The amino acid sequence required for 5' -> 3' exonuclease activity of Bacillus caldotenax DNA polymerase

We studied the 5' 3' exonuclease activity of Bacillus caldotenaxDNA polymerase by site-directed mutagenesis. Among seven mutantsconstructed, two mutant DNA polymerases with an amino acid substitutionof Glyl84 Asp or Glyl92 Asp were confirmed to be deficientin this exonuclease. The two positions corresponded to thoseof the Escherichia coli DNA polymerase I mutants defective in5' 3' exonuclease, polA480ex and polA214. These results provideexperimental support for the proposed amino acid sequence essentialfor the 5' 3' exonuclease activity associated with eubacterialpolymerase I–like DNA polymerases (family A), includingE.coli and Thermits aquaticus.     

Recombinant-derived interleukin-1{alpha} stabilized against specific deamidation

Recombinant-derived human interleukln-1 (IL-1), purified fromEscherichia coli, was resolved by isoelectric focusing on polyacrylamidegels into two species of isoelectric points (pI) 5.45 and 5.20,which constituted 75% and 25% of the total IL-1 protein respectively.The pI 5.45 and pI 5.20 species were separated by chromatofocusingand subjected to N-terminal sequence analysis. The pI 5.45 speciescontained the expected Asn residue at position 36 of the matureprotein sequence whereas the pI 5.20 species contained an Aspresidue at the same position. A mutant protein in which Asn-36was substituted for a Ser residue was isolated from E.coli andshown to be homogeneous on isoelectric focusing analysis witha pI = 5.45. ¹H-n.m.r. and circular dichroism analyses of wild-typeand the mutant IL-1 indicated a similar conformation which wasalso indicated by the identical receptor binding affinitiesof IL-1 with Asn, Asp or Ser in position 36. The mutant proteinwas stabilized against specific base catalysed and temperature-induceddeamidation, and may be more suitable than the wild-type positionfor physical and structural studies.     

Effect of amino acid deletions in the O-glycosylated region of Aspergillus awamori glucoamylase

Aspergillus awamori glucoamylase (GA) contains globular catalyticand starch-binding domains (residues 1–471 and 509–616,respectively). A heavily O-glycosylated sequence comprises twoparts. The first (residues 441–471) in the crystal structurewraps around an /-barrel formed by residues 1–440. Thesecond (residues 472–508) is an extended, semi-rigid linkerbetween the two domains. To investigate the functional roleof this linker, we made internal deletions to remove residues466–512 (GA1), 485–512 (GA2) and 466–483 (GA3).GA2 and GA3 were expressed in Saccharomyces cerevisiae culturesupernatants at 60 and 20% the wild-type level, respectively,while GA1 was almost undetectable. Western blots comparing extracellularand intracellular fractions indicated that the region deletedin GA3 was critical for secretion, while the region deletedin GA2 contributed to the production of a stable enzyme structure.The activities of purified GA2 and GA3 on soluble and insolublestarch were similar to those of wild-type GA, indicating thatfor soluble starch their deletions did not affect the catalyticdomain and for insoluble starch the linker does not coordinatethe activities of the catalytic and starch-binding domains.The deletions had a significant negative effect on GA2 and GA3thermos tabilities.     

Site-directed mutagenesis of glutathione synthetase from Escherichia coli B: mapping of the {gamma}-L-glutamyl-L-cysteine-binding site

Lysl8, Arg86, Asn283, Ser286, Thr288 and Glu292 of glutathionesynthetase from Escherichia coli B are presumed to be highlyconcerned with the substrate, -L-glutamyl-L-cysteine (-Glu-Cys),binding by X-ray crystallography and affinity labeling studies.Using site-directed mutagenesis, we investigated functionalroles of those residues for -Glu-Cys binding. The mutant enzymesof Arg86 and Asn283 altered their kinetic parameters, especiallythe Michaelis constants of -Glu-Cys. In the case of Asn283,the residue is not likely to have an essential role in -Glu-Cysbinding but its side chain would extend to make a van der Waalscontact with bound -Glu-Cys. Chemical modification of a cysteineresidue with 5,5'-dithiobis(2-nitrobenzoate) (DTNB) showed Arg86would not only be much responsible for -Glu-Cys binding butwould also have a role in maintaining the structural integrityof the enzyme. The other mutant enzymes showed little defectin their kinetic parameters of -Glu-Cys.     

The use of alanine scanning mutagenesis to determine the role of the N-terminus of the regulatory chain in the heterotropic mechanism of Escherichia coli aspartate transcarbamoylase

The location of the first seven residues of the regulatory chainof Escherichia coli aspartate transcarbamoylase has been identifiedby X-ray crystallography to be near the binding site of theregulatory nucleotides. In order to determine the function ofthe N-terminus of the regulatory chain of aspartate transcarbamoylasein heterotropic regulation, alanine scanning mutagenesis wasused. Specifically, Thr2r, His3r, Asp4r, Asn5r, Lys6r and Leu7rwere each replaced with alanine. Analyses of these mutant enzymesindicate that none of these substitutions significantly alterthe catalytic properties of the enzyme. However, three of themutant enzymes, Asp4r Ala, Lys6r Ala and Leu7r Ala, exhibitednotable changes in their response to the regulatory nucleotides,while mutations at Thr2r, His3r and Asn5r exhibited only minorchanges in their heterotropic responses. For the Asp4r Alaenzyme, the responses to ATP and CTP were reduced 30 and 40%respectively, compared with the wild-type enzyme. For the Lys6r Ala enzyme, the response to ATP was reduced 70%, while theCTP response was reduced 50%. In the case of the Leu7r Alaenzyme, a 30 and 20% reduction in response to ATP and CTP respectively,was observed. The synergistk inhibition by UTP in the presenceof CTP for the Lys6r Ala enzyme was reduced 40% compared withthat of the wild type enzyme. For the Leu7r Ala enzyme, thesynergistic inhibition was abolished. In addition, UTP decreasedthe CTP binding affinity of the Leu7r Ala enzyme. Analysisof the kinetic data from these mutant enzymes suggests thatresidues Thr2r, His3r and Asn5r have little effect on the heterotropicmechanism, while residues Asp4r, Lys6r and Leu7r play a moresignificant role in the heterotropic response of the enzymetoward the nucleotides. Furthermore, residue Leu7r appears tobe directly involved in the mechanism for synergistic inhibitionof aspartate transcarbamoylase. In this study alanine scanningmutagenesis has provided a rapid method of identifying thoseresidues in the N-terminal region of the regulatory chain ofaspartate transcarbamoylase important for heterotropic regulation.     

Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures

A total of 19 835 polar residues from a data set of 250 non-homologousand highly resolved protein crystal structures were used toidentify side-chain main-chain (SC-MC) hydrogen bonds. The ratioof the number of SC-MC hydrogen bonds to the total number ofpolar residues is close to 1:2, indicating the ubiquitous natureof such hydrogen bonds. Close to 56% of the SC-MC hydrogen bondsare local involving side-chain acceptor/donor (`i') and a main-chaindonor/acceptor within the window i–5 to i+5. These short-rangehydrogen bonds form well defined conformational motifs characterizedby specific combinations of backbone and side-chain torsionangles. (a) The Ser/Thr residues show the greatest preferencein forming intra-helical hydrogen bonds between the atoms O_iand O_i–4. More than half the examples of such hydrogenbonds are found at the middle of -helices rather than at theirends. The most favoured motif of these examples is _RRRR(g^–).(b) These residues also show great preference to form hydrogenbonds between O_i and O_i–3, which are closely related tothe previous type and though intra-helical, these hydrogen bondsare more often found at the C-termini of helices than at themiddle. The motif represented by _RRRR(g⁺) is most preferredin these cases. (c) The Ser, Thr and Glu are the most frequentlyfound residues participating in intra-residue hydrogen bonds(between the side-chain and main-chain of the same residue)which are characterized by specific motifs of the form ß(g⁺)for Ser/Thr residues and _R(g^–g⁺t) for Glu/Gln. (d) Theside-chain acceptor atoms of Asn/Asp and Ser/Thr residues showhigh preference to form hydrogen bonds with acceptors two residuesahead in the chain, which are characterized by the motifs ß (tt')Rand ß(t)_R, respectively. These hydrogen bonded segments,referred to as Asx turns, are known to provide stability totype I and type I' ß-turns. (e) Ser/Thr residues oftenform a combination of SC-MC hydrogen bonds, with the side-chaindonor hydrogen bonded to the carbonyl oxygen of its own peptidebackbone and the side-chain acceptor hydrogen bonded to an amidehydrogen three residues ahead in the sequence. Such motifs arequite often seen at the beginning of -helices, which are characterizedby the ß(g⁺)_RR motif. A remarkable majority of all thesehydrogen bonds are buried from the protein surface, away fromthe surrounding solvent. This strongly indicates the possibilityof side-chains playing the role of the backbone, in the proteininteriors, to satisfy the potential hydrogen bonding sites andmaintaining the network of hydrogen bonds which is crucial tothe structure of the protein.     

A point mutation of human interferon {gamma} abolishes receptor recognition

We identified a single amino acid mutation that abolished thebioactivity of human IFN. The mutation was identified by screeninga mutagenized IFN expression library for molecules with alteredbiological activity. The mutant protein was expressed at highlevels in Escherichia coli, and remained soluble upon purification.However, the protein was completely inactive in all IFN assaysinvestigated, exhibiting < 0.0006% of the specific activityof native IFN antiviral activity. Sequencing the plasmid DNAencoding this mutant protein showed that the histidine at position111 of native human IFN is changed to aspartic acid (IFN/H111D).Other mutations at this site showed that only hydrophobic aminoacids at position 111 maintain significant, though low, biologicalactivity. Structural characterization of the IFN/H111D proteinby NMR as well as CD spectroscopy demonstrated that the proteinhas limited conformational differences from native IFN. Modelsof the X-ray crystal structure of human IFN [Ealick, P.E., W.J.Cook,S.Vijay-Kumar, M.Carson, T.L.Nagabhushan, P.P.Trotta and C.E.Bugg(1991) Science, 252, 698–702] suggest that this histidineresidue is located at a severe 55° bend in the C-terminalF helix. We conclude that H111 lies within or affects the receptorbinding domain of human IFN.     

Activation of the low oxygen affinity-inducing potential of the Asn108({beta}){->}Lys mutation of Hb-Presbyterian on intramolecular {{alpha}}{{alpha}}-fumaryl cross-bridging

The Asn108ßLys mutation in hemoglobin (HbPresbyterianmutation) endows a low O₂ affinity-inducing propensity to theprotein. Introduction of a fumaryl cross-bridge between itstwo 99 lysine residues also induces a low O₂ affinity into HbA.We have now engineered an -fumaryl cross-bridge into Hb-Presbyterianto determine the synergy or additivity, if any, that can beachieved between these two low O₂ affinity-inducing structuralperturbations. Despite the presence of the additional -aminogroup of Lys108(ß) within the central cavity, the-amino group of Lys99() of deoxy Hb-Presbyterian retained highselectivity for -fumaryl cross-bridging, with an overall efficiencycomparable to that with HbA. The -fumaryl cross-linking of Hb-Presbyterianreduced its O₂ affinity much more significantly than that observedwith HbA, indicating a synergy between the two low O₂ affinity-inducingstructural perturbations. Apparently, the -fumaryl cross-bridgein Hb-Presbyterian activates part of the latent low O₂ affinity-inducingpotential of Lys108(ß) that is generally activatedin the presence of chloride. The synergy between the Asn108(ß)Lysmutation and the -fumaryl cross-bridging was conserved in thepresence of chloride, but not in the presence of DPG. Furthermore,in the presence of chloride and DPG, -fumaryl Hb-Presbyterianaccessed a low O₂ affinity T-state that is accessed by HbA,-HbA and Hb-Presbyterian only in the presence of IHP. Isoelectricfocusing analysis suggested that the -fumaryl cross-linkingof Hb-Presbyterian induces changes in the ionization behaviorof one or more of the functional groups neighboring Lys99()and Lys108(ß) [presumably His103() and/or Glu101(ß)]to compensate for the extra positive charge of Lys108(ß).Molecular modeling studies identified two potential chloridebinding sites per ß dimer within the middle of thecentral cavity of -fumaryl HbA involving residues His103(),Arg104(ß) and Asn108(ß). The affinity ofthese sites is increased in -fumaryl Hb-Presbyterian as a resultof the Asn108(ß)Lys mutation. Thus, the results ofthe present study suggest that the enhanced neutralization ofthe positive charges in the middle of the central cavity ofHb achieved by these two electrostatic modifications, one (the-fumaryl cross-bridge) acting directly and the other (the Presbyterianmutation) acting indirectly through the mediation of chlorideion binding, facilitates the - fumaryl-Hb Presbyterian to accessa low O₂ affinity T-state structure much more readily than eitherHb-Presbyterian or -fumaryl HbA.     

Mutational analysis of structure--activity relationships in human tumor necrosis factor-alpha

To determine the region of human tumor necrosis factor-alpha(TNF-), essential for cytotoxic activity against mouse L-M cells,single amino-acid-substituted TNF- mutant proteins (muteins)were produced in Escherichia coli by protein engineering techniques.An expression plasmid for TNF- was mutagenized by passage throughan E.coli mutD5 mutator strain and by oligonucleotide-directedmutagenesis. Approximately 100 single amino-acid-substitutedTNF- muteins were produced and assayed for cytotoxic activity.The cytotoxic activities of purified TNF- muteins, e.g. TNF-31T,-32Y, -82D, -85H, -115L, -141Y, -144K and -146E, were < 1%of that of parent TNF-. These results indicate that the integrityof at least four distinct regions of the TNF- molecule is requiredfor full biological activity. These regions are designated asfollows: region I, from position 30 to 32; region II, from position82 to 89; region III, from position 115 to 117; region FV, fromposition 141 to 146. In addition, TNF-141Y could not completelycompete with parent TNF- for binding to the receptor. This demonstratesthat region IV, and at least aspartk acid at position 141, mustbe involved in the TNF receptor binding site.     

A point mutation that decreases the thermal stability of human interferon {gamma}

We have identified a mutation of human gamma-interferon (IFN)causing a temperature-sensitive phenotype. We used a randomizedoligonucleotide to mutagenize a synthetic human IFN gene, thenscreened the resulting mutants produced in Escherichia colifor proteins with altered biological activity. One mutant proteinselected for detailed characterization exhibited < 0.3% ofthe specific biological activity of native IFN in an antiviralactivity assay performed at 37°C. However, the protein boundthe human IFN receptor with native efficiency at 4°C. Sequencingthe plasmid DNA encoding this protein snowed that the mutationchanged the lysine residue at amino acid 43 to glutamic acid(IFN/K43E). Site-specific mutagenesis at amino acid 43 showedthat this protein's phenotype resulted from positioning a negativecharge at position 43. Structural characterization of IFN/K43Eusing CD demonstrated that the protein had native conformationat 25°C, but assumed an altered conformation at 37°C.IFN/K43E in this altered conformation bound poorly to the IFNreceptor at 37°C, providing a rationale for the mutant'sdecreased antiviral activity.     

Starch-binding domain shuffling in Aspergillus niger glucoamylase

Aspergillus niger glucoamylase (GA) consists mainly of two forms,GAI [from the N-terminus, catalytic domain + linker + starch-bindingdomain (SBD)] and GAII (catalytic domain + linker). These domainswere shuffled to make RGAI (SBD + linker + catalytic domain),RGAIL (SBD + catalytic domain) and RGAII (linker + catalyticdomain), with domains defined by function rather than by tertiarystructure. In addition, Paenibacillus macerans cyclomaltodextringlucanotransferase SBD replaced the closely related A.nigerGA SBD to give GAE. Soluble starch hydrolysis rates decreasedas RGAII GAII GAI > RGAIL RGAI GAE. Insoluble starchhydrolysis rates were GAI > RGAIL > RGAI >> GAE RGAII > GAII, while insoluble starch-binding capacitieswere GAI > RGAI > RGAIL > RGAII > GAII > GAE.These results indicate that: (i) moving the SBD to the N-terminusor replacing the native SBD somewhat affects soluble starchhydrolysis; (ii) SBD location significantly affects insolublestarch binding and hydrolysis; (iii) insoluble starch hydrolysisis imperfectly correlated with its binding by the SBD; and (iv)placing the P.macerans cyclomaltodextrin glucanotransferaseSBD at the end of a linker, instead of closely associated withthe rest of the enzyme, severely reduces its ability to bindand hydrolyze insoluble starch. Received June 20, 2002; revised May 23, 2003; accepted June 6, 2003.     

Family of G protein {alpha} chains: amphipathic analysis and predicted structure of functional domains

The G proteins transduce hormonal and other signals into regulationof enzymes such as adenylyl cyclase and retinal cGMP phosphodiesterase.Each G protein contains an subunit that binds and hydrolyzesguanine nucleotides and interacts with ß subunitsand specific receptor and effector proteins. Amphipathic andsecondary structure analysis of the primary sequences of fivedifferent chains (bovine _s, _t1 and _t2, mouse _i, and rat _o)predicted the secondary structure of a composite chain (_avg).The chains contain four short regions of sequence homologousto regions in the GDP binding domain of bacterial elongationfactor Tu (EF-Tu). Similarities between the predicted secondarystructures of these regions in _avg and the known secondary structureof EF-Tu allowed us to construct a three-dimensional model ofthe GDP binding domain of _avg. Identification of the GDP bindingdomain of _avg defined three additional domains in the compositepolypeptide. The first includes the amino terminal 41 residuesof _avg, with a predicted am phipathic helical structure; thisdomain may control binding of the chains to the ßcomplex. The second domain, containing predicted ßstrands and helices, several of which are strongly amphipathic,probably contains sequences responsible for interaction of chains with effector enzymes. The predicted structure of thethird domain, containing the carhoxy terminal 100 amino acids,is predominantly ß sheet with an amphipathic helixat the carboxy terminus. We propose that this domain is reponsiblefor receptor binding. Our model should help direct further experimentsinto the structure and function of the G protein chain.     

Inhibition of {beta}S-chain dependent polymerization by synergistic complementation of contact site perturbations of {alpha}-chain: application of semisynthetic chimeric {alpha}-chains

Mouse _1–30-horse _31–141 chimeric -chain, a semisyntheticsuper-inhibitory -chain, inhibits ß^S-chain dependent polymerizationbetter than both parent -chains. Although contact site sequencedifferences are absent in the _1–30 region of the chimericchain, the four sequence differences of the region _17-22 couldinduce perturbations of the side chains at ₁₆, ₂₀ and ₂₃, thethree contact sites of the region. A synergistic complementationof such contact site perturbation with that of horse _31–141probably results in the super-inhibitory activity of the chimeric-chain. The inhibitory contact site sequence differences, bythemselves, could also exhibit similar synergistic complementation.Accordingly, the polymerization inhibitory activity of Hb Le-Lamentin(LM) mutation [His20()Gln], a contact site sequence difference,engineered into human–horse chimeric -chain has been investigatedto map such a synergistic complementation. Gln20() has littleeffect on the O₂ affinity of HbS, but in human–horse chimeric-chain it reduces the O₂ affinity slightly. In the chimeric-chain, Gln20() increased sensitivity of the ßßcleft for the DPG influence, reflecting a cross-talk betweenthe ₁ß₁ interface and ßß cleft in this semisyntheticchimeric HbS. In the human -chain frame, the polymerizationinhibitory activity of Gln20() is higher compared with horse_1–30, but lower than mouse _1–30. Gln20() synergisticallycomplements the inhibitory propensity of horse _31–141.However, the inhibitory activity of LM–horse chimeric-chain is still lower than that of mouse–horse chimeric-chain. Therefore, perturbation of multiple contact sites inthe _1–30 region of the mouse–horse chimeric -chainand its linkage with the inhibitory propensity of horse _31–141has been now invoked to explain the super-inhibitory activityof the chimeric -chain. The `linkage-map' of contact sites canserve as a blueprint for designing synergistic complementationof multiple contact sites into -chains as a strategy for generatingsuper-inhibitory antisickling hemoglobins for gene therapy ofsickle cell disease.     

Site-directed mutagenesis in hemoglobin: test of functional homology of the F9 amino acid residues of hemoglobin {alpha} and {beta} chains

The cysteine residue at F9(93) of the human hemoglobin (Hb A)ß chain, conserved in mammalian and avian hemoglobins,is located near the functionally important 1–ß2interface and C-terminal region of the ß chain and isreactive to sulfhydryl reagents. The functional roles of thisresidue are still unclear, although regulation of local bloodflow through allosteric S-nitrosylation of this residue is proposed.To clarify the role of this residue and its functional homologyto F9(88) of the chain, we measured oxygen equilibrium curves,UV-region derivative spectra, Soret-band absorption spectra,the number of titratable -SH groups with p-mercuribenzoate andthe rate of reaction of these groups with 4,4'-dipyridine disulfidefor three recombinant mutant Hbs with single amino acid substitutions:AlaCys at 88 (rHb A88C), CysAla at 93ß (rHb C93ßA)and CysThr at 93ß (rHb C93ßT). These Hbs showedincreased oxygen affinities and impaired allosteric effects.The spectral data indicated that the R to T transition upondeoxygenation was partially restricted in these Hbs. The numberof titratable -SH groups of liganded form was 3.2–3.5for rHb A88C compared with 2.2 for Hb A, whereas those for rHbC93ßA and rHb C93ßT were negligibly small. The reductionof rate of reaction with 4,4'-dipyridine disulfide upon deoxygenationin rHb A88C was smaller than that in Hb A. Our experimentaldata have shown that the residues at 88 and 93ß have definiteroles but they have no functional homology. Structure–functionrelationships in our mutant Hbs are discussed.     

Functional expression in insect cells, one-step purification and characterization of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp)

Phospholipase D (PLD) is an important enzyme involved in signaltransduction, vesicle trafficking and membrane metabolism. Inthis study, large amounts of a recombinant plant PLD were secretedinto the culture medium of baculovirus-infected insect cellsand purified to homogeneity in the form of a fully active enzyme.The transient production of recombinant PLD yielded a protein(rPLDa, 88 kDa) together with a shorter form (rPLDb, 87 kDa),which accumulated in the medium. N-Terminal amino acid sequencingof the rPLDa and rPLDb showed that rPLDb resulted from proteolyticcleavage at Gly8–Ile9. Immunoblotting showed that bothrPLDa and rPLDb are recognized by a polyclonal antibody previouslyraised against native soybean PLD. One-step calcium-dependentoctyl-Sepharose chromatography was used to obtain the two highlypurified forms of rPLD, as attested by gel electrophoresis,N-terminal amino acid sequence and mass spectrometry. The N-terminalregion of PLD is homologous with the C2 domains which are presentin a number of enzymes known to be involved in signal transductionand/or phospholipid metabolism. The truncated rPLDb lacks thefirst acidic amino acid in its N-terminus, which is probablyinvolved in the calcium binding site. The rPLDb was thus easilyeluted from the octyl-Sepharose column by decreasing the calciumconcentration of the buffer from 50 to 30 mM, whereas, the rPLDawas eluted after chelating calcium ions with EDTA. The purifiedrPLD yield reached a level of 10 mg per liter of serum-freeculture medium. The availability of baculovirus-derived rPLDconstitutes a valuable source of enzyme for future crystallographicstudies to determine its three-dimensional structure.     

Altered specificities of genetically engineered {alpha}1 antitrypsin variants

Seven active site variants of human ₁-antitrypsin (₁AT) wereproduced in Escherichia coli following site-specific mutagenesisof the ₁AT complementary DNA. ₁AT (Ala ³⁵⁸), ₁AT (Ile³⁵⁸ and₁AT (Val³⁵⁸), were efficient inhibitors of both neutrophil andpancreatic elastases, but not of cathepsin G. ₁AT (Ala³⁵⁸, Val³⁵⁸)and ₁AT (Phe³⁵⁸ specifically inhibited pancreatic elastase andcathepsin G respectively. The most potent inhibitor of neutrophilelastase was ₁AT (Leu³⁵⁸), which also proved to be effectiveagainst cathepsin G. The ₁AT (Arg³⁵⁸) variant inactivated thrombinwith kinetics similar to antithrombin III in the presence ofheparin. Electrophoretic analysis showed that SDS-stable highmol. wt complexes were formed between the mutant inhibitorsand the cognate proteases in each case. These data indicatethat effective inhibition occurs when the ₁AT P1 residue (position358) corresponds to the primary specificity of the target protease.Moreover, alteration of the P3 residue (position 356) can furthermodify the reactivity of the inhibitor. Two of the variantshave therapeutic potential: ₁AT (Leu³⁵⁸ may be more useful thanplasma ₁AT in the treatment of destructive lung disorders and₁ (Arg³⁵⁸ could be effective in the control of thrombosis.     

Increasing the thermostability of a neutral protease by replacing positively charged amino acids in the N-terminal turn of {alpha}-helices

The 247–260 and 289–299 -helices of Bacillus subtilisneutral protease have a lysine in their N-terminal turn. Theselysines were replaced by Ser or Asp in order to improve electrostaticinteractions with the -helix dipole. After replacing Lys bySer at positions 249 or 290, the thermostability of the enzymewas increased by 0.3 and 1.0°C, respectively. The Asp249and Asp290 mutants exhibited a stabilization of 0.6 and 1.2°C,respectively. The results show the feasibility of stabilizingenzymes by introducing favourable residues at the end of -helices.     

Folding and stability of the active N-terminal domain of tissue inhibitor of metalloproteinases-1 and -2

The truncated forms of tissue inhibitor of metalloproteinase-1and -2 (TIMP-1 and -2), comprising the N-terminal active domain,are ideal molecules for structural analysis by intrinsic fluorescenceas each contains a single conserved tryptophan residue. In thispaper we describe studies on their conformational stability,unfolding/refolding kinetics and the environment of the uniquetryptophan as judged by its fluorescence properties in the nativestate and exposure to an external quencher, acrylamide. Twoforms of TIMP-2 were studied: TIMP-2 T21 derived from the full-lengthcDNA clone isolated from a mixed-tumour library, and TIMP-2A21 containing the highly conserved V18IRAK22 sequence. In allthree TIMP proteins the tryptophan environments in the nativestate appeared to be similar, but substantial differences wereseen in their conformational stabilities and refolding kinetics.TIMP-1 was approximately twice as stable as TIMP-2 T21 and 1.4-foldmore stable than TIMP-2 A21. This stability difference betweenTIMP-1 and TIMP-2 was shown to be independent of N-linked glycosylation.TTMP-1 and TIMP-2 A21 both showed simple two-state refoldingkinetics, whereas TIMP-2 T21 refolding was more complex andbiphasic in character. These differences between TIMP-2 T21and A21 suggest that residue 21 is a structurally importantsite in the TIMP protein.All three truncated molecules can beconsidered as stable independent folding domains ideally suitedfor further structural analysis     

A Pore-forming protein with a protease-activated trigger

Hemolysin (HL) is a 293 amino acid pore-forming toxin, whichis secreted as a water-soluble monomer by Staphylococcus aureus.By forming a hexameric pore, HL damages the plasma membranesof target cells. Previous studies established that HL proteinswith nicks near the midpoint of a central glycine-rich loopare held together by a domain-domain interaction and are hemolyticallyactive. In contrast, HL proteins comprising two HL truncationmutants that overlap in the central loop have no or greatlyreduced pore-forming activity, even though the two chains againform a tight complex. Based on these findings, overlap mutantshave now been designed that are activated when redundant aminoacids in the loop are removed by proteases. Further, the identityof the activating enzyme can be specified by additional mutagenesisof the protease recognition site in the overlap sequence. Mutantsof aHL that are activated by tumor-associated proteases mightbe useful components of immunotoxins     

Structure of {alpha}-{alpha}-hairpins with short connections

This paper presents the results of detailed stereochemical analysisof structures and sequences of --hairpins with short connections.It is shown that --hairpins of each given type have very similarpatterns of hydrophobic, hydrophilic and glycine residues intheir amino acid sequences. These results can be used in theprediction of --hairpin conformation as well as in protein designand engineering.