bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and crystal structures of Aib‐containing oligopeptides Boc‐Leu4‐Aib‐Leu4‐OBzl and Boc‐(Leu4‐Aib)2‐OBzl
Authors: Okuyama K. , Saga Y. , Nakayama M. , Narita M. 
Published: December 2004

AbstractSample peptides Boc‐Leu4‐Aib‐Leu4‐OBzl and Boc‐(Leu4‐Aib)2‐OBzl, were crystallized by the solvent‐evaporation method. Both crystals are monoclinic, with space group of P21 and Z = 2. The cell parameters are a = 16.580(7), b = 21.105(7), c = 11.583(4) Å, and β = 104.90(3)° (Boc‐Leu4‐Aib‐Leu4‐OBzl), and a = 15.247(9), b = 19.04(l), c = 16.311(9) Å, and β = 117.10(1)° [Boc‐(Leu4‐Aib)2‐OBzl]. Crystal structures were solved by the direct method and refined to R values of 0.096 (the former peptide) and 0.112 (the latter). Peptide backbones fold into a right‐handed α‐helix, except for the C‐terminal Aib residue in Boc‐(Leu4‐Aib)2‐OBzl. Both peptide molecules are stabilized by six (the former) or seven (the latter) intramolecular (5 → 1) hydrogen bonds, and arranged in the head‐to‐tail fashion, which makes an infinite column. In this column, one (the former) or two (the latter) intermolecular hydrogen bonds link the neighboring molecules. In the case of Boc‐Leu4‐Aib‐Leu4‐OBzl, the solvent molecule N, N‐dimethylformamide was found in the difference Fourier map. There was a hydrogen bond between peptide and solvent molecule. Along the lateral direction, only hydrophobic contacts were observed between adjacent peptide molecules.
Ionization of clusters. IV. Cooperativity and allosterism derived from shared clusters in macromolecules
Authors: Saroff Harry A. 
Published: December 2004

AbstractClusters of ionizable groups are examined for conditions that develop cooperativity (1) on the binding of protons, and (2) on the binding of an associated ligand when the clusters are shared between domains or subunits in macromolecules. Cooperative binding isotherms for protons have long been observed (but not emphasized as cooperative binding) when studies have been done on clusters for the evaluation of metal ion complexation [A. E. Martell & M. Calvin (1952) Chemistry of the Metal Chelate Compounds, Prentice‐Hall, Englewood Cliffs, New Jersey]. Reactions are formulated in this paper to show that anions, chelating to positively charged clusters, are also capable of developing the cooperative binding of protons. Extension of these simple reactions to those where clusters of ionizable groups are shared between domains of macromolecules provides models for cooperative binding, which include the allosteric, Bohr, anion, and cation effects in proteins.
Electric birefringence imaging of electrokinetic agarose orientation
Authors: Lanan Maureen , Shick Reed , Morris Michael D. 
Published: December 2004

AbstractTime‐resolved and steady‐state electric birefringence imaging with a slow‐scan video camera is used to study orientation during DNA agarose gel electrophoresis. The hydrodynamically induced gel distortion is shown to be the major source of birefringence under electrophoresis running conditions and to generate a birefringence image that approximates the image of the DNA concentration gradient in the electric field direction. A fluid kinematic model is presented to describe the spatial distribution of steady‐state birefringence and is verified with fluorescence measurements of DNA distribution. The stress‐optic coefficient of 1% agarose gel is measured by mechanical compression and used to evaluate the magnitude of the induced strain on the gel during electrophoresis.
Structural versatility of peptides from Cα,α‐disubstituted glycines: Preferred conformation of the chiral isovaline residue
Authors: Nebel K. , Altmann E. , Mutter M. , Bardi R. , Piazzesi A. M. , Crisma M. , Bonora G. M. , Toniolo C. 
Published: December 2004

AbstractThe molecular structures of four protected isovaline‐ (Iva‐) containing peptides to the pentamer level have been determined by x‐ray diffraction. The peptides are t‐Boc‐Ala‐(S)‐Iva‐Ala‐OMe (t‐Boc : tert‐butyloxycarbonyl; OMe : methoxy) and its (R)‐Iva diastereomer, and t‐Boc‐[Ala‐(R)‐Iva]2‐Ala‐OH and its (S)‐Iva diastereomeric methyl ester analogue. The two tripeptides are folded in an open type II β‐bend conformation. The fully developed right‐handed 310‐helix formed by the (R)‐Iva pentapeptide, which includes an unusual intramolecular (acid) OH ⃛OC(peptide) H bond, is partially unfolded (near the C‐terminus) in the (S) ‐Iva pentapeptide. 1H‐nmr and Fourier transform ir absorption studies suggest that in CDCl3 solution (a) the two tripeptides maintain a type II β‐bend conformation of comparable stability and (b) both diastereomeric pentapeptide sequences adopt a fully developed 310‐helix. A comparison with the preferred conformation of other extensively investigated Cα,α‐disubstituted glycines is made and the implications for the use of the Iva residue in designing conformationally constrained analogues of bioactive peptides are briefly discussed.
Induced CD and interaction of some porphyrin derivatives with α‐helical polypeptides in aqueous solutions
Authors: Ikeda Shoichi , Nezu Takashi , Ebert Gotthold 
Published: December 2004

AbstractAbsorption spectra and induced CD have been measured on aqueous solutions of water‐soluble porphyrins with α‐helical poly(L‐glutamic acid) or α‐helical poly (L‐lysine) at different mixing ratios. For the former, porphyrin is porphine‐meso‐tetra (4‐N‐methylpyridinium) (TMpyP), and for the latter, it is porphine‐meso‐tetra (4‐benzenesulfonate) (TPPS) or porphine‐meso‐tetra(4‐benzoate) (TPPC). All the solutions of porphyrin‐polypeptide systems show hypochromism in the Soret band and induced CD in the Soret region. The CD is characterized by a positive band at a shorter wavelength and a stronger negative band at a longer wavelength. The hypochromicity and the magnitude of molar ellipticities are much larger for the TPPS– and TPPC–poly (L‐lysine) systems than for the TMpyP–poly (L‐glutamic acid) system. Porphyrin ions bind to the α‐helix electrostatically, and the two components of the Soret transition of porphyrin are subject to dissymmetric perturbation. TMpyP ions bind to the α‐helix at isolated sites, while TPPS ions and TPPC ions are in pairs on the α‐helix, that is, two ions bind consecutively and dissymmetrically. In the TMpyP–poly (L‐glutamic acid) system a single CD band is associated with each of the two components of the Soret transition, and these are of opposite sign. In the TPPS– and TPPC–poly (L‐lysine) systems, a pair of positive and negative CD bands is associated with each of the two components, thus giving apparently a single pair of CD bands with a shoulder, owing to partial overlapping.
The interaction of auramine O with calmodulin: Location of the binding site on the connecting strand
Authors: Steiner Robert F. , Albaugh Sharon , Nenortas Elizabeth , Norris Lynn 
Published: December 2004

AbstractThe cationic dye auramine O forms a fluorescent complex with Ca2+‐liganded calmodulin. One moderately strong binding site is present, as well as one or more weaker sites. The binding site for auramine O is different from those for toluidinyl‐naphthalene sulfonate. The dependence of binding upon electrolyte concentration suggests a substantial electrostatic component of the free energy of binding. The splitting of the bond between residues 77 and 78 by trypsin digestion abolishes auramine O binding; the N‐ and C‐terminal half‐molecules have virtually no binding capacity. This suggests that the primary binding site is located near the midpoint of the connecting strand and includes elements of both half‐molecules. Thrombin digestion, which splits calmodulin between residues 106 and 107, also substantially reduces auramine O binding; this may be interpreted in terms of the stabilization of the structure of the connecting strand by interaction with residues within binding domain IV. The binding affinity at pH 5.0, where the helical organization of the connecting strand may be intact, is greater than at neutral pH.
The interactions of neuropeptides with membrane model systems: A case study
Authors: Hicks Rickey P. , Beard Debbie J. , Young John K. 
Published: December 2004

AbstractThe interactions between the positively charged neuropeptides substance P (SP), bradykinin (BK), and zwitterionic Met‐enkephalin (ME) neuropeptides, and negatively charged SDS and zwitterionic lysophosphatidylcholine (LPC) membrane model systems, have been investigated using one‐ and two–dimensional nmr experiments. Proton longitudinal relaxation studies were used to characterize these interactions as intrinsic or extrinsic. An extrinsic interaction are similar to those observed for extrinsic membrane proteins. An intrinsic interaction are similar to those observed for intrinsic membrane proteins, and would require that the hydrophobic residues penetrate or insert into the hydrophobic core of the membrane. The interactions between both SP and BK and SDS, based on nmr results, may be characterized as intrinsic, and the interaction between ME and SDS may be characterized as extrinsic. Two–dimensional nuclear Overhauser enhancement spectroscopy experiments proved the insertion of the phenylalanine residues on both SP and BK into the hydrophobic core of SDS micelles. The interaction between SP and BK with LPC based on nmr results are characterized as extrinsic, with the interaction between ME and SDS characterized as weakly intrinsic.
Studies on the yeast α‐mating factor: A model for mammalian peptide hormones
Authors: Naider Fred , Gounarides John , Xue Chu‐Biao , Bargiota Effimia , Becker Jeffrey M. 
Published: December 2004

AbstractSmall peptides initiate sexual conjugation in the yeast Saccharomyces cereuisiae and this phenomenon is an ideal paradigm for studying the mode of action of mammalian peptide hormones, 1H‐nmr spectroscopy was used to examine the conformation of linear and cyclic analogues of the α‐factor (WHWLQLKPGQPMY) in aqueous solution. In all cases peptides that exhibit nmr parameters expected for a type II β‐turn have higher biological activities than those that do not appear to assume this conformation. Based on a simple model for the interaction of the pheromone with its receptor, we prepared fragments of the α‐factor. Several of these fragments either antagonize or potentiate the activity of the α‐factor. The latter represent the first example of peptide fragments that synergize the activity of the parent pheromone.
Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units
Authors: Gerber Paul R. 
Published: December 2004

AbstractThe central ingredient of any structure modeling tool is a molecular model or force field that accounts for proper geometry and energy calculation. For protein and peptide modeling based on entire amino acids as building blocks, we describe a peptide force field in which each amino acid is represented by a single point in space, taken at the position of the α‐carbon atom. Apart from the positional coordinates, these units carry the two torsional angles φ and Ψ as additional degrees of freedom to account for the orientations of the peptide links. While some of the energy terms are analogous to expressions in atomic force fields, the presence of the angular variables leads to fundamental differences with new features and additional terms with no atomic counterparts.The force field reproduces secondary structure elements with very good accuracy. Globular parts of tertiary packing stay near the experimental structures with a rms deviation in C‐α positions of 0.1–0.3 nm and about 25° in φ and Ψ depending on the size of the structure. A tendency for larger discrepancies is observed in exposed loops or terminal segments the conformations of which may be strongly influenced by neighboring domains.Finally, a scope of possible applications is presented. They range from modeling activities, such as model building by homology, to coarse scanning of conformation space in conformation analysis and structure determination. An extension to a dynamics model would offer the possibility to eliminate the less interesting high‐frequency modes that in all‐atom force‐field dynamics absorb most of the computational effort.
Conformations in solution of angiotensin II, and its 1–7 and 1–6 fragments
Authors: Cushman J. A. , Mishra P. K. , Bothner‐By A. A. , Khosla M. S. 
Published: December 2004

AbstractHigh‐resolution proton spectra at 620 MHz of human angiotensin II (1–8), angiotensin II (1–7), and angiotensin II (1–6) have been obtained in aqueous solution at acidic pH, and in dimethylsulfoxide solution. Complete chemical shift assignments for all three angiotensin peptides were made based on two‐dimensional (2D) correlated spectroscopy and 2D‐CA‐MELSPIN spectra. Based on the measured values of 3J HNCH, the pattern of observed transverse Overhauser effects, and side‐chain coupling constants, it is concluded that all three analogues exist in H2O or DMSO‐d6 as a mixture of conformers that is largely extended, with negligible content of folded structures, such as β‐turns, γ‐turns, or helix content. The results fit well with those of Nikiforovich et al.1, 2. © 1992 John Wiley & Sons, Inc.
Shape distributions of protein topography
Authors: Connolly Michael L. 
Published: December 2004

AbstractA method is presented for measuring protein surface shape. It is an improvement of an earlier method that intersects a sphere with the solvent‐excluded volume of a protein molecule. The new method, called a shape distribution, produces a more sophisticated description of the region of the sphere inside the protein than is provided by simply measuring the region's area or solid angle. This method is applied to the prediction of molecular complexes in three systems: the hemoglobin nonallosteric interface, trypsin and trypsin inhibitor, and heme and apomyoglobin. It does not uniquely predict the correct structure, even though the individual structures are taken from the experimentally determined complex structure. However, it does provide a list of several hundred predicted complexes, one of which is correct, and from which the correct complex might be extracted by a subsequent chemical filter. © 1992 John Wiley & Sons, Inc.
Variable ranges of interactions in polypeptide conformations with a method to complement molecular modeling
Authors: Jacchieri S. G. , Jernigan R. L 
Published: December 2004

AbstractFormulations of conformational weights for helix‐coil transitions can be extended to substantially more complex situations than are usually pursued. General rules for matrix multiplication that depend parametrically on the interaction ranges and numbers of rotamers of residues are presented. The orders of the matrices of statistical weights can be increased with chain length, so that an individual matrix element can represent any specified single conformation, as needed. By the appropriate choice of interaction ranges and numbers of available conformers, approximations can be introduced in which: (1) an average of the conformations of any chain segment is obtained, (2) specific residue‐residue interactions are excluded, or (3) the conformation of a part of the chain is restricted or fixed. The method is appropriate for treating specific interactions in peptides and could be used together with available experimental information to develop models of conformational transitions. As such, the methods represent a class of calculations aimed at more rigorous calculations built around known features of a molecule. The aim is to facilitate calculations that bridge the gap between nonquantitative molecular model building and more rigorous but less directed molecular mechanics calculations. The method can directly include any desired longer range of interactions, if the interaction range is not too long to make impossible the manipulation of the requisite matrices. An outline is presented of an application to treat salt bridges in the C peptide of ribonuclease A. © 1992 John Wiley & Sons, Inc.
Nmr studies of an extrahelical cytosine in an A·T rich region of a deoxyribodecanucleotide
Authors: Morden Kathleen M. , Maskos Karol 
Published: December 2004

AbstractOne‐dimensional and two‐dimensional (2D) nmr experiments were carried out on an oligonucleotide duplex that contains an unpaired cytosine, d(GCGAACAAGCG)·d(CGCTTTTCGC), which will be referred to as the C‐bulge decamer. Evidence from one‐dimensional nuclear Overhauser effect (NOE) experiments on the exchangeable protons indicates that the unpaired cytosine is extrahelical. This conclusion is also supported by numerous cross‐peaks in the 2D NOE spectroscopy (NOESY) spectrum of the nonexchangeable protons. The assignments for all of the resonances, with the exception of the H5′ and H5″ resonances, have been made through the use of 2D NOESY, correlated spectroscopy (COSY), and relayed COSY experiments. The temperature dependence of the C(H6) resonance chemical shifts indicates that the unpaired cytosine shows unusual behavior compared to other cytosines in the duplex. A comparison of chemical shifts for all, the assigned resonances of the duplexes with and without the unpaired cytosine suggests that the majority of the structural perturbation is localized in the A·T tract surrounding the unpaired base. The behavior of the imino resonances as a function of temperature also indicates that the perturbation to the duplex is localized and destabilizes the A·T base pairs adjacent to the unpaired base. © 1993 John Wiley & Sons, Inc.
Degree of linear polarization method for determination of intrinsic optical anisotropy of southern bean mosaic virus
Authors: Sano Yoh 
Published: December 2004

AbstractSouthern bean mosaic virus (SBMV) is a spherical plant virus. It possesses an intrinsic (structural) anisotropy due to the orientation of valence bonds of the amino acid and/or nucleic acid residues. According to the light scattering theory of Rayleigh and Gans for optically anisotropic spheres, the degree of linear polarization of the scattered light depends on the intrinsic anisotropy, the relative refractive index of the sphere to the solvent, the scattering angle, and the inclination angle of linearly polarized incident light to the scattering plane. By using the theoretical expression of the degree of linear polarization, the intrinsic anisotropy parameter of southern bean mosaic virus in the compact spherical state was calculated with the appropriate experimental values. This novel method should be useful in elucidating the internal structure of spherical viruses and other spherical complexes of macromolecules. © 1993 John Wiley & Sons, Inc.
Application of distance geometry to the proton assignment problem
Authors: Oshiro C. M. , Kuntz I. D. 
Published: December 2004

AbstractAssignment of the hydrogen spectrum is the first step in the conventional procedure for the determination of molecular structure by 1H‐nmr. In this paper, we explore the possibility of directly exploiting the distances derived from nuclear Overhauser effect experiments to generate a three‐dimensional structure that is then assigned based on knowledge of the connectivity or primary sequence. This effort is analogous to that of the protein crystallographers in tracing electron density of the peptide chain. In particular, we compare structures produced by distance geometry to known peptide secondary structures to see what level of information is required to “trace” the backbone α‐carbon and amide hydrogens and the β‐carbon hydrogens. We conclude that this approach is only useful with excellent quality stereo‐resolved data. © 1993 John Wiley & Sons, Inc.
Kinetic analysis of the hydrodynamic transition accompanying protein folding using size exclusion chromatography. 2. Comparison of spectral and chromatographic kinetic analyses
Authors: Shalongo William , Jagannadham Medicherla , Stellwagen Earle 
Published: December 2004

AbstractThe kinetics of the hydrodynamic volume change associated with the unfolding and refolding of a globular protein can be observed using high performance size exclusion chromatography. Chromatographic profiles that evidence such dynamics can be simulated using equations in which Chromatographic partitioning and the conformational transition are described in terms of a finite difference algorithm incorporating an apparent binding model to generate broad and asymmetric peaks. Application of these equations to the simple two‐state unfolding transition of ribonuclease A in guanidine hydrochloride indicates that reliable kinetic parameters can be obtained using these equations. © 1993 John Wiley & Sons, Inc.
Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization
Authors: Vajda S. , Jafri M. S. , Sezerman O. U. , DeLisi C. 
Published: December 2004

AbstractLow energy conformations have been generated for melittin, pancreatic polypeptide, and ribonuclease S‐peptide, both in the vicinity of x‐ray structures by energy refinement and by an unconstrained search over the entire conformational space. Since the structural polymorphism of these medium‐sized peptides in crystal and solution is moderate, comparing the calculated conformations to x‐ray and nmr data provides information on local and global behavior of potential functions. Local analysis includes standardization calculations, which show that models with standard geometry can approximate good resolution x‐ray data with less than 0.5 Å rms deviation (RMSD). However, the atomic coordinates are shifted up to 2 Å RMSD by local energy minimization, and thus 2 Å is generally the smallest RMSD value one can target in a conformational search using the same energy evaluation models.The unconstrained search was performed by a buildup‐type method based on dynamic programming. To accelerate the generation of structures in the conformational search, we used the ECEPP potential, defined in terms of standard polypeptide geometry. A number of low energy conformations were further refined by relaxing the assumption of standard bond lengths and bond angles through the use of the CHARMM potential, and the hydrophobic folding energies of Eisenberg and McLachlan were calculated. Each conformation is described in terms of the RMSD from the native, hydrogen‐bonding structure, solvent‐acessible surface area, and the ratio of surfaces corresponding to nonpolar and polar residues.The unconstrained search finds conformations that are different from the native, sometimes substantially, and in addition, have lower conformational energies than the native. The origin of deviations is different for each of the three peptides, but in all examples the refined x‐ray structures have lower energies than the calculated incorrect folds when (1) the assumption of standard bond lengths and bond angles is relaxed; (2) a small and constant effective dielectric permittivity (ε < 10) is used; and (3) the hydrophobic folding energy is incorporated into the potential. © 1993 John Wiley & Sons, Inc.