Hydrogen bonding in peptide helices - Analysis of two independent helices in the crystal structure of a peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe

The crystal structure determination of the heptapeptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe reveals two peptide helices in the asymmetric unit, Crystal parameters are: space group P2(1), a = 10.356(2) Angstrom, b = 19.488(5) Angstrom, c = 23.756(6) Angstrom, beta = 102.25(2)degrees), V = 4685.4 Angstrom(3), Z = 4 and R = 5.7% for 7615 reflections [I>3 sigma(I)]. Both molecules adopt largely alpha-helical conformations with variations at the C-terminus, Helix type Is determined by analysing both 4-->1 and 5-->1 hydrogen-bond interactions and comparison with the results of analysis of protein structures. The presence of two 4-->1 hydrogen-bond interactions, besides four 5-->1 interact ions in both the conformations provides an opportunity to characterize bifurcated hydrogen bonds at high resolution, Comparison of the two helical conformations with related peptide structures suggests that distortions at the C-terminus are more facile than at the N-terminus.

Sijaissotilasjärjestelmä ja väenotot : Taloudellis-sosiaalinen tutkimus sijaissotilaiden käytöstä Ala-Satakunnan väenotoissa vuosina 1631-1648

The dissertation describes the conscription of Finnish soldiers into the Swedish army during the Thirty Years' War. The work concentrates on so-called substitute soldiers, who were hired for conscription by wealthier peasants, who thus avoided the draft. The substitutes were the largest group recruited by the Swedish army in Sweden. The substitutes made up approximately 25-80% of the total number of soldiers. They recieved a significant sum of money from the peasants: about 50-250 Swedish copper dalers, corresponding to the price of a little peasant house. The practice of using substitutes was managed by the local village council. The recruits were normally from the landless population. However, when there was an urgent need of men, even the yeoman had to leave their homes for the distant garrisons across the Baltic. Conscription and its devastating effect on agricultural production also reduced the flow of state revenues. One of the tasks of the dissertation is the correlation between the custom of using substitutes and the abandonment of farmsteds (= in to the first place, to the non-ability to pay taxes). In areas where there were no substitutes available the peasants had to join the army themselves, which normally led to abandonment and financial ruin because agricultural production was based on physical labour. This led to rise of large farms at the cost of smaller ones. Hence, the system of substitutes was a factor that transformed the mode of settlement.

Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

An apolar synthetic analog of the first 10 residues at the NH2-terminal end of zervamicin IIA crystallizes in the triclinic space group P1 with cell dimensions a = 10.206 +/- 0.002 A, b = 12.244 +/- 0.002 A, c = 15.049 +/- 0.002 A, alpha = 93.94 +/- 0.01 degrees, beta = 95.10 +/- 0.01 degrees, gamma = 104.56 +/- 0.01 degrees, Z = 1, C60H97N11O13 X 2H2O. Despite the relatively few alpha-aminoisobutyric acid residues, the peptide maintains a helical form. The first intrahelical hydrogen bond is of the 3(10) type between N(3) and O(0), followed by five alpha-helix-type hydrogen bonds. Solution 1H NMR studies in chloroform also favor a helical conformation, with seven solvent-shielded NH groups. Continuous columns are formed by head-to-tail hydrogen bonds between the helical molecules along the helix axis. The absence of polar side chains precludes any lateral hydrogen bonds. Since the peptide crystallizes with one molecule in a triclinic space group, aggregation of the helical columns must necessarily be parallel rather than antiparallel. The packing of the columns is rather inefficient, as indicated by very few good van der Waals' contacts and the occurrence of voids between the molecules.

Observation of a mixed antiparallel and parallel beta-sheet motif in the crystal structure of Boc-Ala-Ile-Aib-OMe

A diastereomeric mixture of the tripeptide Boc-Ala-Ile-Aib-OMe crystallized in the space group P1 from CH3OH/H2O. The unit cell parameters are a = 10.593(2) A, b = 14.377(3) A, c = 17.872(4) A, alpha = 104.41(2) degrees, beta = 90.55(2) degrees, gamma = 106.91(2) degrees, V = 2512.4 A3, Z = 4. X-Ray crystallographic studies show the presence of four molecules in the asymmetric unit consisting of two pairs of diastereomeric peptides, Boc-L-Ala-L-Ile-Aib-OMe and Boc-L-Ala-D-Ile-Aib-OMe. The four molecules in the asymmetric unit form a rarely found mixed antiparallel and parallel beta-sheet hydrogen bond motif. The Ala and (L,D)-Ile residues in all the four molecules adopt the extended conformations, while the phi, psi values of the Aib residues are in the right-handed helical region. In one of the molecules the Ile sidechain adopts the unusual gauche conformation about the C beta-C gamma bond.

An incipient 310 helix in Piv-Pro-Pro-Ala-NHMe as a model for peptide folding

The molecular mechanism of helix nucleation in peptides and proteins is not yet understood and the question of whether sharp turns in the polypeptide backbone serve as nuclei for protein folding has evoked controversy1,2. A recent study of the conformation of a tetrapeptide containing the stereochemically constrained residue alpha-aminoisobutyric acid, both in solution and the solid state, yielded a structure consisting of two consecutive beta-turns, leading to an incipient 310 helical conformation3,4. This led us to speculate that specific tri- and tetra-peptide sequences may indeed provide a helical twist to the amino-terminal segment of helical regions in proteins and provide a nucleation site for further propagation. The transformation from a 310 helical structure to an alpha-helix should be facile and requires only small changes in the phi and psi conformational angles and a rearrangement of the hydrogen bonding pattern5. If such a mechanism is involved then it should be possible to isolate an incipient 310 helical conformation in a tripeptide amide or tetrapeptide sequence, based purely on the driving force derived from short-range interactions. We have synthesised and studied the model peptide pivaloyl-Pro-Pro-Ala-NHMe (compound I) and provide here spectroscopic evidence for a 310 helical conformation in compound I.

Monoclinic polymorph of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe(anhydrous). Parallel packing of 3(10)-/alpha-helices and a transition of helix type

The structures of two crystal forms of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe have been determined. The triclinic form (P1, Z = 1) from DMSO/H2O crystallizes as a dihydrate (Karle, Sukumar & Balaram (1986) Proc, Natl, Acad. Sci. USA 83, 9284-9288). The monoclinic form (P2(1), Z = 2) crystallized from dioxane is anhydrous. The conformation of the peptide is essentially the same in both crystal system, but small changes in conformational angles are associated with a shift of the helix from a predominantly alpha-type to a predominantly 3(10)-type. The r.m.s. deviation of 33 atoms in the backbone and C beta positions of residues 2-8 is only 0.29 A between molecules in the two polymorphs. In both space groups, the helical molecules pack in a parallel fashion, rather than antiparallel. The only intermolecular hydrogen bonding is head-to-tail between helices. There are no lateral hydrogen bonds. In the P2(1) cell, a = 9.422(2) A, b = 36.392(11) A, c = 10.548(2) A, beta = 111.31(2) degrees and V = 3369.3 A for 2 molecules of C60H97N11O13 per cell.

Aggregation studies in crystals of apolar helical peptides: Boc-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe

In the crystal, the backbone of Boc-(Aib-Val-Ala-Leu)2-Aib-OMe adopts a helical form with four alpha-type hydrogen bonds in the middle, flanked by 3(10)-type hydrogen bonds at either end. The helical molecules stack in columns with head-to-tail hydrogen bonds, either directly between NH and CO, or bridged by solvent molecules. The packing of the helices is parallel, even in space group P2(1). Cell parameters are a = 9.837(2) A, b = 15.565(3) A, c = 20.087(5) A, beta = 96.42(2) degrees, dcalc = 1.091 g/cm3 for C46H83N9O12.1.5H2O.0.67CH3OH. There appears to be some hydration of the backbone in this apolar helix.

Cystine peptides Antiparallel β-sheet conformation of the cyclic biscystine peptide [Boc-Cys-Ala-Cys-NHCH3]2

The crystal structure analysis of the cyclic biscystine peptide [Boc-Cys1-Ala2-Cys3-NHCH3]2 with two disulfide bridges confirms the antiparallel ?-sheet conformation for the molecule as proposed for the conformation in solution. The molecule has exact twofold rotation symmetry. The 22-membered ring contains two transannular NH ? OC hydrogen bonds and two additional NH ? OC bonds are formed at both ends of the molecule between the terminal (CH3)3COCO and NHCH3 groups. The antiparallel peptide strands are distorted from a regularly pleated sheet, caused mainly by the L-Ala residue in which ?=� 155° and ?= 162°. In the disulfide bridge C? (1)-C? (1)-S(1)-(3')-C?(3')-C?(3'), S�S = 2.030 Å, angles C? SS = 107° and 105°, and the torsional angles are �49, �104, +99, �81, �61°, respectively. The biscystine peptide crystallizes in space group C2 with a = 14.555(2) Ã…, b = 10.854(2) Ã…, c = 16.512(2)Ã…, and ?= 101.34(1) with one-half formula unit of C30H52N8O10S4· 2(CH3)2SO per asymmetric unit. Least-squares refinement of 1375 reflections observed with |F| > 3?(F) yielded an R factor of 7.2%.

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac)

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.

Hydration and distortion of peptide helices in crystals. α-Helical structure of a dodecapeptide, Boc-(Ala-Leu-Aib)4-OMe

The dodecapeptide Boc-(Ala-Leu-Aib)(4)-OMe crystallized with two independent helical molecules in a triclinic cell. The two molecules are very similar in conformation, with a 3(10)-helix turn at the N-terminus followed by an alpha-helix, except for an elongated N(7)...O(3) distance in both molecules. All the helices in the crystal pack in a parallel motif. Eleven water sites have been found in the head-to-tail region between the apolar helices that participate in peptide-water hydrogen bonds and a network of water-water hydrogen bonds. The crystal parameters are as follows: 2(C58H104N12O15)+ca. 10H(2)O, space group P1 with a = 12.946(2), b = 17.321(3), c = 20.465(4) Angstrom, alpha = 103.12(2), beta = 105.63(2), gamma = 107.50(2)degrees, Z = 2, R = 10.9% for 5152 data observed > 3 sigma(F), resolution 1.0 Angstrom. In contrast to the shorter sequences [Karle et al. (1988)Proc. Natl. Acad. Sci. USA 85, 299-303] and Boc-(Ala-Leu-Aib)(2)-OMe [Karle et al. (1989) Biopolymers 28, 773-781], no insertion of a water molecule into the helix is observed. However, the elongated N---O distance between Ala(7) NH and Aib(3) CO in both molecules (molecule A, 3.40 Angstrom; molecule B, 3.42 Angstrom) is indicative of an incipient break in the helices. (C) Munksgaard 1994.

Crystal structures of a nonapeptide helix containing alpha,alpha-di-n-butylglycine (Dbg), Boc-Gly-Dbg-Ala-Val-Ala-Leu-Aib-Val-Leu-OMe

Two crystals structures of a nonapeptide (anhydrous and hydrated) containing the amino acid residue alpha, alpha-di-n-butylglycyl, reveal a mixed 3(10)/alpha-helical conformation. Residues 1-7 adopt phi, psi values in the helical region, with Val(8) being appreciably distorted. The Dbg residue has phi, psi values of -40, -37 degrees and -46, -40 degrees in two crystals with the two butyl side chains mostly extended in each. Peptide molecules in the crystals pack into helical columns. The crystal parameters are C50H91N9O12, space group P2(1), with a = 9.789(1) Angstrom, b = 20.240(2) Angstrom, c = 15.998(3) Angstrom, beta = 103.27(1); Z = 2, R = 10.3% for 1945 data observed >3 sigma(F) and C50H91N9O12. 3H(2)O, space group P2(1), with a = 9.747(3) Angstrom, b = 21.002(8) Angstrom, c = 15.885(6) Angstrom, beta = 102.22(3)degrees, Z = 2, R = 13.6% for 2535 data observed >3 sigma(F). The observation of a helical conformation at Dbg suggests that the higher homologs in the alpha, alpha-dialkylated glycine series also have a tendency to stabilize peptide helices. (C) Munksgaard 1996.

A combined extended and helical backbone for Boc-(Ala-Leu-Ac(7)c-)(2)-OMe

The structure of the peptide Boc-Ala-Leu-Ac(7)c-Ala-Leu-Ac(7)c-OMe (Ac(7)c,1-aminocycloheptane-1-carboxylic acid) is described in crystals. The presence of two Ac(7)c residues was expected to stabilize a 3(10)-helical fold. Contrary to expectation the structural analysis revealed an unfolded amino terminus, with Ala(1) adopting an extended beta-conformation (phi = -93degrees,psi = 112degrees). Residues 2-5 form a 3(10)-helix, stabilized by three successive intramolecular hydrogen bonds. Notably, two NH groups Ala(1) and Ac(7)c(3) do not form any hydrogen bonds in the crystal. Peptide assembly appears to be dominated by packing of the cycloheptane rings that stack against one another within the molecule and also throughout the crystal in columns.

Sukupuoli ala-asteen uskonnon ja elämänkatsomustiedon oppikirjojen kuvissa

Tutkimuksen kohteena ovat 2000-luvun alun ala-asteen uskonnon ja elämänkatsomustiedon oppikirjat. Tutkimuksessa kysytään yhtäältä, miten sukupuolia esitetään oppikirjoissa. Toisaalta tarkastellaan oppikirjojen tarjoamia kuvia uskonno(i)sta sukupuolinäkökulmasta katsottuna. Tutkimus sijoittuu uskontososiologian kenttään, koska siinä tarkastellaan, miten uskonnon ja elämänkatsomustiedon opetusmateriaalit suhteutuvat yhteiskunnassamme eläviin sukupuolistereotypioihin. Oppikirjat heijastavat osaltaan yhteiskunnassamme vallitsevia arvoja ja käytäntöjä. Tutkimuksen lähtökohdat ovat kriittisessä feministisessä tutkimuksessa. Tarkoituksena on paljastaa, miten sukupuolia tehdään tutkituissa oppikirjoissa; taustalla on ajatus, että sukupuolet ovat poliittisesti, historiallisesti ja diskursiivisesti tuotettuja kategorioita. Sukupuolijärjestelmään sisältyy sukupuolten erilläänpito, hierarkia ja heteronormatiivisuus. Siihen liittyy myös aina vallankäyttöä: kun jotain määritellään normaaliksi ja ensisijaiseksi, jää sen ulkopuolelle joukko epänormaaliuksia ja toissijaisuuksia. Tutkimus kytkeytyy siis myös teorioihin diskurssien kautta operoivasta, kaikkialla läsnäolevasta ja verkostoituneesta vallasta. Tutkimusaineistona on WSOY:n kustantama uskonnon oppikirjasarja, Suuri kertomus (neljä kirjaa), Otavan kustantama uskonnon oppikirjasarja Tähti (viisi kirjaa), sekä Opetushallituksen kustantamat elämänkatsomustiedon Miina ja Ville kirjat (kaksi kirjaa). Tutkimuksessa tarkastellaan sisällönanalyyttisin keinoin ensisijaisesti kirjojen sisältämiä kuvia, mutta myös tekstejä siltä osin, kuin ne olennaisesti liittyvät analysoituihin kuviin. Koska kyseessä ovat oppikirjat, sivutaan myös niiden suhdetta perusopetuksen opetussuunnitelmien näille oppiaineille määrittelemiin tavoitteisiin. Kuvat on analyysissa jaettu kahteen luokkaan, uskontoon liittyviin ja arkisiin kuviin. Aineisto on käyty läpi etsien vastauksia seuraaviin kysymyksiin: kuinka monessa kuvassa esiintyy tyttö/nainen, poika/mies tai molempia sukupuolia? Miten usein tyttö/nainen, poika/mies tai molemmat sukupuolet ovat kuvassa pääasiallisena toimijana tai kuvan etualalla? Millaisia toimijuuksia eri sukupuolille on annettu, ovatko ne stereotyyppisiä? Löytyykö aineistosta heteronormista poikkeavia esityksiä? Kuvia, joissa stereotyyppisiä sukupuolirooleja erityisesti vahvistetaan tai murretaan, on otettu analyysissa tarkempaan tarkasteluun. Lähempää luettujen kuvien kautta analyysissa käsitellään kulttuurissamme ja yhteiskunnassamme vallitsevia sukupuolittavia käytäntöjä sekä niiden taustalla olevia arvoja ja rakenteita. Uskontoon liittyvien kuvien kohdalla analyysiin kietoutuvat erityisesti uskonno(i)ssa elävät käsitykset sukupuolten järjestyksistä ja paikoista. Keskiöön nousee myös evankelis-luterilaisen kristillisyyden tarjoamat käsitykset sukupuolista ja niiden asemista uskonnonharjoituksessa. Lisäksi tutkimuksessa vertaillaan uskonnon ja elämänkatsomustiedon kirjasarjoista tehtyjä analyyseja keskenään: näkyykö näiden oppiaineiden välillä eroja sukupuolten esittämisessä? Tutkimuksen tulokset ovat suurelta osin samankaltaiset aiemman sukupuolinäkökulmasta tehdyn oppikirjatutkimuksen tulosten kanssa. Poikia ja miehiä esiintyy kuvissa huomattavasti enemmän kuin tyttöjä ja naisia, ja miessukupuolelle on annettu enemmän ja monipuolisempia toimijuuksia kuin naissukupuolelle. Maskuliinisia samastumiskohteita tarjotaan enemmän kuin feminiinisiä. Sukupuolten esitykset ovat enimmäkseen stereotyyppisiä, vaikka joitakin poikkeuksia aineistossa onkin. Vaihtoehtoja heteroseksuaalisuudelle ei aineistossa tuoda esiin. Elämänkatsomustiedon kirjoissa poiketaan stereotyyppisistä esityksistä useammin kuin uskonnon kirjoissa, mutta niidenkin kuvasto on miesvaltainen ja pääosin heteronormatiivinen. Uskontoja esitellään niiden virallisen ja julkisen harjoittamisen kautta, mikä antaa uskonnoista huomattavan mieslähtöisen ja -valtaisen kuvan. Ei esimerkiksi tuoda juurikaan esiin sitä, että monissa uskonnoissa miehet ovat oikeutettuja erilaisiin rooleihin kuin naiset. Naisten uskonnollisuus ohitetaan aineistossa lähes täysin. Taustalla on nähtävissä käsitys miesten ja miehisten elämänpiirien ensisijaisuudesta, kun taas naiset ja naisten elämänpiirit nähdään toiseuden kautta. Tämä ajatusrakennelma on koko kulttuurissamme ja sen perusteissa niin läpikäyvänä, että siihen ei usein kiinnitetä lainkaan huomiota: se näyttäytyy itsestäänselvänä ja ikään kuin luonnollisena asiaintilana. Sukupuolten välinen eriarvoisuus kytkeytyy kuitenkin ihmisten jokapäiväiseen elämään kuten työhön, palkkaan, perhe-elämään ja mahdollisuuksiin toteuttaa itseään ja kehittää taipumuksiaan. Tutkimuksen tulokset tukevat näkemyksiä, joiden mukaan sukupuolten välinen tasa-arvo ei ole yhteiskunnassamme vielä toteutunut. Avainsanat Nyckelord Keywords sukupuoli, oppikirjat, uskonto, elämänkatsomustieto, kuva-analyysi, stereotypia, heteronormatiivisuus, tasa-arvo, sukupuoliroolit, toimijuus

Stabilization of unusual structures in peptides using alpha,beta-dehydrophenylalanine: Crystal and solution structures of Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe

The structures of two dehydropentapeptides, Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe (I) and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe (II) (Boc: t-butoxycarbonyl), have been determined by nuclear magnentic resonance (NMR), circular dichroism (CD), and X-ray, crystallographic studies. The peptide I assumes a S-shaped flat beta-bend structure, characterized by two partially overlapping type II beta-bends and absence of a second 1 <- 4 (N4-H center dot center dot center dot O1') intramolecular hydrogen bond. This is in contrast to the generally observed 3(10)-helical conformation in peptides with Delta Phe at alternate positions. This report describes the novel conformation assumed by peptide I and compares it with that of the conserved tip of the V3 loop of the HIV-1 envelope glycoprotein gp120 (sequence, G:P319 to F:P324, PDB code IACY). The tip of the V3 loop also assumes a S-shaped conformation with Arg:P322, making an intramolecular side-chain-backbone interaction with the carbonyl oxygen of Gly:P319. Interestingly, in peptide I, C(gamma)HVal(3) makes a similar side-chain-backbone C-H center dot center dot center dot O hydrogen bond with the carbonyl oxygen of the Boc group. The observed overall similarity indicates the possible use of the peptide as a viral antagonist or synthetic antigen. Peptide 11 adopts a unique turn followed by a 3(10)-helix. Both peptides I and II are classical examples of stabilization of unusual structures in oligopeptides.