value of Ki, the dissociation constant of barstar and barnase, calculated from the ratio k-1/k1 is 1.3 x 10(-14) M, which corresponds to a delta G of -18.9 kcal/mol at 25 degrees C. The dissociation constant increases with decreasing pH according to the ionization of an acid in free barnase of pKa 6.4, with very weak, if any, binding to the protonated form. This pH dependence for dissociation of the complex can be attributed almost entirely to residue His102 in barnase, as determined by a His102-->Ala mutation. Analysis of the pH dependence of the kinetic constants indicates that binding is, at least, a two-step process. The first, and rate-determining, step is association at close to the diffusion-controlled rate. There is then the precise docking of the complex. The value of Ki increases to 2.4 x 10(-11) M in the presence of 500 mM NaCl, and to 1.6 x 10(-11) M at pH 5 (100 mM NaCl). The binding site of barstar on barnase was mapped by measuring the values of Ki for a broad range of site-specific mutants of barnase. Mutagenesis of residues Lys27, Arg59, Arg87, and His102 to Ala increases the values of Ki by a factor of 10(4).(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗
PubMed2004

Redesign of carnitine acetyltransferase specificity by protein engineering.

In eukaryotes, L-carnitine is involved in energy metabolism by facilitating beta-oxidation of fatty acids. Carnitine acetyltransferases (CrAT) catalyze the reversible conversion of acetyl-CoA and carnitine to acetylcarnitine and free CoA. To redesign the specificity of rat CrAT toward its substrates, we mutated Met564. The M564G mutated CrAT showed higher activity toward longer chain acyl-CoAs: activity toward myristoyl-CoA was 1250-fold higher than that of the wild-type CrAT, and lower activity toward its natural substrate, acetyl-CoA. Kinetic constants of the mutant CrAT showed modification in favor of longer acyl-CoAs as substrates. In the reverse case, mutation of the orthologous glycine (Gly553) to methionine in carnitine octanoyltransferase (COT) decreased activity toward its natural substrates, medium- and long-chain acyl-CoAs, and increased activity toward short-chain acyl-CoAs. Another CrAT mutant, M564A, was prepared and tested in the same way, with similar results. We conclude that Met564 blocks the entry of medium- and long-chain acyl-CoAs to the catalytic site of CrAT. Three-dimensional models of wild-type and mutated CrAT and COT support this hypothesis. We show for the first time that a single amino acid is able to determine the substrate specificity of CrAT and COT.

Acetyl Coenzyme A↗
PubMed1993

Arthrobacter D-xylose isomerase: protein-engineered subunit interfaces.

Mutants of Arthrobacter D-xylose isomerase were constructed in which one or two disulphide bridges or additional salt bridges were introduced at the A-A* subunit interfaces. These showed no change in enzyme activity or stability compared with the wild-type enzyme. However, a Tyr253 mutant in which a disulphide bridge was introduced at the A-B* subunit interface showed reduced thermostability that was identical in both oxidized and reduced forms, and also reduced stability in urea. X-ray-crystallographic analysis of the Mn(2+)-xylitol form of oxidized Y253C (the Tyr253-->Cys mutant) showed a changed conformation of Glu185 and also alternative conformations for Asp254, which is a ligand to the Site-[2] metal ion. With fructose, Mg(2+)-Y253C has a similar Km to that of the wild-type, and its Vmax. is also similar below pH 6.4, but declined thereafter. In the presence of Co2+, Y253C has lower activity than wild-type at all pH values, but its activity also declines at alkaline pH. These results suggest that electrostatic repulsion from the new position of Glu185 causes Asp254 to move when His219 is unprotonated, thereby preventing M2+ binding at Site [2]. These results also suggest that subunit dissociation does not lie on the pathway of thermal inactivation of D-xylose isomerase, but that movements of active-site groups are a trigger for conformational changes that initiate the unfolding process.

Aldose-Ketose Isomerases↗
PubMed2001

Improved oligosaccharide synthesis by protein engineering of beta-glucosidase CelB from hyperthermophilic Pyrococcus furiosus.

Enzymatic transglycosylation of lactose into oligosaccharides was studied using wild-type beta-glucosidase (CelB) and active site mutants thereof (M424K, F426Y, M424K/F426Y) and wild-type beta-mannosidase (BmnA) of the hyperthermophilic Pyrococcus furiosus. The effects of the mutations on kinetics, enzyme activity, and substrate specificity were determined. The oligosaccharide synthesis was carried out in aqueous solution at 95 degrees C at different lactose concentrations and pH values. The results showed enhanced synthetic properties of the CelB mutant enzymes. An exchange of one phenylalanine to tyrosine (F426Y) increased the oligosaccharide yield (45%) compared with the wild-type CelB (40%). Incorporation of a positively charged group in the active site (M424K) increased the pH optimum of transglycosylation reaction of CelB. The double mutant, M424K/F426Y, showed much better transglycosylation properties at low (10-20%) lactose concentrations compared to the wild-type. At a lactose concentration of 10%, the oligosaccharide yield for the mutant was 40% compared to 18% for the wild-type. At optimal reaction conditions, a higher ratio of tetrasaccharides to trisaccharides was obtained with the double mutant (0.42, 10% lactose) compared to the wild-type (0.19, 70% lactose). At a lactose concentration as low as 10%, only trisaccharides were synthesized by CelB wild-type. The beta-mannosidase BmnA from P. furiosus showed both beta-glucosidase and beta-galactosidase activity and in the transglycosylation of lactose the maximal oligosaccharide yield of BmnA was 44%. The oligosaccharide yields obtained in this study are high compared to those reported with other transglycosylating beta-glycosidases in oligosaccharide synthesis from lactose.

Amino Acid Sequence↗
PubMed1989

Structural transition in the metal-free hexamer of protein-engineered [B13 Gln]insulin.

For hexamer formation of native insulin the repulsive potential of six B13 Glu carboxylate groups coming together in the centre is overcome by zinc binding to B10 His. Substitution of Gln for Glu in position B13 by site-directed mutagenesis, i.e. replacement of the repelling carboxylates by amide groups, which are offering H-bonding potential, enhances association and allows a metal-free hexamer to form. Merely upon addition of zinc ions this hexamer undergoes the T6----T3R3 respectively T6----R6 structural transition which in the native 2Zn insulin hexamer is inducible only by additives like inorganic anions or phenolic compounds. [B13 Gln]Insulin hexamers are transformed by phenolic compounds, but not by anions, even in the absence of any metal. The structural transformation of insulin can thus be brought about in two ways: By inorganic ions with the zinc ions as their points of attack, which preexist in the nontransformed hexamer, and by phenol, for which the binding sites close to the B5 histidines come into existence only with the transformation. Therefore transformed and non-transformed hexamers, i.e. molecules with helical and extended B chain N-terminus, must be related in a dynamic equilibrium. Phenol acts as a wedge jamming the structure in the transformed state and trapping the zinc ions. Combination of transformed 2Zn[B13 Gln]insulin and metal-free native insulin in the absence of additives results in a redistribution of the zinc ions in favour of native insulin which is an outcome of the dynamic equilibrium and also demonstrates an influence of B13 charge on metal binding affinity. Transformation of a single subunit in a hexamer would lead to bad contacts.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism↗
PubMed1991

Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering.

Of two closely related species of geese, one, the greylag goose, lives in the Indian plains all year round, while the other, the bar-headed goose, lives at the Tibetan lakes and migrates across the Himalayas to winter in India. Another species, the Andean goose, lives in the High Andes all year round. Possession of a Hb with high oxygen affinity helps to adapt bar-headed and Andean geese to high altitudes. The Hb amino acid sequences of the bar-headed and the greylag geese differ by four substitutions, of which only one is unique among bird sequences: Pro-119 alpha (H2)----Ala. Perutz proposed that the two-carbon gap left by this substitution at the alpha 1 beta 1 contact raises the oxygen affinity, because it relaxes the tension in the deoxy or T structure [Perutz, M. F. (1983) Mol. Biol. Evol. 1, 1-28]. It was later found that the Hb of the Andean goose has a gap in the same position, due to the complementary substitution Leu-55 beta (D6)----Ser. We have tested Perutz's hypothesis by introducing each of these substitutions into human globin synthesized in Escherichia coli. The reconstituted Hbs combine cooperatively with oxygen. Their oxygen affinities exceed that of normal human Hb by an even larger factor than that found between the high-flying geese and the greylag goose. The mutant Hb Met-55 beta (D6)----Ser was crystallized. Its structure is the same as that of HbA, except in the immediate environment of the gap left by the substitution of the serine for the methionine side chain, which evidently causes the increased oxygen affinity of this Hb.

Adaptation, Physiological↗
PubMed1995

Improvement of solubility and stability of the antimicrobial peptide nisin by protein engineering.

Nisin is a 3.4-kDa antimicrobial peptide that, as a result of posttranslational modifications, contains unsaturated amino acids and lanthionine residues. It is applied as a preservative in various food products. The solubility and stability of nisin and nisin mutants have been studied. It is demonstrated that nisin mutants can be produced with improved functional properties. The solubility of nisin A is highest at low pH values and gradually decreases by almost 2 orders of magnitude when the pH of the solution exceeds a value of 7. At low pH, nisin Z exhibits a decreased solubility relative to that of nisin A; at neutral and higher pH values, the solubilities of both variants are comparable. Two mutants of nisin Z, which contain lysyl residues at positions 27 and 31, respectively, instead of Asn-27 and His-31, were produced with the aim of reaching higher solubility at neutral pH. Both mutants were purified to homogeneity, and their structures were confirmed by one- and two-dimensional 1H nuclear magnetic resonance. Their antimicrobial activities were found to be similar to that of nisin Z, whereas their solubilities at pH 7 increased by factors of 4 and 7, respectively. The chemical stability of nisin A was studied in the pH range of 2 to 8 and at a 20, 37, and 75 degrees C. Optimal stability was observed at pH 3.0. Nisin Z showed a behavior similar to that of nisin A. A mutant containing dehydrobutyrine at position 5 instead of dehydroalanine had lower activity but was significantly more resistant to acid-catalyzed chemical degradation than wild-type nisin Z.

Base Sequence↗
PubMed1988

Conformational properties of the guanine-binding site of ribonuclease T1 inferred from the X-ray structure and protein engineering.

Recognition by ribonuclease T1 of guanine bases via multidentate hydrogen bonding and stacking interactions appears to be mediated mainly by a short peptide segment formed by one stretch of a heptapeptide, Tyr42-Asn43-Asn44-Tyr45-Glu46-Gly47- Phe48. The segment displays a unique folding of the polypeptide chain--consisting of a reverse turn, Asn44-Tyr45-Glu46-Gly47, stabilized by a hydrogen-bond network involving the side chain of Asn44, the main-chain atoms of Asn44, Gly47 and Phe48 and one water molecule. The segment is connected to the C terminus of a beta-strand and expands into a loop region between Asn43 and Ser54. Low values for the crystallographic thermal parameters of the segment indicate that the structure has a rigidity comparable to that of a beta-pleated sheet. Replacement of Asn44 with alanine leads to a far lower enzymatic activity and demonstrates that the side chain of Asn44 plays a key role in polypeptide folding in addition to a role in maintaining the segment structure. Substitution of Asn43 by alanine to remove a weak hydrogen bond to the guanine base destabilized the transition state of the complex by 6.3 kJ/mol at 37 degrees C. In contrast, mutation of Glu46 to alanine to remove a strong hydrogen bond to the guanine base caused a destabilization of the complex by 14.0 kJ/mol. A double-mutant enzyme with substitutions of Asn43 by a histidine and Asn44 by an aspartic acid, to reproduce the natural substitutions found in ribonuclease Ms, showed an activity and base specificity similar to that of the wild-type ribonuclease Ms. The segment therefore appears to be well conserved in several fungal ribonucleases.

Amino Acid Sequence↗
PubMed2002

Protein engineering of nitrile hydratase activity of papain: molecular dynamics study of a mutant and wild-type enzyme.

The mechanism of hydrolysis of the nitrile (N-acetyl-phenylalanyl-2-amino-propionitrile, I) catalyzed by Gln19Glu mutant of papain has been studied by nanosecond molecular dynamics (MD) simulations. MD simulations of the complex of mutant enzyme with I and of mutant enzyme covalently attached to both neutral (II) and protonated (III) thioimidate intermediates were performed. An MD simulation with the wild-type enzyme.I complex was undertaken as a reference. The ion pair between protonated His159 and thiolate of Cys25 is coplanar, and the hydrogen bonding interaction S(-)(25).HD1-ND1(159) is observed throughout MD simulation of the mutant enzyme.I complex. Such a sustained hydrogen bond is absent in nitrile-bound wild-type papain due to the flexibility of the imidazole ring of His159. The nature of the residue at position 19 plays a critical role in the hydrolysis of the covalent thioimidate intermediate. When position 19 represents Glu, the imidazolium ion of His159-ND1(+).Cys25-S(-) ion pair is distant, on average, from the nitrile nitrogen of substrate I. Near attack conformers (NACs) have been identified in which His159-ImH(+) is positioned to initiate a general acid-catalyzed addition of Cys-S(-) to nitrile. Though Glu19-CO(2)H is distant from nitrile nitrogen in the mutant.I structure, MD simulations of the mutant.II covalent adduct finds Glu19-CO(2)H hydrogen bonded to the thioimide nitrogen of II. This hydrogen bonded species is much less stable than the hydrogen bonded Glu19-CO(2)(-) with mutant-bound protonated thioimidate (III). This observation supports Glu19-CO(2)H general acid catalysis of the formation of mutant.III. This is the commitment step in the Gln19Glu mutant catalysis of nitrile hydrolysis.

Computer Simulation↗
PubMed2004

Protein engineering of toluene ortho-monooxygenase of Burkholderia cepacia G4 for regiospecific hydroxylation of indole to form various indigoid compounds.

Previous work showed that random mutagenesis produced a mutant of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 containing the V106A substitution in the hydroxylase alpha-subunit (TomA3) that changed the color of the cell suspension from wild-type brown to green in rich medium. Here, DNA shuffling was used to isolate a random TOM mutant that turned blue due to mutation TomA3 A113V. To better understand the TOM reaction mechanism, we studied the specificity of indole hydroxylation using a spectrum of colored TOM mutants expressed in Escherichia coli TG1 and formed as a result of saturation mutagenesis at TomA3 positions A113 and V106. Colonies expressing these altered enzymes ranged in color from blue through green and purple to orange; and the enzyme products were identified using thin-layer chromatography, high performance liquid chromatography, and liquid chromatography-mass spectroscopy. Derived from the single TOM template, enzymes were identified that produced primarily isoindigo (wild-type TOM), indigo (A113V), indirubin (A113I), and isatin (A113H and V106A/A113G). The discovery that wild-type TOM formed isoindigo via C-2 hydroxylation of the indole pyrrole ring makes this the first oxygenase shown to form this compound. Variant TOM A113G was unable to form indigo, indirubin, or isoindigo (did not hydroxylate the indole pyrrole ring), but produced 4-hydroxyindole and unknown yellow compounds from C-4 hydroxylation of the indole benzene ring. Mutations at V106 in addition to A113G restored C-3 indole oxidation, so along with C-2 indole oxidation, isatin, indigo, and indirubin were formed. Other TomA3 V106/A113 mutants with hydrophobic, polar, or charged amino acids in place of the Val and/or Ala residues hydroxylated indole at the C-3 and C-2 positions, forming isatin, indigo, and indirubin in a variety of distributions. Hence, for the first time, a single enzyme was genetically modified to produce a wide range of colors from indole.

Base Sequence↗
PubMed1998

Use of protein engineering to explore subunit interactions in an allosteric enzyme: construction of inter-subunit hybrids in Clostridium symbiosum glutamate dehydrogenase.

Hybrids of different forms of clostridial glutamate dehydrogenase (GDH) have been constructed in order to probe the basis of allosteric interaction in this hexameric enzyme. It was shown that the C320S mutant, which is fully active and shows allosteric behaviour similar to that of the wild-type enzyme, can also be renatured after unfolding in urea. Mixtures of unfolded wild-type and C320S subunits gave rise to hybrids upon refolding. A purely random reassembly would lead to a simple binomial distribution. However there was a slightly better overall recovery of wild-type subunits and there appears to be a tendency for rapidly formed structured wild-type subunits in a mixture to nucleate further refolding in a way that biases the final distribution against the formation of C320S hexamers. Only the wild-type subunits in such hybrid mixtures are able to react with Ellman's reagent, 5,5'-dithiobis-(2-nitrobenzoate) (DTNB). Accordingly, after modification of hybrid hexamers with DTNB only the mutant subunits can bind NAD+. This permits fractionation on an NAD+-agarose affinity column. The elution pattern in itself indicates cooperativity since DTNB modification of just one subunit in a 1:5 wild-type/C320S hybrid largely abolished binding to the column. Kinetic studies were carried out on a fractionated preparation in which hexamers containing only one C320S subunit and five wild-type subunits were the predominant active species. Measurements of activity were made both before and after treatment with an excess of beta-mercaptoethanol to remove the blocking thionitrobenzoate moieties. Before beta-mercaptoethanol treatment this sample, with only one active subunit per hexamer, gave strictly hyperbolic (Michaelis-Menten) kinetics with NAD+ at pH 7.0, whereas after beta-mercaptoethanol (all six subunits now active) the markedly kinked Eadie-Hofstee plot characteristic of wild-type enzyme was obtained. On the other hand the sigmoid response to glutamate at high pH persisted (Hill coefficient=3.6) even without beta-mercaptoethanol, reflecting the fact that the inactive subunits can still bind glutamate. Beta-mercaptoethanol treatment restored full positive cooperativity (Hill coefficient=5.2). These results prove beyond doubt that the non-classical kinetic behaviour of clostridial GDH is a direct result of interaction between NAD+ binding sites on the six (normally) identical subunits of a hexamer.

Allosteric Regulation↗
PubMed2005

Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation.

Proteins could be used to carry and deliver small compounds. As a tool for designing ligand binding sites in protein cores, a three-step virtual screening method is presented that has been optimised using existing data on T4 lysozyme complexes and tested in a newly engineered cavity in flavodoxin. The method can pinpoint, in large databases, ligands of specific protein cavities. In the first step, physico-chemical filters are used to screen the library and discard a majority of compounds. In the second step, a flexible, fast docking procedure is used to score and select a smaller number of compounds as potential binders. In the third step, a finer method is used to dock promising molecules of the hit list into the protein cavity, and an optimised free energy function allows discarding the few false positives by calculating the affinity of the modelled complexes. To demonstrate the portability of the method, several cavities have been designed and engineered in the flavodoxin from Anabaena PCC 7119, and the W66F/L44A double mutant has been selected as a suitable host protein. The NCI database has then been screened for potential binders, and the binding to the engineered cavity of five promising compounds and three tentative non-binders has been experimentally tested by thermal up-shift assays and spectroscopic titrations. The five tentative binders (some apolar and some polar), unlike the three tentative non-binders, are shown to bind to the host mutant and, importantly, not to bind to the wild type protein. The three-step virtual screening method developed can thus be used to identify ligands of buried protein cavities. We anticipate that the method could also be used, in a reverse manner, to identify natural or engineerable protein cavities for the hosting of ligands of interest.

Bacteriophage T4↗
PubMed2004

Modular protein engineering for non-viral gene therapy.

Despite the recognized potential of viral vectors for gene therapy, growing biological concerns are prompting the exploration of safer, non-viral vectors to deliver therapeutic nucleic acids. In this context, recombinant proteins can be bioproduced on a large scale, without the need for further in vitro modifications, being free of known or suspected biohazards. For these vehicles to act as efficient gene-delivery devices, they must perform relevant functions that mimic those of viruses; namely, nucleic acid condensation, targeted cell attachment and internalization, endosomal escape and nuclear transfer. Modular engineering enables the construction of chimeric polypeptides in which selected domains, potentially from different origins, provide the required activities. An equilibrate combination and spatial distribution of such partner elements has generated promising prototypes, able to deliver expressible DNA to tissue culture but also to specific cell-types in whole organisms.

Animals↗