Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences.

abstract：:We have previously proposed a model for the delta-opioid receptor binding conformation of the high affinity tetrapeptide Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) based on experimental and theoretical conformational analysis of this peptide and a correlation of conformational preferences of further conformationally restricted...

journal_title：Biopolymers

authors： Mosberg HI,Dua RK,Pogozheva ID,Lomize AL

更新日期：1996-09-01 00:00:00

abstract：:The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single-molecule methods is usually hindered by the intrinsic tendency of such biopolymers to ...

journal_title：Biopolymers

authors： Alemany A,Ritort F

更新日期：2014-12-01 00:00:00

abstract：:The large abundance of bioactive single- and multiple-stranded cystine-rich peptides in nature has fostered the development of orthogonal thiol-protection schemes and of efficient chemistries for regioselective disulfide formation in synthetic replica for decades. In parallel to these entirely synthetic strategies, an...

journal_title：Biopolymers

authors： Moroder L,Musiol HJ,Götz M,Renner C

更新日期：2005-01-01 00:00:00

abstract：:Collagen is a natural protein, which is used as a vital biomaterial in tissue engineering. The major concern about native collagen is lack of its thermal stability and weak resistance to proteolytic degradation. In this scenario, the crosslinking compounds used for stabilization of collagen are mostly of chemical natu...

journal_title：Biopolymers

authors： Usharani N,Jayakumar GC,Kanth SV,Rao JR

更新日期：2014-08-01 00:00:00

abstract：:Amyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's, and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril-forming proteins revealed coexistence of alternative aggregation modes (amyloid...

journal_title：Biopolymers

authors： Berhanu WM,Masunov AE

更新日期：2012-01-01 00:00:00

abstract：:The hinge region links the antigen binding Fab part to the constant Fc domain in immunoglobulins. For the hinge peptide derivative [AcThr(OtBu)-Cys-Pro-Pro-Cys-Pro-Ala-ProNH2]2 the assignment of the 1H and 13C resonances was achieved by two-dimensional nmr techniques: total correlation spectroscopy (TOCSY), nuclear Ov...

journal_title：Biopolymers

authors： Kessler H,Mronga S,Müller G,Moroder L,Huber R

更新日期：1991-09-01 00:00:00

abstract：:In the native structure of hen egg white lysozyme (HEL), the amino acid sequence 87-97 (HEL 87-97) forms an amphiphilic helix, with hydrophilic residues in the sequence directed toward the solvent. A synthetic version of the HEL 87-97 sequence (with the cysteine corresponding to position 94 of HEL replaced by alanine)...

journal_title：Biopolymers

authors： Vuilleumier S,Mutter M

更新日期：1993-03-01 00:00:00

abstract：:We applied dynamic light scattering technique on the model system of hen egg lysozyme in salt-free aqueous ethanol solution to study the mechanism of denaturation and aggregation of protein. At low ethanol concentration [0-63% (v/v)], the fast relaxation mode was observed, which was caused by lysozyme molecules in the...

journal_title：Biopolymers

authors： Tanaka S,Oda Y,Ataka M,Onuma K,Fujiwara S,Yonezawa Y

更新日期：2001-10-15 00:00:00

abstract：:A secondary structure sequence is a symbolic string composed of three kinds of letters, indicating the helix, strand, and coil (including turns), respectively. A graphic representation for this abstract symbolic sequence is proposed here, called the S curve. The S curve is the unique representation for a given seconda...

journal_title：Biopolymers

authors： Zhang CT,Zhang R

更新日期：2000-06-01 00:00:00

abstract：:We present a method for analysis of a fitness landscape of a biopolymer with significantly epistatic sites. The analysis is based on a quasi-additive fitness model. The fitness model is constructed with additive terms conducted by "site-fitness" and epistatic terms conducted by "pair-fitness," where the site-fitness i...

journal_title：Biopolymers

authors： Aita T,Hamamatsu N,Nomiya Y,Uchiyama H,Shibanaka Y,Husimi Y

更新日期：2002-07-05 00:00:00

abstract：:Multiple, independent sites or domains behave, on chemical change, in a manner predicted by Langmuir. Distortions of this behavior have been attributed to interactions between the domains, which vary with the progress of the changes occurring at the sites or domains. The two main models for nearest neighbor interactio...

journal_title：Biopolymers

authors： Saroff HA,Kiefer JE

更新日期：1999-05-01 00:00:00

abstract：:The thermal conformational transitions of two sonicated samples of schizophyllan were studied in water-dimethylsulfoxide (DMSO) mixtures by high-sensitivity differential scanning calorimetry (DSC). Two transitions were observed over most of the range of solvent compositions. These were assigned to an internal change o...

journal_title：Biopolymers

authors： Kitamura S,Kuge T

更新日期：1989-02-01 00:00:00

abstract：:This report details the observation of (a) the intact double helix of DNA at 0% relative humidity in poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) films, (b) the fractal-like growth of DNA crystals in films of poly(dA).poly(dT), and (c) poly(dA).poly(dT) with adenines in the B form and thymines in the A form. Observat...

journal_title：Biopolymers

authors： Sclavi B,Peticolas WL,Powell JW

更新日期：1994-08-01 00:00:00

abstract：:The conformation and intermolecular association of [D-Hyi2, L-Hyi4] meso-valinomycin [cyclo[-D-Val-D-Hyi-L-Val-L-Hyi-(D-Val-L-Hyi-L-Val-D-+ ++Hyi)2-], C60H102N6O18] in a crystal form obtained from ethanol solution has been determined by x-ray crystallography. Two depsipeptides and one ethanol molecule per asymmetric u...

journal_title：Biopolymers

authors： Pletnev VZ,Ivanov VT,Langs DA,Burkhart BM,Duax WL

更新日期：1997-11-01 00:00:00

abstract：:The conformational study on Arg-Gly-Asp (RGD)-containing tetrapeptides in the unhydrated and hydrated states has been carried out using the force field ECEPP/3 and the hydration shell model. The tetrapeptides studied here are H-RGDX-OH (X = Trp, Tyr, Phe, Leu, Val, Cys, Gln, and Ser), which show the inhibitory activit...

journal_title：Biopolymers

authors： Park HS,Kim C,Kang YK

更新日期：2002-04-15 00:00:00

abstract：:The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism t...

journal_title：Biopolymers

authors： Durell SR,Ben-Naim A

更新日期：2017-08-01 00:00:00

abstract：:Synthesis and CD and (13)C(alpha)-NMR studies in a near-neutral saline buffer are reported for a 65-residue peptide ((190)Tm(254)) comprising residues 190-254 of the alpha-tropomyosin chain. CD on a version disulfide cross-linked via the N-terminal cysteine side chains indicates that this dimer is highly helical and m...

journal_title：Biopolymers

authors： Emerson Holtzer M,Mints L,Hogue Angeletti R,d'Avignon DA,Holtzer A

更新日期：2001-10-05 00:00:00

abstract：:The phase content of amylose-water mixtures (0.7/0.3 w/w) has been analyzed by transmission Fourier transform infrared (FTIR) spectroscopy in the 1175-950 cm(-1) region. Spectra are obtained under three different conditions: (a) as a function of temperature (T) from 25 to 97 degrees C; (b) at room temperature (RT), af...

journal_title：Biopolymers

authors： Bernazzani P,Chapados C,Delmas G

更新日期：2001-03-01 00:00:00

abstract：:Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as d...

journal_title：Biopolymers

authors： Bolt HL,Williams CEJ,Brooks RV,Zuckermann RN,Cobb SL,Bromley EHC

更新日期：2017-07-01 00:00:00

abstract：:A three-dimensional model of DNA/RNA triple helix that contains a poly(L-deoxyadenosine) (L-dA) chain is proposed based on computer-assisted model building and energy calculations. The model building was performed by a new method that systematically searches possible conformations of nucleotide units in the helical ch...

journal_title：Biopolymers

authors： Tomioka N,Itai A

更新日期：1992-12-01 00:00:00

abstract：:The constraints on combinations of nearest neighbors in nucleic acid sequences and the numbers of independent sequences needed to describe nearest-neighbor properties of oligomers and polymers are derived and summarized. It has been pointed out in previous work [D. M. Gray and I. Tinoco, Jr. (1970) Biopolymers, Vol. 9...

journal_title：Biopolymers

authors： Gray DM

更新日期：1997-12-01 00:00:00

abstract：:alpha,beta-Dehydro amino acid residues are known to constrain the peptide backbone to the beta-bend conformation. A pentapeptide containing only one alpha,beta-dehydrophenylalanine (delta Phe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc-Leu-...

journal_title：Biopolymers

authors： Rajashankar KR,Ramakumar S,Mal TK,Jain RM,Chauhan VS

更新日期：1995-02-01 00:00:00

abstract：:Xylanase XYNII from Trichoderma longibrachiatum is a small protein of the molecular weight 21 kDa, belonging to the family 11 of glycosyl hydrolases, which catalyses hydrolysis of xylan. This article reports thermal stability study of xylanase XYN II conformation in the temperature range 15-65 degrees C by the small a...

journal_title：Biopolymers

authors： Kozak M

更新日期：2006-12-15 00:00:00

abstract：:Second-generation dendrimers have been prepared on solid phase by successive additions of branched polyproline building blocks starting from two different branching units anchored to the solid support. The preparation of Pro-rich building blocks was carried out by stepwise solid-phase synthesis and their iterative add...

journal_title：Biopolymers

authors： Sanclimens G,Crespo L,Giralt E,Royo M,Albericio F

更新日期：2004-01-01 00:00:00

abstract：:Nodal, a member of the transforming growth factor-β superfamily, is a potent embryonic morphogen also implicated in tumor progression. Up to date structural information on the interaction of Nodal with its molecular partners are unknown. To deepen our understanding about mechanisms underlying both embryonic developmen...

journal_title：Biopolymers

authors： Calvanese L,Marasco D,Doti N,Saporito A,D'Auria G,Paolillo L,Ruvo M,Falcigno L

更新日期：2010-11-01 00:00:00

abstract：:The thermodynamics of the stacking to unstacking transitions of 24 single-stranded DNA sequences (ssDNA), 10-12 bases in length, in sodium phosphate buffer were determined from 10 to 95 degrees C, using differential scanning calorimetry (DSC). An additional 22 ssDNA sequences did not exhibit an S<=>U transition in thi...

journal_title：Biopolymers

authors： Ramprakash J,Lang B,Schwarz FP

更新日期：2008-11-01 00:00:00

abstract：:The spatial variation in the composition of nonexpanded biopolymer blends prepared by extrusion of mixtures of gelatin with either native or pregelatinized waxy maize starch was studied using a 30-microm aperture FTIR microspectroscopy technique. The ratio of the areas of the "saccharide" bands (953-1180 cm(-1)) and t...

journal_title：Biopolymers

authors： Mousia Z,Farhat IA,Pearson M,Chesters MA,Mitchell JR

更新日期：2001-01-01 00:00:00

abstract：:The creation of peptide libraries by site-selective modification of a few peptide substrates would increase the efficiency of discovery processes, but still is a real synthetic challenge. The site-selective modification of small peptides at serine or threonine residues, by using a short scission-addition procedure, al...

journal_title：Biopolymers

authors： Romero-Estudillo I,Saavedra C,Boto A,Álvarez E

更新日期：2015-09-01 00:00:00

abstract：:Ultraviolet hyperchromicity experiments indicate that in DNA duplex formation, a C-T mismatch is destabilizing in the center of a duplex, but behaves as a stable base pair at the terminus of a duplex. The C-T base pair is thought to contain two hydrogen bonds, but has thermodynamic parameters (delta Ho and delta Go of...

journal_title：Biopolymers

authors： Vanhommerig SA,van Genderen MH,Buck HM

更新日期：1991-08-01 00:00:00

abstract：:Using high precision densimetric and ultrasonic measurements, we have determined, at 25 degrees C, the apparent molar volumes PhiV and the apparent molar compressibilities PhiK(S) of four nucleic acid duplexes-namely, the DNA duplex, poly(dIdC)poly(dIdC); the RNA duplex, poly(rA)poly(rU); and the two DNA/RNA hybrid du...

journal_title：Biopolymers

authors： Chalikian TV,Völker J,Srinivasan AR,Olson WK,Breslauer KJ

更新日期：1999-10-15 00:00:00