Метод конформационного поиска для длинных полипептидных цепей, основанный на анализе энергетической функции

The algorithm is proposed to search a conformational space of long flexible polypeptide chains. It consists in performing a series of geometry optimization runs by a gradient-based method using the atom-atom pairwise potential sum as a target function. Only a portion of pairwise terms is taken into account in each run. The algorithm was employed for the conformational analysis of the loop-like 125–167 fragment of human serum albumin treating the rest of the molecule as a rigid structure. Several stable conformers of the fragment were obtained that considerably differ by their 3D-structure from the original one. Some of the newly found conformers have no major attractive nonbonded contacts with the protein globule, and some of them form hydrogen bonds with other domains of the molecule. The latter enables us to suppose that the conformational transition of the 125–167 fragment can affect the mutual mobility of domains

Divergencija postojane duljine polufleksibilnog homopolimernog lanca u granici krutog lanca

We revisit analytical calculation [Mishra et al., Physica A 323 (2003) 453 and Mishra, NewYork Sci. J. 3 (1) (2010) 32 ] of the persistent length of a semiflexible homopolymer chain in the extremely stiff chain limit, k → 0, where, k is the stiffness of the chain, for the directed walk lattice model in two and three dimensions. Our study for the two-dimensional (square and rectangular) and three-dimensional (cubic) lattice case clearly indicates that the persistent length diverges according to the expression (1−gc) −1 , where gc is the critical value of the step fugacity required for polymerization of an infinitely long linear semiflexible homopolymer chain, and nature of the divergence is independent of the space dimension. This is obviously true because, in the case of extremely-stiff chain limit, the polymer chain is a onedimensional object and its shape is like a rigid rod.Obnavljamo analitički račun [Mishra et al., Physica A 323 (2003) 453 i Mishra, NewYork Sci. J. 3 (1) (2010) 32 ] za postojanu duljinu polufleksibilnog homopolimernog lanca u granici krajnje krutog lanca, k → 0, gdje je k krutost lanca, za model rešetke s usmjerenim hodom u dvije i tri dimenzije. Proučavanje dvodimenzijske (kvadratne i pravokutne) i trodimenzijske (kubične) rešetke jasno pokazuje da postojana duljina divergira kao (1−gc) −1 , gdje je gc nepostojanost potrebna za polimerizaciju beskonačno dugog linearnog polufleksibilnog homopolimernog lanca, i priroda divergencije ne ovisi o prostornoj dimenziji. To je očito tako jer u slučaju krajnje krutog lanca, polimerski lanac je jednodimenzijski predmet i on ima oblik krutog štapa

Mjerenje prinosa međusustavnog prijelaza s4U u tRNA vremenski-razlučenim izbjeljivanjem

The rare base 4-thiouridine (s4U), present in various transfer RNA (tRNA) molecules from Escherichia coli, occupies usually the strategically important 8 th position between the double helices of the acceptor and the dihydrouridine stems of the cloverleaf. This unusual base is largely used as an intrinsic build-in probe for RNA conformational and RNA(DNA)–protein interaction studies through triplet excited state photochemistry related to covalent adducts formation. Here, by applying laser transient absorption saturation spectroscopy, we measured the intersystem crossing yield ϕST and the excited triplet state absorption εT−T of s4U within tRNA. While the incorporation of s4U in tRNA induced appreciable changes in the latter, no important variation of the intersystem crossing yield was observed, which is in contrasts with the published data.Rijetka baza 4-thiouridine (s4U), koju nalazimo u raznim prijenosnim molekulama RNA (tRNA) Escherichie coli, obično uzima strateški važan 8. položaj između dviju zavojnica primatelja i dihidrouridinskih stapki lista djeteline. Ta se neobična baza najviše rabi kao unutarnja ugradbena proba za proučavanje interakcija konformalne RNA s RNA(DNA)–proteinima preko fotokemije tripletnog uzbuđenog stanja, povezanog sa stvaranjem kovalentnih adukata. U ovom smo radu primjenom laserske prijelazne apsorpcijske spektroskopije sa zasićenjem mjerili prinos međusustavnih prijelaza ϕST i apsorpciju tripletnog stanja εT−T s 4U u tRNA. Dok ugrađivanje s4U u tRNA uzrokuje prilične promjene u tRNA, nismo opazili promjene prinosa međusustavnih prijelaza, što nije u skladu s objavljenim rezultatima

Teorijsko ab initio proučavanje učinaka električnog polja na građu i stabilnost baznog para G:C

The effect of applied external electric field on DNA occurs mostly at high field intensity. The results of a theoretical ab initio study of effects of applied electric field on G:C base pair components are reported. The geometries of the local minima were optimized without the symmetry restrictions by the gradient procedure at density-functional level of the theory and were verified by calculations of the second derivative of energy. The standard CEP-31G basis set was used. The geometrical parameters, relative stability and interaction energies are reported. The electric field mutation could be classified as a multi-point mutation.Učinak vanjskog električnog polja na DNA javlja se najčešće za jaka polja. Izvješćujemo o ishodima proučavanja učinaka vanjskog električnog polja na sastavnice baznog para G:C polazeći od osnova teorije. Razmještaj lokalnih minimuma smo optimizirali bez ograničenja na uvjete simetrije rabeći gradijentan postupak na razini teorije funkcionala gustoće i provjerili računima drugih derivacija energije. Primijenili smo uobičajen osnovni skup CEP-31G. Izvješćujemo o promjenama razmaka, stabilnosti i energijama međudjelovanja. Mutacije električnim poljem mogle bi se razvrstati u višemjesne mutacije

Спостереження іон-фосфатних коливань макромолекули ДНК

It is shown that, in the low-frequency Raman spectra of Cs-DNA, the mode of ion-phosphate vibrations exists. Together with the modes of H-bond stretching in base pairs, it forms the band near 100 cm−1 with intensity about twice as much than that in the spectra of Na-DNA. The mode of Na-DNA ion-phosphate vibrations is much lower in intensity and is located within a broad band near 180 cm−1

Laserska izravna dvofotonska fotoliza guanina u DNK

Nanosecond laser-induced oxidative lesions at guanines within DNA were investigated using sequencing gel electrophoresis analysis. Strong sequence-specific lesions on guanines were revealed by either Fpg or piperidine treatments and assigned to 8-oxoG and oxazolone, respectively. It was shown that both the biphotonic ionization process and the chemical reactivity of the radical cation (G+) are dependent on the DNA sequence. The former were explained by the occurrence of energy and charge migration phenomena, while the latter in terms of local DNA hydration peculiarities.Istraživali smo lomove DNK izazvane nanosekundnim laserskim impulsima primjenom gel elektroforeze za određivanje nizova. Otkrili smo snažne nizovno specifične lomove kod guanina djelovanjem sa Fpg ili piperidinom i oni se pripisuju 8-oxoG odnosno oxazolonu. Pokazali smo da su i dvofotonski ionizacijski proces i kemijska reaktivnost radikala kationa (G+) nizovno ovisni. Prvi se objašnjava selenjem energije i naboja, a drugi kao posebnosti lokalnog hidriranja DNK

Divergencija postojane duljine polufleksibilnog homopolimernog lanca u granici krutog lanca

We revisit analytical calculation [Mishra et al., Physica A 323 (2003) 453 and Mishra, NewYork Sci. J. 3 (1) (2010) 32 ] of the persistent length of a semiflexible homopolymer chain in the extremely stiff chain limit, k → 0, where, k is the stiffness of the chain, for the directed walk lattice model in two and three dimensions. Our study for the two-dimensional (square and rectangular) and three-dimensional (cubic) lattice case clearly indicates that the persistent length diverges according to the expression (1−gc) −1 , where gc is the critical value of the step fugacity required for polymerization of an infinitely long linear semiflexible homopolymer chain, and nature of the divergence is independent of the space dimension. This is obviously true because, in the case of extremely-stiff chain limit, the polymer chain is a onedimensional object and its shape is like a rigid rod.Obnavljamo analitički račun [Mishra et al., Physica A 323 (2003) 453 i Mishra, NewYork Sci. J. 3 (1) (2010) 32 ] za postojanu duljinu polufleksibilnog homopolimernog lanca u granici krajnje krutog lanca, k → 0, gdje je k krutost lanca, za model rešetke s usmjerenim hodom u dvije i tri dimenzije. Proučavanje dvodimenzijske (kvadratne i pravokutne) i trodimenzijske (kubične) rešetke jasno pokazuje da postojana duljina divergira kao (1−gc) −1 , gdje je gc nepostojanost potrebna za polimerizaciju beskonačno dugog linearnog polufleksibilnog homopolimernog lanca, i priroda divergencije ne ovisi o prostornoj dimenziji. To je očito tako jer u slučaju krajnje krutog lanca, polimerski lanac je jednodimenzijski predmet i on ima oblik krutog štapa

Laserska izravna dvofotonska fotoliza guanina u DNK

Nanosecond laser-induced oxidative lesions at guanines within DNA were investigated using sequencing gel electrophoresis analysis. Strong sequence-specific lesions on guanines were revealed by either Fpg or piperidine treatments and assigned to 8-oxoG and oxazolone, respectively. It was shown that both the biphotonic ionization process and the chemical reactivity of the radical cation (G+) are dependent on the DNA sequence. The former were explained by the occurrence of energy and charge migration phenomena, while the latter in terms of local DNA hydration peculiarities.Istraživali smo lomove DNK izazvane nanosekundnim laserskim impulsima primjenom gel elektroforeze za određivanje nizova. Otkrili smo snažne nizovno specifične lomove kod guanina djelovanjem sa Fpg ili piperidinom i oni se pripisuju 8-oxoG odnosno oxazolonu. Pokazali smo da su i dvofotonski ionizacijski proces i kemijska reaktivnost radikala kationa (G+) nizovno ovisni. Prvi se objašnjava selenjem energije i naboja, a drugi kao posebnosti lokalnog hidriranja DNK

Mjerenje prinosa međusustavnog prijelaza s4U u tRNA vremenski-razlučenim izbjeljivanjem

The rare base 4-thiouridine (s4U), present in various transfer RNA (tRNA) molecules from Escherichia coli, occupies usually the strategically important 8 th position between the double helices of the acceptor and the dihydrouridine stems of the cloverleaf. This unusual base is largely used as an intrinsic build-in probe for RNA conformational and RNA(DNA)–protein interaction studies through triplet excited state photochemistry related to covalent adducts formation. Here, by applying laser transient absorption saturation spectroscopy, we measured the intersystem crossing yield ϕST and the excited triplet state absorption εT−T of s4U within tRNA. While the incorporation of s4U in tRNA induced appreciable changes in the latter, no important variation of the intersystem crossing yield was observed, which is in contrasts with the published data.Rijetka baza 4-thiouridine (s4U), koju nalazimo u raznim prijenosnim molekulama RNA (tRNA) Escherichie coli, obično uzima strateški važan 8. položaj između dviju zavojnica primatelja i dihidrouridinskih stapki lista djeteline. Ta se neobična baza najviše rabi kao unutarnja ugradbena proba za proučavanje interakcija konformalne RNA s RNA(DNA)–proteinima preko fotokemije tripletnog uzbuđenog stanja, povezanog sa stvaranjem kovalentnih adukata. U ovom smo radu primjenom laserske prijelazne apsorpcijske spektroskopije sa zasićenjem mjerili prinos međusustavnih prijelaza ϕST i apsorpciju tripletnog stanja εT−T s 4U u tRNA. Dok ugrađivanje s4U u tRNA uzrokuje prilične promjene u tRNA, nismo opazili promjene prinosa međusustavnih prijelaza, što nije u skladu s objavljenim rezultatima

Teorijsko ab initio proučavanje učinaka električnog polja na građu i stabilnost baznog para G:C

The effect of applied external electric field on DNA occurs mostly at high field intensity. The results of a theoretical ab initio study of effects of applied electric field on G:C base pair components are reported. The geometries of the local minima were optimized without the symmetry restrictions by the gradient procedure at density-functional level of the theory and were verified by calculations of the second derivative of energy. The standard CEP-31G basis set was used. The geometrical parameters, relative stability and interaction energies are reported. The electric field mutation could be classified as a multi-point mutation.Učinak vanjskog električnog polja na DNA javlja se najčešće za jaka polja. Izvješćujemo o ishodima proučavanja učinaka vanjskog električnog polja na sastavnice baznog para G:C polazeći od osnova teorije. Razmještaj lokalnih minimuma smo optimizirali bez ograničenja na uvjete simetrije rabeći gradijentan postupak na razini teorije funkcionala gustoće i provjerili računima drugih derivacija energije. Primijenili smo uobičajen osnovni skup CEP-31G. Izvješćujemo o promjenama razmaka, stabilnosti i energijama međudjelovanja. Mutacije električnim poljem mogle bi se razvrstati u višemjesne mutacije