Neutral Amino Acid Substitutions Research Articles

Electrically neutral microheterogeneity of human plasma transthyretin (prealbumin) detected by isoelectric focusing in urea gradients.

Mutants of the human plasma transthyretin (TTR, prealbumin) have attracted interest due to their rather frequent association with the autosomal dominant disease familial amyloidotic polyneuropathy (FAP). Some three quarters of known TTR mutations produce electrically neutral amino acid substitutions undetectable via separation by charge. We have developed an electrophoretic procedure sensitive to differences in the stability of tetramers and monomers under partially denaturing conditions. The differential folding states were found to be fully reversible. Applying the procedure we found 14 electrically silent mutants of TTR among 2000 plasma samples from German donors. We demonstrate that the normal TTR monomer exists in different forms of variable stability and/or charge due to binding of sulfhydryls from plasma to the unique cysteine at position 10 of the primary structure as well as due to modification by treatment with an oxidant. We found that reduction of Cys10 increases the stability of the folded monomeric and tetrameric conformations. The conformational changes of TTR induced by isoelectric focusing in a urea gradient were found to be associated by a gain of three positive charge units. Using published crystallographic data we present structural sites in the TTR molecule which could explain the observed effects.

Detection of neutral and charged mutations in α- and β-human globin chains by capillary zone electrophoresis in isoelectric, acidic buffers

A simple and reliable method, for screening for point mutations in α- and β-human globin chains, is reported here, utilizing capillary zone electrophoresis in isoelectric, acidic buffers. A solution of 50 m M iminodiacetic acid (p I 2.23) containing 7 M urea and 0.5% hydroxyethylcellulose (apparent pH 3.2) is used as background electrolyte for fast separation of heme-free, denatured globin (α and β) chains. Due to the low conductivity of such buffers, high voltage gradients (600 V/cm) can be applied, thus reducing the separation time to only a few minutes. In presence of neutral to neutral amino acid substitutions, it is additionally shown that the inclusion of 3% surfactant (Tween 20) in the sample and background electrolyte induces the separation of the wild-type and mutant chains, probably by a mechanism of hydrophobic interaction of the more hydrophobic mutant with the detergent micelle, via a mechanism similar to “micellar electrokinetic chromatography”. At this low operative pH, however, charged mutants, involving substitutions of acidic amino acids (Glu and Asp) are not detected, since these residues are extensively protonated. Curiously, however, they are still separated in presence of detergent, due to the large variation in hydrophobicity involved in such mutations. Of the 19 mutants analyzed, all but one were resolved: Hb St Nazaire (β103 Phe→Ile). This is due to the fact that the Δ G (in kcal/mol) in the substitution Phe→Ile is zero, thus no separation can possibly take place between two chains exhibiting the same hydrophobicity parameter.

Identification of the principal proteoglycan-binding site in LDL. A single-point mutation in apo-B100 severely affects proteoglycan interaction without affecting LDL receptor binding.

The subendothelial retention of LDLs through their interaction with proteoglycans has been proposed to be a key process in the pathogenesis of atherosclerosis. In vitro studies have identified eight clusters of basic amino acids in delipidated apo-B100, the protein moiety of LDL, that bind the negatively charged proteoglycans. To determine which of these sites is functional on the surface of LDL particles, we analyzed the proteoglycan-binding activity of recombinant human LDL isolated from transgenic mice. Substitution of neutral amino acids for the basic amino acids residues in site B (residues 3359-3369) abolished both the receptor-binding and the proteoglycan-binding activities of the recombinant LDL. Chemical modification of the remaining basic residues caused only a marginal further reduction in proteoglycan binding, indicating that site B is the primary proteoglycan-binding site of LDL. Although site B was essential for normal receptor-binding and proteoglycan-binding activities, these activities could be separated in recombinant LDL containing single-point mutation. Recombinant LDL with a K3363E mutation, in which a glutamic acid had been inserted into the basic cluster RKR in site B, had normal receptor binding but interacted defectively with proteoglycans; in contrast, another mutant LDL, R3500Q, displayed defective receptor binding but interacted normally with proteoglycans. LDL with normal receptor-binding activity but with severely impaired proteoglycan binding will be a unique resource for analyzing the importance of LDL- proteoglycan interaction in atherogenesis. If the subendothelial retention of LDL by proteoglycans is the initial event in early atherosclerosis, then LDL with defective proteoglycan binding may have little or no atherogenic potential.

The carbohydrate recognition domain of surfactant protein A mediates binding to the major surface glycoprotein of Pneumocystis carinii.

Pneumocystis carinii is a common cause of life-threatening pneumonia in immunodeficient patients. Pulmonary surfactant protein A (SP-A), an alveolar glycoprotein containing collagen-like and carbohydrate recognition domains (CRD), binds P. carinii and enhances adherence to alveolar macrophages. In this study, we examined the structural basis of the interaction between SP-A and the major surface glycoprotein of P. carinii (MSG). Rat SP-A bound to purified rat P. carinii-derived MSG in a saturable and calcium-dependent manner, which was partially reversible by coincubation with excess monosaccharides, or pretreatment of MSG with N-glycanase. Mutant recombinant SP-As with neutral amino acid substitutions for the predicted calcium- and carbohydrate-coordinating residues of the CRD were synthesized in insect cells using baculovirus vectors and tested for binding to MSG. Substitutions of negatively charged (Glu195, Glu202, and Asp215) and polar residues (Asn214) of the CRD with alanine but not substitution of the Arg197 with glycine reduced the binding of SP-A to mannose-Sepharose beads and to MSG. Deletion of the N-linked oligosaccharides from SP-A by mutagenesis of the consensus sequences for glycosylation had no effect on binding. We conclude that the CRD mediates the binding of SP-A to oligosaccharides attached to MSG.

Screening and biochemical characterization of transthyretin variants in the Portuguese population.

The study of pathogenic and nonpathogenic transthyretin (TTR) variants is very important for the understanding of such TTR-related diseases as hereditary amyloidosis and also to establish a relationship between the structure and function of the molecule. Variants with clinical manifestations can be easily detected, but clinically silent variants can be detected only by population screening programs using specialized techniques. Hybrid isoelectric focusing (HIEF) in extremely flattened immobilized pH gradients (IPG) allows the detection of even neutral amino acid substitutions and has been used to analyze approximately 5,000 samples from the Portuguese population. Comparison with samples from carriers of three known TTR mutations (Met 30 associated with hereditary amyloidosis, Met 119, and Asn 90) was also made. In this study we detected: (1) 8 individuals carriers of TTR Met 30, (2) 35 carriers of TTR Met 119, (3) 12 carriers of TTR Asn 90, (4) 1 compound heterozygote for TTR Met 30/Met 119, and (5) 5 variants that presented a different pattern from the controls used. We also performed DNA sequencing analyses of two of the variants with the different band pattern in HIEF. The individuals were found to be carriers of TTR Ile 122 and TTR Thr 190, respectively. All the mutations detected, except for Asn 90, result from substitutions in CpG hot spots and thus can be rather frequent in the populations. Studies on the clinical evolution of the compound heterozygotes and on the physical-chemical properties of these hybrid TTRs will help to understand the pathogenicity associated with TTR.

Screening and biochemical characterization of transthyretin variants in the Portuguese population

The study of pathogenic and nonpathogenic transthyretin (TTR) variants is very important for the understanding of such TTR-related diseases as hereditary amyloidosis and also to establish a relationship between the structure and function of the molecule. Variants with clinical manifestations can be easily detected, but clinically silent variants can be detected only by population screening programs using specialized techniques. Hybrid isoelectric focusing (HIEF) in extremely flattened immobilized pH gradients (IPG) allows the detection of even neutral aminoacid substitutions and has been used to analyze ∼5,000 samples from the Portuguese population. Comparison with samples from carriers of three known TTR mutations (Met 30 associated with hereditary amyloidosis, Met 119, and Asn 90) was also made. In this study we detected: (1) 8 individuals carriers of TTR Met 30, (2) 35 carriers of TTR Met 119, (3) 12 carriers of TTR Asn 90, (4) 1 compound heterozygote for TTR Met 30/Met 119, and (5) 5 variants that presented a different pattern from the controls used. We also performed DNA sequencing analyses of two of the variants with the different band pattern in HIEF. The individuals were found to be carriers of TTR Ile 122 and TTR Thr 109, respectively. All the mutations detected, except for Asn 90, result from substitutions in CpG hot spots and thus can be rather frequent in the populations. Studies on the clinical evolution of the compound heterozygotes and on the physical-chemical properties of these hybrid TTRs will help to understand the pathogenicity associated with TTR. Hum Mutat 9:226–233, 1997 © 1997 Wiley-Liss, Inc.

Reversal of the surface charge asymmetry in purple membrane due to single amino acid substitutions

Twenty-seven mutant bacteriorhodopsin's were screened to determine the PKa for reversal of the permanent electric dipole moment. The photoelectric response of an aqueous purple-membrane suspension was used to determine the direction of the purple-membrane dipole moment as a function of pH. The pK(a) for the dipole reversal of wild-type bacteriorhodopsin is 4.5. Six of the 27 mutant bacteriorhodopsin's were found to have a pK(a) for dipole reversal larger than that of wild-type bacteriorhodopsin. Two of these mutants, L93T and L93W, involve a neutral amino acid substitution in the interior of the protein. The direction of the purple-membrane permanent electric dipole moment is determined by the purple-membrane surface charge asymmetry. We conclude that these two substitutions, which do not involve charge replacement, alter the pK(a) for the reversal of the purple-membrane surface charge asymmetry. We suggest that these changes to the pK(a) are due to altered protein folding at the surface of the purple-membrane induced by single-site substitutions in the protein interior.

Molecular basis of the complement C7 M/N polymorphism. A neutral amino acid substitution outside the epitope of the allospecific monoclonal antibody WU 4-15.

The allotypes of the C7 M/N polymorphism are determined by comparing the ELISA reaction pattern of the allospecific mAb WU 4-15 with polyclonal anti-C7 IgG. To characterize the molecular basis of this polymorphism, the WU 4-15 epitope was mapped by expression of cDNA fragments. It was found to be located within the boundary region of the two short consensus repeats of C7 (amino acid residues 595-612). Coincidentally an A or C substitution was found in the course of investigation of the gene structure at nucleotide 1759. This leads to an electrically neutral Pro/Thr substitution at residue 565 and alternative Sau961 or RsaI restriction sites, respectively. Enzymatic digestion or sequencing of PCR-amplified genomic DNA from C7 M/N-typed individuals showed a perfect correspondence of the genotype with the phenotype of the C7 M/N polymorphism. In contrast, no association was found with the genotypes of a second polymorphic site at residue 367. Thus, a threonine at amino acid residue 565 allows access of WU 4-15 to its epitope but its substitution with proline almost completely inhibits access in the native molecule, although the epitope is about 40 amino acid residues distant from the polymorphic site in the primary structure. Furthermore, the different conformational structure is probably responsible for the hypomorphic appearance of C7*N.

Mistranslation of human phosphoglycerate kinase in yeast in the presence of paromomycin

Missense errors in the translation of mRNAs in Saccharomyces cerevisiae were screened by looking for charge heterogeneity of proteins on two-dimensional gels resulting from the substitution of charged and neutral amino acids. No such mistranslation was detected in wild-type yeast strains grown in the presence of the translational error-inducing antibiotic paromomycin. However, paromomycin-induced mistranslation of a heterologous mRNA, encoding human phosphoglycerate kinase expressed in yeast, was seen. We suggest that the combination of error-prone translation of a heterologous mRNA, and growth in the presence of paromomycin, leads to an accumulation of mistranslated proteins that can be detected by two-dimensional gel electrophoresis.

A mutation in the Norrie disease gene (NDP) associated with X-linked familial exudative vitreoretinopathy.

Familial exudative vitreoretinopathy (FEVR) is a hereditary disorder characterized by an abnormality of the peripheral retina. Both autosomal dominant (adFEVR) and X-linked (XLFEVR) forms have been described, but the biochemical defect(s) underlying the symptoms are unknown. Molecular analysis of the Norrie gene locus (NDP) in a four generation FEVR family (shown previously to exhibit linkage to the X-chromosome markers DXS228 and MAOA (Xp11.4-p11.3)) reveals a missense mutation in the highly conserved region of the NDP gene, which caused a neutral amino acid substitution (Leu124Phe), was detected in all of the affected males, but not in the unaffected family members, nor in normal controls. The observations suggest that phenotypes of both XLFEVR and Norrie disease can result from mutations in the same gene.

The C7 M/N polymorphism is determined by a neutral amino acid substitution outside the epitope of the allospecific monoclonal antibody WU 4-15

The C7 M/N polymorphism is determined by a neutral amino acid substitution outside the epitope of the allospecific monoclonal antibody WU 4-15

Allelic Variations of Human Keratins K4 and K5 Provide Polymorphic Markers Within the Type II Keratin Gene Cluster on Chromosome 12

To appreciate point mutations in keratin genes as causes for hereditary epithelial diseases, the normal variation of these gene sequences in the population must be known. Because genetic polymorphism of keratins at the protein level due to allelic variation has been described for the type II keratins 4 and 5, we have analyzed their corresponding genes using single-strand conformation polymorphism gel electrophoresis and sequence analysis of polymerase chain reaction amplified genomic DNA. Although no sequence variations were found in the carboxyl-terminal and rod domains we were able to map the molecular differences among the alleles to their amino-terminal domains. In particular, we have identified three alleles of keratin 4. Two alleles differed by a nucleotide transition causing a neutral amino acid substitution (alanine to valine) and one allele had a 42-bp in-frame deletion corresponding to 14 amino acids within the V1 subdomain. Three alleles were also recognized for the keratin 5 locus, all being elicited by single nucleotide substitutions. Of these, only one altered the amino acid sequence, replacing an uncharged (glycine) with a charged (glutamic acid) amino acid in the H1 subdomain. Pedigree analyses in three families showed the alleles to be inherited as autosomal Mendelian traits. Thus, these normal alleles of keratins 4 and 5 will provide favorable polymorphic markers for linkage analysis directly within the cluster of type II keratin genes located on chromosome 12q to elucidate the potential involvement of these and other keratin genes in disorders of squamous cell differentiation.

Haemoglobin I: a new beta-globin chain variant found in sheep of Italian breeds.

A rather common haemoglobin variant was detected in the Sardinian and Altamurana sheep breeds. The mutated globin chain appears to be produced under the control of an allele at the HBB locus and due to a neutral amino acid substitution. The variant will be provisionally referred to as the Hb I.

Role of the charge pair aspartic acid-237-lysine-358 in the lactose permease of Escherichia coli.

Using a lactose permease mutant devoid of Cys residues (C-less permease), Asp237 and Lys358 were replaced with Cys or other amino acids to pursue the proposal that the two residues form a charge pair [King, S. C., Hansen, C. L., & Wilson, T.H. (1991) Biochim. Biophys. Acta 1062, 177-186]. Individual replacement of Asp237 with Cys, Ala, or Lys or replacement of Lys358 with Cys, Ala, or Asp virtually abolishes active lactose transport. However, simultaneous replacement of both residues with Cys and/or Ala yields permease with high activity. Therefore, neutral amino acid substitutions at either position are detrimental only because they leave the opposing charge unpaired. Strikingly, moreover, when Asp237 is interchanged with Lys358, high activity is observed. The results indicate strongly that Asp237 and Lys358 interact to form a salt bridge and that neither residue nor the salt bridge per se is important for activity. Immunoblots reveal low membrane levels of the active mutants lacking the putative salt bridge, suggesting a role for the salt bridge in either permease folding or stability and raising the possibility that the salt bridge may exist in a folding intermediate but not in the mature protein. Remarkably, however, a mutant with Cys in place of Asp237 is restored to full activity by carboxymethylation which recreates a negative charge at position 237. Pulse-chase analysis and heat-inactivation studies indicate that the stability of the double mutant with Cys at positions 237 and 358 is comparable to C-less. Therefore, the interaction between Asp237 and Lys358 is likely to be important for permease folding and is maintained in the mature protein.(ABSTRACT TRUNCATED AT 250 WORDS)

River buffalo ( Bubalus bubalis L.) AA phenotype haemoglobins: characterization by immobiline polyacrylamide gel electrophoresis and high performance liquid chromatography and determination of the primary structure of the constitutive chains by mass spectrometry

1. 1. Polyacrylamide gel electrophoresis in ultra-narrow immobilized pH gradient shifted the “Hb fast” band of AA buffalo phenotype haemoglobin into two components which were named Hb1 and Hb3. 2. 2. Urea/Triton electrophoresis and reversed-phase HPLC demonstrated that Hb1 and Hb3 differ in the presence of two structurally distinct α chains (α 1 and α 3), also suggesting that the α chains must differ for neutral amino acid substitution. 3. 3. Extensive mass spectrometric analysis on several digests (FAB overlapping) meant to determine the complete sequence of the constituent chains. 4. 4. Two amino acid replacements (Lys 18→His and Asn 116→His) were present in the β chain with respect to the bovine (A phenotype chain, whereas the α 1 and α 3 globins were found to contain four amino acid replacements compared to the bovine α, three of which were identical (Glu 23→Asp, Glu 71→Gly and Phe 117→Cys) and, notably, an insertion of Ala at position 123–124. 5. 5. Furthermore, α 1 contains Phe at position 130 whereas α 3 contains Ser at position 132 (following the modified numbering as a consequence of the Ala insertion).

Haemophilia B mutations in a complete Swedish population sample: a test of new strategy for the genetic counselling of diseases with high mutational heterogeneity

Carrier and prenatal diagnosis based on the identification of the gene defect (direct diagnosis) increases the proportion of haemophilia B families that can be offered precise genetic counselling from the 50-60% attainable by DNA markers, to 100% and they also provide information on the molecular biology of the disease. We propose that in order to maximize the practical and scientific benefits of direct diagnosis the gene defect of complete (possibly national) populations of patients should be characterized and the information stored in appropriate confidential databases. We demonstrate the feasibility of such a strategy by characterizing the mutations of all the patients registered with the Malmö haemophilia centre. These patients (44 male and 1 female) are from 45 unrelated families and 24 (53%) have negative family history. The 25 patients with similar reduction of factor IX:C and factor IX:Ag (24 male + 1 female) have: two gross deletions, three frameshifts, four translation stops, six mutations expected to affect pre-mRNA splicing and 10 amino acid substitutions. The six patients with greater reduction of factor IX:C than factor IX:Ag and the seven with reduced IX:C and normal IX:Ag have only amino acid substitutions. Patients with inhibitors have: one complete deletion, one frameshift and three translation stops. One patient has both a translation stop and a functionally neutral amino acid substitution (His257----Tyr). Characterization of the factor IX mutation was successful in every case, usually entailed 4 person-days work, and has led to the identification of 12 amino acid residues essential for the factor IX structure and function.

Mutagenesis of lysine 460 in the human insulin receptor. Effects upon receptor recycling and cooperative interactions among binding sites.

Mutations in the insulin receptor gene can cause insulin resistance. Previously, we have identified a mutation substituting glutamic acid for lysine at position 460 in the alpha-subunit of the insulin receptor in a patient with a genetic form of insulin resistance. In the present work, we have investigated the effect upon receptor function of amino acid substitutions at position 460. Decreasing the pH from 8.0 to 5.5 caused a progressive acceleration of the dissociation of 125I-insulin from the wild-type insulin receptor. Substitution of acidic amino acids (Glu or Asp) for Lys460 decreased the ability of acid pH to accelerate dissociation of 125I-insulin. In contrast, substitution of Arg or neutral amino acids (Val, Met, Thr, or Gln) had no effect upon the sensitivity to acid pH. Correlated with decreased sensitivity to acid pH, substitution of Glu or Asp at position 460 retarded the dissociation of 125I-insulin from intracellular receptors subsequent to receptor-mediated endocytosis. Furthermore, retardation of dissociation of 125I-insulin from the internalized receptor was associated with a decreased half-life of the receptor. In summary, the Glu460 mutation appears to cause insulin resistance by accelerating receptor degradation and, thereby, decreasing the number of insulin receptors on the cell surface. Additional studies suggested that Lys460 may provide the amino groups whereby disuccinimidyl suberate cross-links the two alpha-subunits to each other. Consistent with the hypothesis that Lys460 is located at the interface between adjacent alpha-subunits, substitutions at position 460 impair cooperative interactions among insulin binding sites. The Glu460 mutation decreases positively cooperative binding interactions; the Arg460 mutation impairs negative cooperativity. Mutations at position 460 in the alpha-subunit did not decrease the ability of insulin to stimulate receptor tyrosine kinase.

Discrimination between adaptive and neutral amino acid substitutions in vertebrate hemoglobins

A discriminant analysis on the basis of the physicochemical properties of amino acid residues is developed to investigate the accumulation pattern of amino acid substitutions in a family of proteins. The application of this analysis to vertebrate hemoglobins reveals the following new results. (1) The major components of teleost fish and amphibian hemoglobins showing the Root effect are sharply discriminated from mammalian hemoglobins in several regions of the alpha and beta chains, whereas shark, minor components of teleost fish and amphibian, reptile, and bird hemoglobins showing no Root effect exhibit a gradual change to mammalian hemoglobin in a straightforward way. This result suggests at least two lines of molecular evolution in vertebrate hemoglobins. (2) The nonadult hemoglobin chains are allocated to the latter line, i.e., tadpole, zeta, and pi chains are similar to shark and trout I chains, and epsilon and gamma chains are similar to some of the reptile chains. (3) In any case, most of the amino acid residues causing the discrimination are located near the sites that carry the amino acid residues conserved well throughout all classes of vertebrates, suggesting that modifications adapting to the respective living conditions or respiratory organs have taken place effectively near the amino acid residues essential for the manifestation of cooperative oxygen binding. (4) The amino acid residues at other sites are changed from one to another species even within the same class, showing a constant substitution rate as a whole. These amino acid substitutions may be nearly neutral, being under a weak functional constraint. The number of sites allowing such neutral substitutions is rather small, less than one-half of all the sites in the adult hemoglobins of bird and mammal, whereas it amounts to two-thirds in teleost fish hemoglobins.

Biochemical and genetic studies on rabbit hemoglobin. II. Electrophoretic polymorphism of the?-chain

A genetic polymorphism of rabbit (Oryctolagus cuniculus) hemoglobin alpha chain is demonstrated by means of acid starch gel electrophoresis. The polymorphism is not detected by isoelectric focusing and may be based upon neutral for neutral amino acid substitutions in accordance with previous findings by means of amino acid sequencing. Segregation analysis was performed on 15 matings with 49 offspring and confirmed the initial genetic hypothesis of three common codominant alleles at an autosomal locus. The calculated gene frequencies in a random sample of 86 unrelated individuals are HBA*1 = 0.73, HBA*2 = 0.22, and HBA*3 = 0.05.

High-performance liquid chromatography as a method to identify haemoglobin abnormalities.

This short review summarizes data obtained with two different high-performance liquid chromatography (HPLC) methods, useful in the study of numerous haemoglobinopathies. The first concerns the use of a cation exchange HPLC column which, when developed with specific gradient elution systems, will allow the separation of many normal and abnormal haemoglobins in blood from adults and newborn babies. The method has great diagnostic value. The second procedure uses a reverse-phase HPLC system and acetonitrile-H2O-trifluoroacetic acid developers at low pH for the separation of globin chains (alpha, zeta, beta, delta, G gamma, A gamma, epsilon). The method can be applied as an analytical as well as a preparative tool; it is ideally suited to separate several normal and abnormal chains with neutral amino acid substitutions, including the three gamma chains (G gamma = gamma 75Ile; 136Gly, A gamma = gamma 75Ile; 136Ala, A gamma T = gamma 75Thr; 136Ala).