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1

KSZTAŁT WIELKOŚĆ I STRUKTURA DRUGORZĘDOWA CZĄSTECZEK KWASÓW NUKLEINOWYCH W ROZTWORACH W ŚWIETLE ICH WŁAŚCIWOŚCI FIZYKOCHEMICZNYCH

100%
Wierzchowski K. L.
Postępy Mikrobiologii
|
1963
|
tom 2
|
nr 3
2

Intramolecular electron transfer between tryptophan radical and tyrosine in oligoproline-bridged model peptides and hen egg-white lysozyme

100%
Wierzchowski K. L.
Acta Biochimica Polonica
|
1997
|
tom 44
|
nr 4
Long range electron transfer (LRET) across protein matrix underlies all one-electron cellular redox reactions. Elucidation of molecular electron transfer pathways and parametrization of their relative efficiency is one of the most challenging problems in the studies on LRET in proteins. In this paper results of pulse radiolysis investigations on kinetics of LRET accompanying intramolecular radical transformation Trp. --> TyrO. in model peptides built of tryptophan and tyrosine bridged by an oligoproline fragment are reviewed, along with an interpretation of the observed distance dependence of the rate of LRET in terms of conformational properties of the peptides, and partitioning of LRET between electron transfer pathways through space and through peptide backbone. This review on model peptide systems is supplemented with recapitulation of similar studies on the same intramolecular transformation in hen egg-white lysozyme, which allowed to identify Trp./Tyr redox pairs and associated electron transfer pathways involved in LRET in this protein.
3

HOMOLGIA SEKWENCJI KWASU DEZOKSYRYBONUKLEINOWEGO U BAKTERIOFAGÓW SERII T

75%
Wierzchowski K. L.
Postępy Mikrobiologii
|
1962
|
tom 1
|
nr 1
4

Evaluation of mixed-salt effects on thermodynamic and kinetic parameters of RNA polymerase - promoter DNA complexes in terms of equivalent salt concentrations. General applicability to DNA complexes

63%
Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
2009
|
tom 56
|
nr 4
695-702
 Facile evaluation of mixed-salt effect on the strongly salt-dependent thermodynamic and kinetic parameters of protein-DNA complexes is of importance for relevant biochemical and biophysical studies. In pursuit of this aim, binding isotherms for open transcription complex (RPo) of Escherichia coli RNA polymerase (R) at λPR promoter DNA (P) were determined as a function of salt concentration in pure NaCl and Tris/HCl solutions, and as a function of [NaCl] in the presence of fixed concentrations of MgCl2 and Tris/HCl. A concept of equivalent salt concentrations, i.e. concentrations at which the binding equilibrium constant is the same, was introduced and applied for prediction of binding isotherms in mixed salt solutions. Full coincidence between the experimental and predicted isotherms indicated that individual contributions of salts to the global salt-effect are additive in a broad range of salt concentrations. A generalized formula for calculation of salt equivalents characteristic for any of the thermodynamic or kinetic parameters of a complex (e.g., free energy, binding equilibrium and association/dissociation kinetic rate constants) is presented and its applicability to a number of protein-DNA complexes and dsDNA melting demonstrated using authors' own and literature data.
5

Professor Jozef Heller, 1896-1982. Biographical note

63%
Szarkowski J. W., Wierzchowski K. L.
Acta Biochimica Polonica
|
1984
|
tom 31
|
nr 1
6

Photochemistry of model oligo- and polynucleotides. II. Homopolymers of adenylic, guanylic and cytidylic acids and several heteropolymers

63%
Wierzchowski K. L., Shugar D.
Acta Biochimica Polonica
|
1960
|
tom 07
|
nr 2-3
7

Photochemistry of cytosine nucleosides and nucleotides. II

63%
Wierzchowski K. L., Shugar D.
Acta Biochimica Polonica
|
1961
|
tom 08
|
nr 2
8

Further studies on the photochemistry of pyrimidines, with special reference to 5- and 6-substituted derivatives in relation to photoreactivation in the T-even bacteriophages

63%
Wierzchowski K. L., Shugar D.
Acta Biochimica Polonica
|
1960
|
tom 07
|
nr 1
9

Synthesis and properties of some 2-, 4- and 5-aminopyrimidines. Effect of -NH2 and ortho-c methylation on protolytic equilibria and electronic absorption spectra

63%
Proba Z., Wierzchowski K. L.
Acta Biochimica Polonica
|
1975
|
tom 22
|
nr 2
10

Studies of reversible photolysis in oligo-and poly-uridylic acids

63%
Wierzchowski K. L., Shugar D.
Acta Biochimica Polonica
|
1959
|
tom 06
|
nr 3
11

Effect of Mg2plus on kinetics of oxidation of pyrimidines in duplex DNA by potassium permanganate

63%
Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 2
Po tas sium per manga nate ox i da tion of py rim i dine bases is of ten used to probe sin­gle-stranded re gions in func tional DNA-pro tein com plexes. How ever, so far re ac tiv- ity of these bases in double-stranded DNA has not been studied quantitatively. We have investigated the kinetics of oxidation of pyrimidines in supercoiled pDS3 plasmid dsDNA by quan ti ta tive KMnO4 footprinting, in con nec tion with par al lel stud ies on the ef fect of Mg2+ on ki net ics of ox i da tion of in di vid ual thymines in the sin­gle-stranded re gion of the open tran scrip tion com plex of Escherichiacoli RNA poly­mer ase at a cog nate Pa pro moter con tained in this plasmid. Rate con stants of ox i da­tion for pyrimidines, kj, in selected regions of pDS3 DNA, including Pa promoter, were de ter mined un der sin gle-hit re ac tion con di tions in the ab sence and pres ence of 10 mM MgCl2. Their val ues ap peared to be se quence-dependent and were: (i) the larg­est for Ts in 5 TA3' and 5 TC3' steps, while 2-4 times smaller for 5'-adja cent ones in TT(A,G,C) and TTT(A) runs, (ii) for Cs in 5'TC3' steps 2-4 fold smaller than for ad ja- cent Ts, and (iii) in the pres ence of Mg2+ gen er ally larger by a se quence-dependent fac­tor: in 5' TC3' steps of about 2 and 4 for Ts and Cs, re spec tively, in 5 TA3' steps of TTA and TTTA se quences for 3 -ter mi nal Ts of about 3, while for their 5 -neigh bors of a dis­tinctly smaller value of about 2. Com par i son of kj data for cor re spond ing Ts lo cated be tween +1 and -10 re gions of Pa pro moter in dsDNA and in ssDNA form in the open transcription complex, reported elsewhere, demonstrates that reactivity of pyrimi­dines in dsDNA is by 2-3 or ders of mag ni tude smaller. The ef fect of Mg 2+ in dsDNA is in ter preted in terms of elec tro static bar rier to dif fu sion of MnO4- on DNA surface, which is low ered by dif fu sive bind ing of these ions to back bone phos phates, in volv ing also se quence-specific con tacts with bases in the mi nor and major grooves of B-DNA.
12

Effect of reversed orientation and length of An.Tn DNA binding sequences in the -35 and spacer domains of a consensus-like Escherichia coli promoter on its strength in vivo and gross structure of the open complex in vitro

63%
Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
1996
|
tom 43
|
nr 1
In continuation of an earlier study (Łoziński ct at., 1991 Nucleic Acids Res. 19, 2947-2953) a series of consensus-like E. coli promoters with bending An Tn sequences of different length (n = 3-8) and orientation in the -35 and spacer domains was constructed, cloned into the plasmid pDS3 and their strength in vivo measured in relation to an internal transcriptional standard. Gel mobilities of free DNA restriction fragments carrying these promoters and of open transcriptional complexes with cognate RNA polymerase were determined by polyacrylamide gel electrophoresis and the gross structure of the complexes interpreted in terms of the theoretically predicted superstructure of DNA restriction fragments. The results obtained together with those reported earlier show that bending of the DNA helix axis immediately upstream of the -35 domain generally lowers the promoter strength in vivo and brings about shortening of the mean square end-to-end distance between free DNA ends in the open complex in vitro. T4Í-34...-37) and Ts(-34...-38) tracts located in the nontemplate DNA strand had the largest and comparable effect on the promoter strength, while the As T5 (-37...-41) sequence in either orientation (As tract in the template or nontemplate strand) exerted a much smaller effect. Promoters with the spacer bent by about 40° but in different directions, by two An (n = 5 or 6) tracts aligned in phase with the B-DNA repeat and located either in the template or nontemplate strands, had somewhat lower strength in vivo but the gross geometry of the respective open complexes was the same as that of a control promoter with straight spacer. Implications of these findings are discussed in connection with the existing model of E. coli transcriptional open complex.
13

Mg2plus ions do not induce expansion of the melted DNA region in the open complex formed by Escherichia coli RNA polymerase at a cognate synthetic Pa promoter. A quantitative KMnO4 footprinting study

63%
Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 2
Footprinting studies of prokaryotic open transcription complexes (RP O), based on oxidation of pyrimidine residues by KMnO4 and/or OsO4 at a single oxidant dose, have suggested that the extent of DNA melt ing in the tran scrip tion bub ble re gion in­creases in the presence of Mg2+. In this work, quantitative KMnO4 footprinting in func tion of the ox i dant dose of RPo, us ing EscherichiacoliRNA poly mer ase (Es7 ) at a fully func tional syn thetic pro moter Pa hav ing -35 and -10 con sen sus hexamers, has been used to de ter mine in di vid ual rate con stants of ox i da tion of T res i dues in this re­gion at 37° C in the ab sence of Mg2+ and in the pres ence of 10 mM MgCl2, and to eval u- ate there from the ef fect of Mg on the ex tent of DNA melt ing. Pop u la tion dis tri bu­tions of end-labeled DNA frag ments cor re spond ing to ox i dized Ts were quan ti fied and an a lyzed ac cord ing to the sin gle-hit ki netic model. Pseudo-first or der re ac tiv ity rate con stants, kx, thus ob tained dem on strated that Mg2+ ions bound to RPo merely en­hanced the re ac tiv ity of all 11ox i diz able thymines be tween the +3 and -11 pro moter sites by a po si tion-dependent fac tor: 3-4 for those lo cated close to the tran scrip tion start point +1 in ei ther DNA strand, and about 1.6 for those lo cated more dis tantly there from. On the ba sis of these ob ser va tions, we con clude that Mg2+ ions bound to RPo at Pa do not in flu ence the length of the melted DNA re gion and pro pose that the higher re ac tiv ity of thymines re sults mainly from lower lo cal re pul sive elec tro static bar ri ers to MnO4- dif fu sion around carboxylate bind ing sites in the cat a lytic cen ter of RPo and pro moter DNA phos phates.
14

Influence of polynucleotide secondary structure on thymine photodimerization

51%
Tramer Z., Wierzchowski K. L., Shugar D.
Acta Biochimica Polonica
|
1969
|
tom 16
|
nr 1
15

Photochemistry of 2,4-diketopyrimidines. Photodimerization, photohydration and stacking association of 1,3-dimethyluracil in aqueous solution

51%
Stepien E., Lisewki R., Wierzchowski K. L.
Acta Biochimica Polonica
|
1973
|
tom 20
|
nr 3
16

Cyclobutane dimers of 1-methylthymine: isolation, identyfication and properties

51%
Stepien E., Lisewski R., Wierzchowski K. L.
Acta Biochimica Polonica
|
1973
|
tom 20
|
nr 3
17

Conformation of the N(CH3)2 group in cytosine and in simple model pyrimidines and pyridines. Steric effects of orthomethyl substitution on infrared spectra and molecular dipole moments

51%
Litonska E., Proba Z., Kulakowska I., Wierzchowski K. L.
Acta Biochimica Polonica
|
1979
|
tom 26
|
nr 1-2
18

CD investigations on conformation of H-X-[Pro]n-Y-OH peptides [X-Trp, Tyr; Y-Tyr, Met]; models for intramolecular long range electron transfer

51%
Wierzchowski K. L., Majcher K., Poznanski J.
Acta Biochimica Polonica
|
1995
|
tom 42
|
nr 2
Conformations of three series of peptides: H-Trp-(Pro)n-Tyr-OH (n = 1-5), H-Trp-(Pro)n-Met-OH (n = 1-3) and H-Tyr-(Pro)n-Met-OH (n = 1-3), used as models in studies on long range electron transfer through protein matrix, were investigated by CD spectroscopy in aqueous solution at pH 5.2 in the temperature range of 10°C-90°C. CD spectra of their component N- and C-terminal dipeptide and oligoproline fragments were also measured under similar conditions. In interpretation of the spectra the cis <-> trans equilibrium about X-Pro bonds was taken into account and CD spectra of Trp-Pro and Tyr-Pro chromophores in trans and cis configuration of the peptide bond were evaluated. The spectra of n = 3-5 peptides from the first series and those with n = 2-3 from the other two series exhibit a strong negative band in the 202-207 nm region, the strength of which is proportional to the number of Pro residues in the (Pro)n bridge, and characterized by a large temperature decrement. In view of close similarity between characteristics of this band and the 206 nm band of aqueous oligoproline peptides = 3), known to attain a left handed helical conformation similar to that of 31 helix of the all-trans poly-L-proline II, this band was attributed to a conformation of the latter type. H-Trp-(Pro)2-Tyr-OH does not form this conformation due to sterical interaction between the two bulky aromatic side chains. Conclusions drawn from analysis of the CD spectra are supported by 1H and C13 NMR data reported elsewhere (Poznański et al., 1993, Biopolymers 33,781-795).
19

Mg2plus does not induce isomerization of the open transcription complex of Escherichia coli RNA polymerase at the model Pa promoter bearing consensus -10 and -35 hexamers

51%
Kolasa I. K., Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 4
The kinetics and thermodynamics of the formation of the transcriptional open com­plex (RPo) by Escherichia coli RNA polymerase at the synthetic Pa promoter bearing consensus -10 and -35 recognition hexamers were studied in vitro. Previously, this promoter was used as a control one in studies on the effect of DNA bending by An • Tn sequences on transcription initiation and shown to be fully functional in E. coli (Łoziński et al., 1991, Nucleic Acids Res. 19, 2947; Łoziński & Wierzchowski, 1996, Acta Biochim. Polon. 43, 265). The data now obtained demonstrate that the mecha­nism of Pa-RPo formation and dissociation conforms to the three-step reaction model: bind-nucleate-melt, commonly accepted for natural promoters. Measurements of the dissociation rate constant of Pa-RPo as a function of MgCl2 concentration allowed us to determine the number of Mg2+ ions, nMg ~ 4, being bound to the RPo in the course of renaturation of the melted DNA region. This number was found constant in the tem­perature range of 25-37°C, which indicates that under these conditions the complex remaines fully open. This observation, taken together with the recent evidence from KMnO4 footprinting studies that the length of the melted region in Pa-RPo at 37°C is independent of the presence of Mg2+ ions (Łoziński & Wierzchowski, 2001, Acta Biochim. Polon. 48, 495), testifies that binding of Mg2+ to RPo does not induce its fur­ther isomerization, which has been postulated for the λPr-RPo complex (Suh et al., 1992, Biochemistry 31, 7815; 1993, Science 259, 358).
20

Effects of distortions by A-tracts of promoter B-DNA spacer region on the kinetics of open complex formation by Escherichia coli RNA polymerase

51%
Kolasa I. K., Lozinski T., Wierzchowski K. L.
Acta Biochimica Polonica
|
2003
|
tom 50
|
nr 4
A-tracts in DNA due to their structural morphology distinctly different from the ca­nonical B-DNA form play an important role in specific recognition of bacterial up­stream promoter elements by the carboxyl terminal domain of RNA polymerase a subunit and, in turn, in the process of transcription initiation. They are only rarely found in the spacer promoter regions separating the -35 and -10 recognition hexamers. At present, the nature of the protein-DNA contacts formed between RNA polymerase and promoter DNA in transcription initiation can only be inferred from low resolution structural data and mutational and crosslinking experiments. To probe these contacts further, we constructed derivatives of a model Pa promoter bearing in the spacer region one or two An (n = 5 or 6) tracts, in phase with the DNA helical repeat, and studied the effects of thereby induced perturbation of promoter DNA structure on the kinetics of open complex (RPo) formation in vitro by Esche­richia coli RNA polymerase. We found that the overall second-order rate constant ka of RPo formation, relative to that at the control promoter, was strongly reduced by one to two orders of magnitude only when the A-tracts were located in the nontemplate strand. A particularly strong 30-fold down effect on ka was exerted by nontemplate A-tracts in the -10 extended promoter region, where an involvement of nontemplate TG (-14, -15) sequence in a specific interaction with region 3 of tf-sub-unit is postulated. A-tracts in the latter location caused also 3-fold slower isomerization of the first closed transcription complex into the intermediate one that precedes formation of RPo, and led to two-fold faster dissociation of the latter. All these findings are discussed in relation to recent structural and kinetic models of RPo formation.
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