Abstract:
:A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by +/- 10 degrees in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (3(7)) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5' end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 10(6) conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques.
journal_name
Biopolymersjournal_title
Biopolymersauthors
Erie DA,Breslauer KJ,Olson WKdoi
10.1002/bip.360330109subject
Has Abstractpub_date
1993-01-01 00:00:00pages
75-105issue
1eissn
0006-3525issn
1097-0282journal_volume
33pub_type
杂志文章相关文献
BIOPOLYMERS文献大全abstract::Laminins are a multifunctional molecule with numerous active sites that have been identified in short peptide sequences. Mixed peptide-conjugated chitosan membranes using laminin-derived active peptides have been previously demonstrated to be useful as a biomaterial for tissue engineering. In this study, two syndecan-...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22303
更新日期:2013-11-01 00:00:00
abstract::In this article, the pulsed double electron-electron resonance in electron spin-echo (PELDOR) technique is applied to study the self-aggregation of spin-labeled zervamicin IIA, a hexadecapeptide antibiotic of fungal origin, which is known to form ion channels in a phospholipid double layer. Measurements of the ion cha...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.10208
更新日期:2002-09-01 00:00:00
abstract::We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation....
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22821
更新日期:2016-06-01 00:00:00
abstract::The discovery of the prototype delta opioid antagonists TIPP (H-Tyr-Tic-Phe-Phe-OH) and TIP (H-Tyr-Tic-Phe-OH) in 1992 was followed by extensive structure-activity relationship studies, leading to the development of analogues that are of interest as pharmacological tools or as potential therapeutic agents. Stable TIPP...
journal_title:Biopolymers
pub_type: 杂志文章,评审
doi:10.1002/(SICI)1097-0282(1999)51:6<411::AID-BIP4>3.
更新日期:1999-01-01 00:00:00
abstract::Purified integral membrane proteins require amphipathic molecules to maintain their solubility in aqueous solutions. These complexes, in turn, are used in studies to characterise the protein structures by a variety of biophysical and structural techniques, including spectroscopy, crystallography, and cryo-electron mic...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.23067
更新日期:2018-08-01 00:00:00
abstract::Human saliva contains hundreds of small proline-rich peptides originated by the proteolytic cleavage of the salivary basic Proline-Rich Proteins. Nevertheless only for few of them a specific biological activity has been assigned to date. Among them, the 1932 Da peptide (p1932) has been patented as an anti-HIV agent. I...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22889
更新日期:2016-09-01 00:00:00
abstract::Designed ligands that inhibit protein-protein interactions involved in gene expression are valuable as reagents for genomics research and as leads for drug discovery efforts. Selective modulation of protein-protein interactions has proven to be a daunting task for synthetic ligands; however, the last decade has seen s...
journal_title:Biopolymers
pub_type: 杂志文章,评审
doi:10.1002/bip.21546
更新日期:2011-01-01 00:00:00
abstract::In our continuing series of measurements of the complex index of refraction for representative samples of biological materials, we measured ovalbumin (egg albumin) over the spectral region from 0.130 (76,923 cm(-1)) to 2.50 microm (4000 cm(-1)). Films of ovalbumin suitable for optical analyses were prepared and measur...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.1004
更新日期:2001-01-01 00:00:00
abstract::Short peptides composed of phenylalanine and sequences derived from amyloidogenic peptides have the ability to self-assemble to form nanostructures including hydrogels. The self-assembly of peptides composed of only hydrophobic amino acids and aliphatic protecting groups have not been investigated in detail. We have e...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.23033
更新日期:2017-11-01 00:00:00
abstract::Simulated ir absorption and vibrational CD (VCD) spectra of four alanine-based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were based on transfer of...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/(SICI)1097-0282(20000415)53:5<380::AID-BIP
更新日期:2000-04-15 00:00:00
abstract::Hexameric insulin is an allosteric protein that undergoes transitions between three conformational states (T(6), T(3)R(3), and R(6)). These allosteric states are stabilized by the binding of ligands to the phenolic pockets and by the coordination of anions to the His B10 metal sites. Raman difference (RD) spectroscopy...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.1020
更新日期:2001-01-01 00:00:00
abstract::CD experiments are reported for several coiled-coil species in the tyrosine/disulfide (approximately 250-350-nm) region. Intact noncross-linked tropomyosin (approximately 3 degrees C) shows a negative nonsymmetric band maximal at 280 nm. This spectrum is the sum over six tyrosines/chain, and has conformational signifi...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360280909
更新日期:1989-09-01 00:00:00
abstract::A series of iota-carrageenans containing different amounts of nu-carrageenan (0-23 monomer %) have been prepared from neutrally extracted carrageenan of Eucheuma denticulatum. nu-Carrageenan is the biochemical precursor of iota-carrageenan. The conformational order-disorder transition and rheological properties of the...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.10250
更新日期:2002-11-15 00:00:00
abstract::We developed dictionaries of two-, three-, and five-residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look-up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that p...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20113
更新日期:2004-10-15 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
pub_type: 杂志文章
doi:10.1002/bip.21517
更新日期:2010-11-01 00:00:00
abstract::The pulsed-field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical pre...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360290408
更新日期:1990-03-01 00:00:00
abstract::Prolonged exposure (>90 days) of bovine beta-lactoglobulin (BLG) to subdenaturing concentrations of either urea or potassium thiocyanate resulted in the formation of ordered polymers in the form of fibrils. The fibrils obtained with each chaotrope showed major differences in morphology, surface properties, thiol acces...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20704
更新日期:2007-05-01 00:00:00
abstract::Thermal unfolding of bovine serum albumin (BSA) has been studied in the presence of 2,2,2-trifluoroethanol (TFE) using high-sensitivity microdifferential scanning calorimetry. Quantitative thermodynamic parameters accompanying the thermal transitions have been evaluated. TFE is observed to be a stabilizer or a destabi...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20262
更新日期:2005-06-05 00:00:00
abstract::The abnormal aggregation of amyloid proteins is reported to play a critical role in the etiology of neurodegenerative disorders. Studies have shown that excessive ferric irons are associated with the misfolding of amyloid proteins, and that (-)-epigallocatechin gallate (EGCG) is a good metallic ion chelator with inhib...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22752
更新日期:2016-02-01 00:00:00
abstract::Different hexameric forms of insulin have been crystallized from a variety of conditions. In the presence of 1% phenol, 1.0 M sodium chloride, and at a pH of 8.5, a rhombohedral form is produced with two monomers in the asymmetric unit, space group R3, a = 79.92 A and c = 40.39 A. The structure has been solved and ref...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360320422
更新日期:1992-04-01 00:00:00
abstract::A large number of potent and selective therapeutic agents, useful for the treatment of several diseases, have been isolated from natural sources. For example, the most active thrombin inhibitors are those secreted by the salivary glands of leeches. One peculiar feature of these agents is the lack of any significant in...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/(SICI)1097-0282(1999)51:1<19::AID-BIP4>3.0
更新日期:1999-01-01 00:00:00
abstract::The beta-subunit of the human chorionic gonadotropin (hCG) hormone, which is believed to be related to certain types of cancer, contains three hairpin-like fragments. To investigate the role of beta-hairpin formation in the early stages of the hCGbeta folding, a 28-residue peptide with the sequence RDVRFESIRLPGSPRGVNP...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/(SICI)1097-0282(19991005)50:4<413::AID-BIP
更新日期:1999-10-05 00:00:00
abstract::Neurokinins and their receptors are a complex system consisting of at least three endogenous agents--substance P (SP), neurokinin A (NKA), and neurokinin B (NKB)--and their corresponding receptor types, respectively, NK-1, NK-2, and NK-3. Investigations on receptors have been made using sensitive and fairly selective ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.360280111
更新日期:1989-01-01 00:00:00
abstract::MD simulations have been carried out to understand the dynamical behavior of the DNA substrate of the Thermus aquaticus DNA methyltransferase (M.TaqI) in the methylation process at N6 of adenine. As starting structures, an x-ray structure of M.TaqI in complex with DNA and cofactor analogue (PDB code: 1G 38) and free d...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.20341
更新日期:2005-10-15 00:00:00
abstract::In this study, we identified and chemically synthesized three cationic and amphipathic peptides (Glycinin-17, BCAS-16, and BCBS-11) from soybean proteins. These peptides had high isoelectric points, high positive net charges, and included multiple hydrophobic amino acids. Subsequently, we identified multiple functions...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.23023
更新日期:2017-07-01 00:00:00
abstract::GSK3β plays an important role in many physiological functions; dysregulated GSK3β is involved in human diseases such as diabetes, cancer, and Alzheimer's disease. This study uses MD simulations to determine the interaction between GSK3β and a peptide derived from GSKIP, a novel GSK3β interacting protein. Results show ...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21603
更新日期:2011-07-01 00:00:00
abstract::Four members of the carcinoembryonic antigen family, CEACAMs 1, 3, 6, and 8, are expressed on human neutrophils and can trigger an activation signal that increases neutrophil adhesion to human umbilical vein endothelial cell (HUVEC) monolayers. To identify active sites on CEACAM1, we previously performed molecular mod...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21447
更新日期:2011-01-01 00:00:00
abstract::Understanding the high temperature behavior of collagen and collagenous tissue is important for surgical procedures and biomaterials processing for the food, pharmaceutical, and cosmetics industries. One primary event for proteins is thermal denaturation that involves unfolding the polypeptide chains while maintaining...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.23017
更新日期:2017-06-01 00:00:00
abstract::Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.21250
更新日期:2009-09-01 00:00:00
abstract::Combinatorial library composed of rigid rod-like peptides with a triple-helical scaffold was constructed. The component peptides were designed to have various combinations of basic and neutral (or hydrophobic) amino acid residues based on collagen-like (Gly-Pro-Yaa)-repeating sequences, inspired from the basic and amp...
journal_title:Biopolymers
pub_type: 杂志文章
doi:10.1002/bip.22791
更新日期:2016-11-04 00:00:00