CC BY
42
Save 10% on Subscription for 2010
Details at www.actanaturae.ru
ActaNaturae
RESEARCH ARTICLES
I Keying appr*mrlir* »w (nrUirr Hnpmnl by implmwiU-in| new algorithm» n| IIm conformational *r itrvh nod new Knrliti (uiicinm inn’thoii lu ••jumntp the trvv energy of ligand binding i Scoring lun<iu>m may includo mhrr rum* |amriii> n( rtuihTulir mnluRKt fijrrt* llrlil» |!|m rittpinral term*. pf. hydrogen twmda drocntifd by »hiur Krami'tncil parameter* |(| In tiiia work W *1udl*d «tacking interac-limn, whtrli w.ually tr* mil prap*tly ukra into Mcmint in widely uaad tcormo (unctn»
TH* PAt aMfTEtt Of $1*0IMG MTC*ACTIONS Of «11 ll»«f van true l)r|M «1 ittlrrartuim in hnannlrtular ««im-|iImi« iMuch a* hydrogen rtnnru hU tNidu». <itc I Itw ituk-mg ot aromatic rabatance* deeervr» ipectal attention. Mott iltuip ini ludi' ammalte (rafiwtili In Ihfir chemical Ktrm-lum, aoc| «Jacking often ptayt a nalalilc roln in their r»<nn • union by protein-target* Wv liav* itvently ahown iu> an vipllcti account >*/ «tacking in «coring funcUMM mrrpun the effiurnry irf ATP ducking |9|. T)»e arumatk inli tartim® ><if nit tii'ii try the mutual im tent a Unit at twn ryctoa it*~ •cribed by geomatrtcal parameter*- th* height h and dw-pUmnrnt d <d dm rytk retail** kt thrdhrr. and tltr angle b«twe«ni theirpUm-t (Fiji I>
Hiiwwr, tlit* rang* o| itw parameter*. wkkh carrv-Nponda to the premncr or a burner of a «lacking contact, is rlltl not very wdl defined and uiually taken u arbitrary Iff, n LVfining it mnrn aci*uruti>ty wmild aaiuat tn devehip-ing more efficient «coring luncttnm and ahuuld Incrta*» ihe pr«*dict«m quality «if th» upatlal itturiiinr» <i( prolem-ligand [onpliti ■ by molecular modeling metliodi. Wltb tliu aun in view <ii' performed an analffti* uf Ih* njwUil uructutM ul protein-lucand cmmplexr» drtrrmmrd mprnmetttally with atnnur trtMlutmn wtitfi* llgamt* rimtainnt »ili*runi< nr glia * nine ub a aubatrurtur*
On* writ-known rxampk1 of «tacking inti-ructlon* It th# parallel packing ul punrw- and pyrimidine nuelenlia*** in DNA|I, H| Some ttiumaltc compuuuda tniil touriaid parjuo-thrulat lonarh utlier fT-«haped stacking), a* tu> tirvii durum lor ammo arid» in pruteina (7, |Ct| and for nualH uf
curium aromatic cydit (Ortum* and naphtalene) |11 - HJ Besides, aiuifi compound* |«urtinpate tu cstum-ai Intiirar-Ilona, flirr» a poaltivvly charged group tnU-nir.ta with the n»gati\r-ly charged r.kaid nf aromatic «t-elprf mm | IS* 17| Taking all that lulo account. wr analyzed lit* distribu-tiMfi of gMimi*ti iral parameter* h. 4. and «t fur con taut* uf adcnitw and guanine mouilci uf ligandr with the ammatii aide chaiiu ot tweplof amino acids Pbe. Tyr. Trp, and Ola. a* wall aa with the pMCitivety clurfnl guamdiiM' gmup uf Arg and ammo group at l.yv Thv mult» obtained for guanine are pn wntnt tn Fig 7
It «an be well that two dltlinrt utlentatioaa ate typical for Plw parallel and pety^ndii'idar ui the guanine plane I Fig 2, thinm in red and grrm. mputllvaly) The dlipfare* meni d lie* In (he tome rang? 11-3 A fur but)* type* of coo-tacta Mi'ttuwhilr, they cUauty differ m the value uf height h. which M <1-5 for paiallel A and <35 A for prrpetulimlat nnmtatlon Similar dUtnbutlma w*»r> obtained for Tyr. Trp. and IIU. though the data are ararrer In th«ne cam f|nw> ev«. the T-«lM|e)l CBiiUrl U nut m typtntl fur Tyr, Trp, ami Ilia aa it la fur Phr
Fij t Gaomatncaf paramatan u»e J to daicnba a ttackmg contact batwaan
DopUcenieni (d) and bat^ht (h) «a calculated lor Ilia cento*
lahwa to anothaf ig'i plana. Angle it calculated at It
wmd mton of both rtnm.
(ftaplacamant A
Trp
dtydAcei
His
m
displacement^
^Lys M
rteipondt In Bhe plan*» of bot1>
SYNTHETIC ANTIBODIES
FOR CUNICAL USE
REGULATING TELOMERASE IN ONCOGENESIS
P. SI «
THE STRUCTURE OF THE MITOCHONDRIAL GENOME AS AN ACTIVATOR OF OPISTHORCHIASIS STACKING INTERACTIONS
HIGHLIGHTS
Y.A. Shtyrya, L.V. Mochalova, N.V. Bovin
Influenza Virus Neuraminidase: Structure and Function
Active site of influenza virus A neuraminidase (N2 subtype) in complex with Neu5Ac2en (2-deoxy-2,3-didehydro-N-acetylneuraminic acid). Neu5Ac2en is presented in black, functional a.a. of the active site — red.
O.A. Patutina, N.L. Mironova, V.V. Vlasov, M.A. Zenkova
New Approaches for Cancer Treatment: Antitumor Drugs Based on Gene-Targeted Nucleic Acids
How antisense oligonucleotides (asON) work. (a) RNA is cleaved as a part of a heteroduplex with the asON by RNase H. (b) Block of translation caused by binding of the oligonucleotide onto the mRNA
T. Shcheglova, S.P. Makker, A. Tramontano
Covalent Binding Antibodies Suppress Advanced Glycation: On the Innate Tier of Adaptive Immunity
enhanced protein glycation
glucose
levels
cellular uptake
AGEs
T
low mol wt glycation products
i/ \
extracellular matrix
Inflammatory cross
signaling links
▼
Apoptosis ^ vascular pathology
Nephropathy
Atherosclerosis
Retinopathy
Advanced Glycation Endproducts in Pathology. Protein glycation due to hyperglycemia or normal aging is further modified in the body to advanced glycation endproducts (AGE). These AGE may be further broken down to glycated peptides and low-molecular-weight AGEs. Both high- and low-molecular weight AGEs could be taken up by vascular tissues, by cellular receptors, and by cross-linking of the extracellular matrix. These modifications account for the cytotoxicity and tissue necrosis and ultimately lead to vascular pathologies, as is seen in diabetic complications
asON
b
Morphology of iPS derived from an endothelium, feeder-free culture. A — Bright field image of iPS colony. B — Image of ESC colony. Bar scale — 100 mkm
M.V. Shutova, A.N. Bogomazova, M.A. Lagarkova, S.L. Kiselev
Derivation and Characterization of Human Induced Pluripotent Stem Cells
№ 2 2009 | ACTA NATURAE | 3
a
