Characterization of a new variant of human red cell carbonic anhydrase I,CA if London (Glu-102→Lys)

A new inherited variant of red cell carbonic anhydrase I (CA I), designated CA If London, was discovered during a survey of 1615 individuals from London, England. No electrophoretic variants of the other isozyme of carbonic anhydrase CA II, were observed in the same survey. Sequence analysis of a lysine-blocked tryptic peptide believed to contain the amino acid substitution in CA If showed that the glutamyl residue at position 102 had been substituted by a lysyl residue. This substitution results in a net increase of two positive charges in the mutant enzyme. Densitometric scanning of the electrophoretically separated forms in the variant hemolysate indicates that the levels of the normal and variant enzymes are approximately equal.Supported in part by U.S. Public Health Service grant GM15,419.     

Hb F-La Grange or alpha 2 gamma 2 101(G3)Glu----Lys; 75Ile; 136Gly: a high oxygen affinity fetal hemoglobin variant observed in a Caucasian newborn

The identification of a newly discovered gamma-chain variant is reported. This abnormal fetal hemoglobin is characterized by a Glu----Lys substitution at position 101(G3) of its gamma chain and was observed in a Caucasian baby girl. Because glutamic acid residue in position gamma 101 is involved in the alpha 1-gamma 2 chain contact, its replacement by a lysine residue results in changes in physicochemical and functional properties. The variant readily forms hybrid hemoglobins at room temperature, is mildly unstable at higher temperature, and has an increased oxygen affinity with a somewhat lower heme-heme interaction.     

Discovery of novel dual inhibitors of receptor tyrosine kinases EGFR and IGF-1R

Novel 4-benzylamino benzo-anellated pyrrolo[2,3-b]pyridines have been synthesized with varied substitution patterns both at the molecular scaffold of the benzo-anellated ring and at the 4-benzylamino residue. With a structural similarity to substituted thieno[2,3-d]pyrimidines as epidermal growth factor receptor (EGFR) inhibitors, we characterized the inhibition of EGFR for our novel compounds. As receptor heterodimerization gained certain interest as mechanism of cancer cells to become resistant against novel protein kinase inhibitors, we additionally measured the inhibition of insulin-like growth factor receptor IGF-1R which is a prominent receptor for such heterodimerizations with EGFR. Structure–activity relationships are discussed for both kinase inhibitions depending on the varied substitution patterns. We discovered novel dual inhibitors of both receptor tyrosine kinases with interest for further studies to reduce inhibitor resistance developments in cancer treatment.     

Studies on cytochrome c. 8. Synthesis of the protected hexadecapeptide (sequence 93-108) of Baker's yeast iso-1-cytochrome c

The synthesis is described of the protected hexadecapeptide corresponding to the C-terminal sequence 93–108 of baker's yeast iso-I-cytochrome c. The cysteine residue in position 107 of the natural sequence has been substituted by a threonine residue. The rationale of this substitution as well as the synthetic route to the preparation of the hexadecapeptide derivative is discussed.     

Discovery of novel heteroaryl-substituted chalcones as inhibitors of TNF-alpha-induced VCAM-1 expression

Novel chalcone derivatives have been discovered as potent inhibitors of TNF-alpha-induced VCAM-1 expression. Thienyl or benzothienyl substitution at the meta-position of ring B helps boost potency while large substitution at the para-position on ring B is detrimental. Various substitutions are tolerated on ring A. A lipophilicity-potency relationship has been observed in several sub-series of compounds.     

A tryptophan-substituted member of the AKH/RPCH family isolated from a stick insect corpus cardiacum.

A neuropeptide, Cam-HrTH-I, has been isolated from the corpus cardiacum of the Indian stick insect Carausius morosus. The peptide causes hyperlipaemia in Locusta migratoria and hypertrehalosaemia in Periplaneta americana and is related to the previously isolated Cam-HrTH-II (pGlu-Leu-Thr-Phe-Thr-Pro-Asn-Trp-Gly-Thr-NH2) by substitution, apparently by a hexose, on the Trp residue. This appears to be the first example of such substitution on a Trp residue.     

Site-directed mutagenesis of aspartic acid 372 at the ATP binding site of yeast phosphoglycerate kinase: over-expression and characterization of the mutant enzyme

A new phosphoglycerate kinase over-expression vector, pYE-PGK, has been constructed which greatly facilitates the insertion and removal of mutant enzyme genes by cleavage at newly introduced BamHI sites. This vector has been used to prepare mutant protein in appreciable (100 mg) quantities for use in kinetic, crystallographic and NMR experiments. Aspartate 372 is an invariant amino acid residue in genes known to code for a functionally active PGK. The function of this acidic residue appears to be to help desolvate the magnesium ion complexed with either ADP or ATP when this substrate binds to the enzyme. Both crystallographic and nuclear magnetic resonance experiments show that the replacement of the residue with asparagine has only minimal effects on the overall structure. The substitution of the charged carboxyl group with that of the neutral amide affects the binding of the nucleotide substrate as predicted but not, as might have been expected, the binding of 3-phosphoglycerate. The overall velocity of the enzymic reaction (Vmax) is reduced 10-fold by the substitution of aspartic acid 372 by an asparagine residue (D372N). This reduction in Vmax is considerably less than one would expect from its known position within the structure of the enzyme. This result therefore poses questions about our understanding of charged groups at the active centres of enzymes and of the reason for their apparent conservation.     

Analysis of glycosaminoglycan substitution in decorin by site-directed mutagenesis

Posttranslational glycosaminoglycan attachment to decorin, a chondroitin/dermatan sulfate proteoglycan, was studied by expression of a wild-type decorin cDNA and several mutagenized forms in two types of mammalian cells. Transfection of the wild-type cDNA resulted in the synthesis of an authentic chondroitin/dermatan sulfate proteoglycan similar to the decorin molecule synthesized by cultured human fibroblasts. Conversion of the serine residue that serves as the attachment site for the sole glycosaminoglycan chain in decorin to a threonine residue greatly reduced the efficiency of the glycosaminoglycan substitution. Less than 10% of the threonine-mutated core protein acquired a glycosaminoglycan chain, whereas most of the core protein was secreted without such substitution. Expression of cDNA in which an alanine residue had been introduced into the substituted serine position resulted in the secretion of core protein with no detectable glycosaminoglycan. Conversion to alanine of either one of the glycine residues that are adjacent to the substituted serine yielded the proteoglycan form of decorin. These results show that the xylosyltransferase responsible for the initiation of the glycosaminoglycan chain on the core protein can use a threonine residue for this substitution instead of a serine residue, but that such substitution is only partial, creating a "part-time" proteoglycan. Moreover, variations are possible in the sequence context of a glycosaminoglycan-substituted serine residue without loss of glycosaminoglycan substitution. The conformation of the substitution site may therefore be important for xylosyltransferase recognition.     

Characterization of hemoglobin Burke [β107 (G9) Gly→Arg]

Hb Burke [107 (G9) GlyArg] was discovered in a young woman with hemolytic anemia. A substitution in this position has not been previously reported either in the human -chain or in any of the animal -chains so far sequenced. The abnormal hemoglobin shows heat instability and a lowered oxygen affinity. The substitution of a large charged arginine residue for the small glycine residue in the G helix next to a heme contact (Leu-106) may be responsible for these effects. Hb Burke is compared with five other hemoglobins having Gly-Arg substitutions in other parts of the molecule.This work was supported in part by U.S. Public Health Service Grants AM-17850 and AM-18006.     

Stabilization of lambda repressor against thermal denaturation by site-directed Gly----Ala changes in alpha-helix 3

Oligonucleotide-directed mutagenesis has been used to replace alpha-helical glycines in the N-terminal domain of lambda repressor with alanines. Since alanine is a significantly better helix-forming residue than glycine, these changes were predicted to have a stabilizing effect. We show that the Gly46----Ala substitution, the Gly48----Ala substitution, and the double substitution increase the melting temperature of the N-terminal domain by 3-6 degrees.     

Human apolipoprotein A-I polymorphism. Identification of amino acid substitutions in three electrophoretic variants of the Münster-3 type

Variant forms of apolipoprotein A-I (apo-A-I) have been shown to exist in the human population. One mutant form, referred to as apo-A-I-Münster-3, is one charge unit more basic than normal apo-A-I on isoelectric focusing gels. This variant has the same immunologic characteristics and molecular weight as normal apo-A-I. The apo-A-I-Münster-3 from subjects in three unrelated families (in two of which the trait has been shown to be transmitted as an autosomal co-dominant) has been analyzed by partial amino acid sequencing to define the cause of the electrophoretic abnormality. In the apo-A-I of family A, the abnormality was shown to occur in the smallest cyanogen bromide fragment, CB-2 (residues 87-112), and amino acid sequencing revealed asparagine instead of the usual aspartic acid at residue 103. Subjects with this mutant form have shown no signs of dyslipoproteinemia. The NH2-terminal cyanogen bromide fragment (CB-1, residues 1-86) from the apo-A-I of family B was shown to differ electrophoretically from normal CB-1, and amino acid sequencing revealed that a substitution of arginine for proline at residue 4 was responsible for this variant form. Analysis of the plasma lipids of one affected family B member demonstrated that the percentage of the total cholesterol that was esterified was somewhat lower than that normally observed. In a third family, family C, a variant having the same electrophoretic abnormality as the other two was determined to have an amino acid substitution at yet a different position. In this variant, histidine was found at residue 3 in the apo-A-I sequence, rather than the usual proline. In all three cases, the substitution could account for the electrophoretic abnormality. It is proposed that these three apo-A-I-Münster-3 variants be designated apo-A-I(Asp103----Asn), apo-A-I(Pro4----Arg), and apo-A-I(Pro3----His), respectively, to indicate the substitution that accounts for the abnormality in isoelectric focusing gels.     

Crystal structure of the W35A mutant thioredoxin h from Chlamydomonas reinhardtii: the substitution of the conserved active site Trp leads to modifications in the environment of the two catalytic cysteines

The conformational analysis of W35A thioredoxin h from the eukaryotic green alga Chlamydomonas reinhardtii in the solid state has been carried out by x-ray diffraction, with the aim to clarify the role of Trp in the catalysis. Comparative analysis of W35A mutant with wild-type (WT) thioredoxin shows that, even if the structural motif of thioredoxin is not perturbed, the substitution of Trp35 by an Ala leads to significant changes in protein conformation near the active site. This rearrangement increases its solvent exposure and explains the change of the pKa values of the catalytic cysteines. The substitution of the Trp residue also influences the crystal packing as well as the recognition ability of thioredoxin. The solid state analysis suggests that the Trp residue has a structural function both to force the active site in the bioactive conformation, and to mediate the protein-protein recognition.     

The role of conserved Glu residue on cyclotide stability and activity: a structural and functional study of kalata B12, a naturally occurring Glu to Asp mutant

Cyclotides are a family of plant defense proteins with a unique cyclic backbone and cystine knot. Their remarkable stability under harsh thermal, enzymatic, and chemical conditions, combined with their range of bioactivities, including anti-HIV activity, underpins their potential as protein drug scaffolds. The vast majority of cyclotides possess a conserved glutamate residue in loop 1 of the sequence that is involved in a structurally important network of hydrogen bonds to an adjacent loop (loop 3). A single native cyclotide sequence, kalata B12, has been discovered that has an aspartic acid in this otherwise conserved position. Previous studies have determined that methylation of the glutamate or substitution with alanine abolishes the membrane disrupting activity that is characteristic of the family. To further understand the role of this conserved structural feature, we studied the folding, structure, stability, and activity of the natural aspartic acid variant kalata B12 and compared it to the prototypical cyclotide kalata B1, along with its glutamate to alanine or aspartate mutants. We show that the overall fold of kalata B12 is similar to the structure of other cyclotides, confirming that the cyclotide framework is robust and tolerant to substitution, although the structure appears to be more flexible than other cyclotides. Modification of the glutamate in kalata B1 or replacing the aspartate in kalata B12 with a glutamate reduces the efficiency of oxidative folding relative to the native peptides. The bioactivity of all modified glutamate cyclotides is abolished, suggesting an important functional role of this conserved residue. Overall, this study shows that the presence of a glutamic acid in loop 1 of the cyclotides improves stability and is essential for the membrane disrupting activity of cyclotides.     

Identification of a new P1 residue mutation (444Arg----Ser) in a dysfunctional C1 inhibitor protein contained in a type II hereditary angioedema plasma

A new reactive-centre P1 residue mutation (444Arg----Ser), has been identified in a dysfunctional C1 inhibitor protein, C1 inhibitor(Ba), contained in a type II hereditary angioedema plasma. This substitution is compatible with a point mutation of the 444Arg codon (CGC----AGC), and represents the first non-histidine, non-cysteine P1 residue mutant described for C1 inhibitor.     

Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix

Cost measure matrices or different amino acid indices have been widely used for studies in many fields of biology. One major criticism of these studies might be based on the unavailability of an unbiased and yet effective amino acid substitution matrix. Throughout this study we have devised a cost measure matrix based on the solvent accessibility, residue charge, and residue volume indices. Performed analyses on this novel substitution matrix (i.e. solvent accessibility charge volume (SCV) matrix) support the uncontaminated nature of this matrix regarding the genetic code. Although highly similar to a number of previously available cost measure matrices, the SCV matrix results in a more significant optimality in the error-buffering capacity of the genetic code when compared to many other amino acid substitution matrices. Besides, a method to compare an SCV-based scoring matrix with a number of widely used matrices has been devised, the results of which highlights the robustness of this matrix in protein family discrimination.     

Single substitution within the RKTR motif impairs kinase activity but promotes dimerization of RAF kinase

The serine/threonine kinase RAF is a central component of the MAPK cascade. Regulation of RAF activity is highly complex and involves recruitment to membranes and association with Ras and scaffold proteins as well as multiple phosphorylation and dephosphorylation events. Previously, we identified by molecular modeling an interaction between the N-region and the RKTR motif of the kinase domain in RAF and assigned a new function to this tetrapeptide segment. Here we found that a single substitution of each basic residue within the RKTR motif inhibited catalytic activity of all three RAF isoforms. However, the inhibition and phosphorylation pattern of C-RAF and A-RAF differed from B-RAF. Furthermore, substitution of the first arginine led to hyperphosphorylation and accumulation of A-RAF and C-RAF in plasma membrane fraction, indicating that this residue interferes with the recycling process of A-RAF and C-RAF but not B-RAF. In contrast, all RAF isoforms behave similarly with respect to the RKTR motif-dependent dimerization. The exchange of the second arginine led to exceedingly increased dimerization as long as one of the protomers was not mutated, suggesting that substitution of this residue with alanine may result in similar a structural rearrangement of the RAF kinase domain, as has been found for the C-RAF kinase domain co-crystallized with a dimerization-stabilizing RAF inhibitor. In summary, we provide evidence that each of the basic residues within the RKTR motif is indispensable for correct RAF function.     

Electrostatic influence of active-site waters on the nucleophilic aromatic substitution catalyzed by 4-chlorobenzoyl-CoA dehalogenase

The 4-chlorobenzoyl-CoA dehalogenase catalyzes the hydrolytic dechlorination of 4-chlorobenzoyl-CoA via a two-step mechanism, namely nucleophilic aromatic substitution and ester hydrolysis. The mutation of an active-site Histidine residue has been shown to reduce the catalytic activity in both the substitution and subsequent hydrolysis steps. In this communication, we report a quantum mechanical/molecular mechanical simulation of the potential of mean force for the substitution step, which confirms the increased barrier height in the H90Q mutant and provides evidence on the electrostatic influence of two active-site waters on the rate-limiting barrier.     

Functional and Structural Analysis of Influenza Virus Neuraminidase N3 Offers Further Insight into the Mechanisms of Oseltamivir Resistance

The influenza virus neuraminidase H274Y substitution is a highly prevalent amino acid substitution associated with resistance to the most heavily used influenza drug, oseltamivir. Previous structural studies suggest that the group specific 252 residue (Y252 in group 1 and T252 in group 2) might be a key factor underlying H274Y resistance. However, H274Y has only been reported in N1 subtypes, which indicates that there must be additional key residues that determine H274Y resistance. Furthermore, we found that members of NA serotype N3 also possess Y252, raising the key question as to whether or not H274Y resistance may also be possible for some group 2 NAs. Here, we demonstrate that the H274Y substitution results in mild oseltamivir resistance for N3. Comparative structural analysis of N3, N1, and their 274Y variants indicates that the interaction of residue 296 (H in N1 and nonaromatic for other serotypes) with conserved W295 is another important determinant of oseltamivir resistance.     

Parvalbumin conformers revealed by steady-state and time-resolved fluorescence spectroscopy

The binding of calcium to whiting (one tryptophan residue) and pike (one tyrosine residue) parvalbumins has been studied by means of kinetic and steady-state fluorescence techniques. The decay curves of the tryptophan and tyrosine fluorescence of the parvalbumins are best fitted by a sum of two exponents for any metal state of the proteins. The data can be interpreted as a nonexponential decay of the fluorescence of a single-type chromophore or in terms of equilibria between compact and relaxed conformers of the parvalbumins in each metal state. Fluorescence quenching by I-ions and effects of H2O/D2O substitution confirm the second interpretation. The constants of the equilibria have been evaluated.