bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer simulation of the conformational properties of retro–inverso peptides. II. Ab initio study, spatial electron distribution, and population analysis of N‐formylglycine methylamide, N‐formyl N′‐acetyldiaminomethane, and N‐methylmalonamide
Authors: Stern P. S. , Chorev M. , Goodman M. , Hagler A. T.
Published: May 2005

Ab initio minimal and split‐valence basis set calculations have been performed on compounds that are involved in retro–inverso modifications, i.e., gem‐diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem‐diaminoalkyl and malonyl derivatives of residues found in the retro‐inverso modified peptides is 5–8 kcal/mol lower than the C conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.
Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. I. Theory and FCS measurements
Authors: Icenogle R. D. , Elson E. L.
Published: May 2005

Fluorescence correlation spectroscopy (FCS) and fluorescence photobleaching recovery (FPR) are two methods that may be used to measure diffusion and chemical reaction kinetics in small, labile systems such as biological cells. These methods are here applied to systems in which a fluorescent ligand can bind to a polyvalent substrate molecule in a multistep reaction sequence. The analytical theory for both FCS and FPR is extended to allow analysis of these kinds of systems. Experimental measurements of the binding of ethidium bromide to DNA by FCS confirm the theoretical analysis. (FPR measurements on the same system are reported in the accompanying paper.) The analysis shows that FCS and FPR perceive multivalent binding reactions differently. This difference results from the selective effect of the photobleaching process in the chemical reaction system. The development and results we report could have useful applications to a wide range of biopolymeric binding and assembly process.
Correlation of Tm, sequence, and ΔH of complementary RNA helices and comparison with DNA helices
Authors: Ornstein Rick L. , Fresco Jacques R.
Published: May 2005

Tm values of 16 fully complementary RNA duplexes with repeating base sequence have been employed as the empirical basis for developing a reliable and practical method for computing apparent enthalpies (ΔHcalc) for their helix → coil transitions. The approach taken is the same as in the accompanying investigation of DNA duplexes, although some of the computational variables of the “best‐fit” function are necessarily different due to the distinguishing structural properties of the RNA‐type helix. An excellent linear correlation was thus obtained between experimental Tm and ΔHcalc values. An equally good fit was obtained between Tm and ΔHcalc for five unrelated (to the 16 RNAs) decaribonucleotide duplexes. The differences in computational variables between the best‐fit methods for RNA and DNA duplexes are shown to be a reflection of differences in cation binding and the effective local dielectric. The greater Tm dependence on G·C content of RNA helices than of DNA helices is shown to be due to a greater latitude of stacking stabilities of complementary dinucleotide fragments containing A·T than A·U base pairs.
Stereochemistry of α‐aminoisobutyric acid peptides in solution: Helical conformations of protected decapeptides with repeating Aib‐L‐Ala and Aib‐L‐Val sequences
Authors: kumar E. K. S. Vijaya , Balaram P.
Published: May 2005

The decapeptides Boc‐(Aib‐L‐Ala)5‐OMe and Boc‐(Aib‐L‐Val)5‐OMe have been studied by 270‐MHz 1H‐nmr in CDCl3 and (CD3)2SO solutions. Intramolecular hydrogen‐bonded NH groups have been delineated using the temperature and solvent dependence of the NH chemical shifts and differential broadening of the NH resonances, induced by addition of a nitroxide radical. Both peptides have eight solvent‐shielded NH groups, suggesting that 310‐helical conformations are maintained in the two solvents. In alternating Aib‐X sequences, the Aib residues appear to play a dominant role in determining the preferred conformations, overriding the intrinsic stereochemical preferences of the X residues.
Hydrodynamic properties of mucous glycoproteins
Authors: Bloomfield Victor A.
Published: May 2005

In order to understand how mucous glycoproteins, or mucins, confer such striking rheological properties on mucous secretions, it is first necessary to understand the structures of the individual glycoproteins and their components. Although significant variability of structure among mucins from different sources is evident, the “bottlebrush” structure is a common motif. For purposes of hydrodynamic calculations, we take the typical mucin monomer to have a molecular weight of 5 × 105, 20% protein and 80% carbohydrate. About 25% of the polypeptide chain is unglycosylated or bare, while the remainder is densely substituted with oligosaccharide chains, averaging about eight sugar residues long. Unless the mucins are treated with S‐S reducing agents, proteases, and denaturants, they are often found to have molecular weights around 2 × 106. Thus, we model the normally occurring form as a tetramer, crosslinked like a star in the bare region.

With these structural ideas as a basis, we have confronted published hydrodynamic data with modern hydrodynamic theories to obtain a picture of mucin molecular structure. To account for the oligosaccharide side chains, we used a treatment developed for partially porous spheres. To model the composite structure of glycosylated and bare regions, we used subunit hydrodynamic theory. To consider the effects of branching, we used published theories for branched random coils and extended the broken‐rod results of Wilemski to cover branched rodlike structures.

The major conclusions are (1) the bare region is probably not highly extended, (2) the glycosylated region is more like a random coil than a rigid rod, and (3) comparison of hydrodynamic properties of monomers and branched tetramers suggests that the monomer is more rigid in the tetramer. This may be due either to understimation of aggregation in the analysis of the experimental data or to a real stiffening effect imposed by polyelectrolyte and steric repulsive interactions with the other chains in the branched mucin.
Polyelectrolyte complexes of glycol chitosan with some mucopolysaccharides: Dielectric properties and electrical conductivity
Authors: Pushpa S. , Srinivasan R.
Published: May 2005

The dielectric properties, DC electrical conductivity, and I‐V characteristics of thin films of polyelectrolyte complexes formed by glycol chitosan (GlChi) with mucopolysaccharides chondroitin sulfate A (CSA), chondroitin sulfate C (CSC), and hyaluronic acid (HA) have been studied at different temperatures. The dielectric constant and the loss factor were measured at frequencies ranging from 1 to 100 kHz at all temperatures. The behavior of GlChi–CSA and GlChi–CSC complexes resembles that of the GlChi–dextran sulfate complex reported earlier. The GlChi–HA complex behaves differently and is similar to the GlChi–alginic acid complex reported [Srinivasan, R. & Kamalam, R. (1982) Biopolymers 21, 251–263, 265–275].
Ethidium binding to deoxyribonucleic acid: Spectrophotometric analysis of analogs with amino, azido, and hydrogen substituents
Authors: Yielding Lerena W. , Yielding K. Lemone , Donoghue Jennifer E.
Published: May 2005

The DNA–ligand interactions of a series of phenanthridinium compounds with various combinations of amino, azido, and hydrogen functions at R3 and R8 were examined to determine the contribution of these particular substituents to ligand binding. Spectrophometric titrations using calf‐thymus DNA emphasized the importance of amino substituents in conferring a strong interaction and also stabilizing the interaction against reversal by high ionic strength. Although azido groups were not as effective as amino groups, they were more effective than hydrogen functions in enhancing the interaction. Furthermore, an amino substitution at R8 was consistently, though only slightly, more effective than an amino substituent at R3. The results from superhelical titrations using plasmid pBR322 DNA demonstrated that analogs with amino and/or azido functions at both R3 and R8 produced the greatest unwinding, and compounds with an amino or an azido function at R8 proved more effective than those with the corresponding amino or azido substituent at R3.
Kinetics of formation of fibrin oligomers. III. Ligation kinetics concurrent with and subsequent to oligomer assembly
Authors: Bale Marsha D. , Janmey Paul A. , Ferry John D. , Lorand Laszlo
Published: May 2005

Human fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ‐γ ligation was determined from the former. The latter provided the size distribution of ligated end‐to‐end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p‐nitrophenyl‐p′‐guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end‐to‐end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ‐γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ‐γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end‐to‐end sequences agreed with a theory based on random ligation of ligatable junctions.
Small‐angle x‐ray scattering studies on yeast inorganic pyrophosphatase and its interactions with divalent metal ions, inorganic phosphate, and hydroxymethane bisphosphonate
Authors: Thiyagarajan P. , Borso C. S. , Banerjee A. , Cooperman B. S.
Published: May 2005

Small‐angle x‐ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
Structure determination of the adduct formed between the signal nucleotide diadenosine 5′, 5‴‐P1, P4‐tetraphosphate (Ap4A) and cis‐[Pt(NH3)2Cl2]
Authors: Segal Evelyne , Girault Jean‐Pierre , Muzard Gabriel , Chottard Geneviève , Chottard Jean‐Claude , Le Pecq Jean‐Bernard
Published: May 2005

Diadenosine 5′,5‴‐P1,P4‐tetraphosphate (Ap4A), an intracellular regulatory nucleotide, has been found to react with the antitumor drug cis‐diamminedichloroplatinum(II) and its aqua derivative to form a single complex. This complex has been purified by high‐performance liquid chromatography and characterized by 1H‐nmr and CD spectroscopy. In this complex, Ap4A takes a very particular conformation. It is an N7‐N7 chelate of the metal with the two adenines in a head‐to‐head arrangement and an anti–anti conformation of the adenosines. Platinum chelation leads to a large decrease of the Ap4A conformational flexibility.
Comments on the “ordinary–extraordinary phase transition” of poly(lysine)
Authors: Schmitz Kenneth S. , Lu Mei , Singh Narinder , Ramsay Donald J.
Published: May 2005

The “ordinary–extraordinary phase transition” of poly(lysine), first reported by Lin et al. [(1978) Biopolymers 17, 1041–1064], has been reexamined as a function of the data collection interval (Δt) and scattering angle (θ). These data suggest that the relaxation domains “split” as the ionic strength is lowered through the transition region. In contrast, fluorescence photobleaching recovery data of Ware and coworkers (personal communication) indicate the tracer diffusion coefficient is not sensitive to the “ordinary–extraordinary phase transition.” The apparent discrepancy between these two techniques is here proposed to be due to small ion effects on both the dynamics and the scattering power of the polyelectrolytes.
Sequential hydration of dry proteins: A direct difference IR investigation of sequence homologs lysozyme and α‐lactalbumin
Authors: Poole P. L. , Finney J. L.
Published: May 2005

Direct difference ir spectra are presented as a function of hydration for lysozyme and α‐lactalbumin, and detailed sequential hydration molecular events identified. Despite the strong sequence homology between the two proteins, and their expected conformational similarity, the hydration behaviour of the polar groups is different for the two proteins. Using a Hill‐type analysis, we conclude that the acid groups ionize and hydrate rapidly and noncooperatively in both proteins, consistent with the known (lysozyme) and postulated (α‐lactalbumin) surface chemistry. The polar group hydration shows a clear cooperativity, which is quantitatively different in the two proteins. Complementary work suggests this cooperativity relates to a hydration‐induced “loosening up” of the lysozyme conformation at about 55 mol water/mol protein. α‐Lactalbumin appears to “open up” more easily for hydration than does lysozyme, consistent with its lower stability against thermal and acid denaturation.
Thermodynamic stability of the ordered conformations of carrageenan polyelectrolytes
Authors: Paoletti Sergio , Smidsrod Olav , Grasdalen Hans
Published: May 2005

Manning's counterion condensation theory has been applied to the temperature‐induced conformational transition of κ‐ and ι‐carrageenan in the solution and gel states. The formalism of the theory has been extended to transitions between conformations with charge densities below or across the counterion condensation threshold. Measurements of the dependence of the melting temperature on ionic strength, and of the enthalpy of melting, are interpreted with the theory as indicating that the conformational transition is intramolecular and that side‐by‐side dimerization of chains gives rise to the gel structure.
Twist and writhing in short circular DNAs according to first‐order elasticity
Authors: Le Bret Marc
Published: May 2005

The distribution of twist and writhing in a closed DNA shorter than its persistence length is examined. In this case, the only energy contribution is elastic. We have in tegrated the equations of elasticity for a homogeneous axially symmetric rod of undeformable infinitely small circular cross section with frictionless reactions, when there is no or only one self‐contact. In the absence of self‐contacts, the central line of the rod is drawn on a toroid. It makes ν turns around the axis of revolution of the toroid and m turns around its core. The integer, ν, is equal to one if the rod is unknotted. We prove that no infinitely thin rod with a positive Poisson ratio is stable in a toroidal conformation if there is no self‐contact. However, m‐leafed roses or rosettes, with but one multiple self‐contact, are shown to actually be stable when their writhing is not too great. When the integer, m, is equal to two, we have figure‐8 conformations. Buckling of the circle into a figure‐8 conformation occurs for the constraint such that the figure‐8 and the circular conformations have the same energy. This constraint is 1.845 turns for a bending‐to‐twisting elastic constants ratio of A/C = 1.5. For the same value of A/C, the figure‐8 conformation is unstable for a constraint greater than 2.4 turns. Corrections caused by a finite value of the radius ratio, a/L, of the cross section to the length of the rod, are estimated. For instance, both the circular conformation and the infinitesimally warped circle are simultaneous solutions for particular values of the β twist. β = A/C (m2 − ν2)½ [1 + (νπa/L)2/2]. The binding of ethidium to DNAs short enough to follow first‐order elasticity has been studied. Buckling occurs at an apparent average constraint of about 0.6. How the DNA molecules are distributed in figure‐8 conformations and circles has been determined as the ethidium concentration is varied.
Diffusion‐controlled protein–DNA association: Influence of segemental diffusion of the DNA
Authors: Berg Otto G.
Published: May 2005

The intrachain reaction theory of Wilemki and Fixman [(1974) J. Chem. Phys. 60, 866–877] is used to assess the influence of internal DNA motions on various protein–DNA association schemes. It is found that, for large proteins, the diffusional association rate can be totally dominated by these motions rather than by the free‐trans‐lational diffusion rates. Also, the time required for the diffusion together of two DNA segments is estimated. This estimate can be used to provide an upper limit for the rate of intrachain cyclization, and also for the effective intrachain transfer rate of a protein bound to a DNA chain.
Theoretical studies on protein–nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments
Authors: Kumar N. Vasant , Govil Girjesh
Published: May 2005

Coulombic interactions between the side chains of charged amino acids (Arg+, Lys+, and His+) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single‐stranded RNA and DNA, respectively. The interaction energies have been calculated by second‐order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys+ and His+ form more stable complexes with RNA than with single‐stranded DNA. On the other hand, Arg+ has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys+ > His+ > Arg+. Further, the basic amino acid residues form more stable complexes with A‐DNA than with B‐DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.
Vibrational analysis of peptides, polypeptides, and proteins. XXIV. Conformation of poly(α‐aminoisobutyric acid)
Authors: Dwivedi Anil M. , Krimm S. , Malcolm B. R.
Published: May 2005

Raman and polarized ir spectra have been obtained on built‐up monomolecular films of poly(α‐aminoisobutyric acid), and analyzed in the context of normal mode calculations on 310‐, α‐, and α′‐helix conformations of this molecule. The average discrepancy between observed and calculated frequencies is significantly smaller for the 310‐helix than for the other structures. This, together with the more satisfactory explanation of several special features of the spectra, indicates that this polypeptide adopts a 310‐helix conformation in such thin films.
Adenylates: Bound and unbound
Authors: Leonard Nelson J.
Published: May 2005

An evaluation is made of the use of adenylate analogs as spatial, dimensional, and fluorescent probes of enzyme‐coenzyme binding sites.
Molecular design of an amplification cascade in vision
Authors: Stryer Lubert
Published: May 2005

The photoexcitation of rhodopsin triggers a cascade that results in the hydrolysis of a large number of molecules of cyclic GMP. The molecular mechanism of this amplification cascade has been delineated. Transducin, a multisubunit perpheral membrane protein, is the information‐carrying intermediate in the activation of the cyclic GMP phosphodiesterase. Photoexcited rhodopsin (R*) castalyzes the exchange of GRP for GDP bound to the α‐subunit of transducin (T). About 500 molecules of Tα‐GTP are formed per absorbed photon at low light levels. Tα‐GTP, rekeased from the β‐ and γ‐subunits of transducin, then activates the phosphodiesterase by relieving an inhibitory constraint imposed by its small sununit. Each actived phosphodiesterase molecule hydrolyzes more than 100 cyclic GMP/s, giving an overall gain of more than 500,000. Photoexcited rhodopsin triggers the activation of a molecule of transducin in a millisecond, which is sufficiently rapid to enable this cascade to participate in visual excitation. Hydrolysis of GTP bound to Tα seves to restore the system to the dark state. Transducin, like the G proteins of the adenylate cyclase casecade, can be specifically ADP‐ribosylated by cholera toxin and pertussis toxin. In both cascades, labling by pertussis toxin blocks the capacity of transducin to interact with the excited receptor, whereas labeling by cholera toxin inhibits the hydrolysis of bound GTP, leading to persistent activation. Moreover, the moleculaar design of the hormone‐triggered cyclic AMP cascade is similar to that of the light‐triggered cyclic GMP cascade. It seems likely that transducin, the stimulatory G protein, the inhibitor G protein, and the ras protein are members of the same family of signal amplifiers. The study of the cyclic nucleotide cascade of vision is providing rewarding views of recurring motifs of signal amplification in nature.
Conformation–function relationships in hydrophobic peptides: Interior turns and signal sequences
Authors: Gierasch L. M. , Rockwell A. L. , Thompson K. F. , Briggs M. S.
Published: May 2005

Two studies are diescribed in which synthetic peptides have been designed and examined to address biochemical problems inherent in hydorphobic environments: (1) The cyclic hexapeptide cyclo‐(D‐Tyr(Bzl)‐Gly‐Ile‐Leu‐Gln‐Pro) was synthesized as a model of an interior β‐turn from the protein lysozyme. Conformational analysis by proton nmr methods, including two‐dimensional nulcear Overhauser effect spectroscopy, revealed that the model peptide adopts one conformation in chloroform/dimethyl sulfoxide (98.2) and tetramethylene sulfone solutions. The conformation consists of two linked β‐turns, one with the same sequence (Gly‐Ile‐Leu‐Gln) and geometry (Type I) as the protein turn. (2) Major portions of the λ‐receptor protein (LamB) signal sequences from E. coli wildtype and mutant strains have been synthesized. The conformational properties and membrane interactions of these synthetic signal peptides correlate with the in vivo export function of the wild type and mutant strains. Functional signal sequences are significantly richer in α‐helix in aaqueous trifluoroethanol, lysolecithin, or sodium do‐decyl sulfate solution than is a nonfunctional mutant signal sequence.
Energetics of protein structure and folding
Authors: Goldenberg David P. , Creighton Thomas E.
Published: May 2005

The available experimental date on the kinetics of unfolding and refolding of small proteins are reviewed. Excluding slow transitions in the unfolded protein due to cis–trans isomerization of peptide bonds, the rate‐limiting transition state in both unfolding and refolding is concluded to be a high‐energy distortion of the fully folded state. Partially folded intermediates are undoubtedly important for folding, but their formation is normally not rate limiting. A simple model is used to illustrate some of the aspects of protein‐folding energetics.
Assembly of fibronection‐containing extracellular matrix: A glimpse of the machinery
Authors: Mosher Deane F. , McKeown‐Longo Paula J.
Published: May 2005

Soluble fibronectin binds specifically and saturably to surfaces of substrate‐attached cells. Bound fibronection is then transferred to the deoxycholate‐insoluble extracellular matrix. During transfer, fibronectin is translocated from the cell surface and organized into disulfide‐bonded multimers by disulfide exchange. Binding is mediated by disulfidelooped, type I homology “fingers” in the amino‐terminal region. Exchange involves disulfides in the same amino‐terminal region.
Diffusion of bovine serum albumin in a neutral polymer solution
Authors: Phillies George D. J.
Published: May 2005

The diffusion coefficient D of bovine serum albumin through various solutions (pH 7.0, 0.5M NaCl) of polythylene oxide (Mw ∼ 1 × 105, 3 × 105) was studied with quasielastic light scattering. In solutions of the 1 × 105 polymer solution at polymer concentrations above 0.5 g/L, D is considerably greater than would have been expected from the viscosity of water:polymer mixtures, the deviations being larger at low protein concentration that at high protein concentration. With either polymer, D falls with increasing protein concentration.
A simple and novel interpretation of the three‐dimensional structure of globular proteins based on quantum‐mechanical computations on small model molecules. I
Authors: Peters David , Peters Jane
Published: May 2005

It is suggested that the three‐dimensional structure of globular proteins is partly determined by a framework of strengthened hydrogen bonds that involves both ionic side chains and water molecules in addition to the polypeptide backbone. This conclusion follows from a combination of the results of ab initio molecular‐orbital computations on small model molecules and high‐accuracy x‐ray data on the rubredoxin molecule. The computations yield the idea of hydrogen‐bonded bridges that are built from tens of atoms, and the experimental information yields the idea that the bridges are assembled into clusters, each of which is built from hundreds of atoms. Some 10 such clusters then form a globular protein.
Efficient monte carlo method for simulation of fluctuating conformations of native proteins
Authors: Noguti Tosiyuki , Gō Noguhiro
Published: May 2005

A powerful Monte Carlo method is described to simulate thermal conformational fluctuations in native proteins by using an empirical conformational energy function in which bond lengths and bond angles are kept fixed and only dihedral angles are independent variables. In this method, collective variables corresponding to eigenvectors of the second‐derivative matrix of the energy function at its minimum point are scaled according to corresponding eigenvalues in such a way that the energy function in terms of the scaled collective variables is isotropic at the minimum point. Simulation is carried out with an isotropic step size in the space of these scaled collective variables. This simulation method is applied to a small protein, bovine pancreatic trypsin inhibitor (BPTI), and its model harmonic system defined by a quadratic energy function with the same second‐derivative matrix as that of BPTI at its minimum point. Efficiency of the simulation method with an isotropic step size in the space of the scaled collective variables is found to be about 500–50 times greater than the conventional method with with an isotropic step in the space of the usual nonscaled variables. One step of this new method generates conformational changes that occur in the real‐time range of 0.05 ps. In a record of 5 × 105 step simulation, the BPTI molecule is observed to migrate beyond a single minimum‐energy region.
Intermolecular association of tetra‐(γ‐benzyl‐L‐glutamate)s in ethylene dichloride solutions
Authors: Imae Toyoko , Ikeda Shoichi
Published: May 2005

Light scattering from ethylene dichloride solutions of tetra‐(γ‐benzyl‐L‐glutamate)s has been measured and their association in solution is examined. One of the peptides is monodisperse o‐nitrophenylthio‐tetra‐(γ‐benzyl‐L‐glutamate) ethylamide prepared by a stepwise condensation method, and the other is low‐molecular‐weight poly(γ‐benzyl‐L‐glutamate) prepared by the N‐carboxyanhydride method with n‐hexilamine initiation at [A]/[I] = 4 and factionated by dosslution in formic acid. Concentration‐dependent association of both peptides occurs noncooperatively, without giving critical micelle concentrations. The aggregate size is small: about 23 for the former tetrapeptide and about 7 for the latter polypeptide. While angular dissymmetry is close to unity, light scattering shows anomalous angular dependence, the intensity being symmetrically low with respect to the scattering angle of 90°. The observed angular dependence is interpreted in terms of the effect of optical anisotropy of peptide units. Formation of the anisotropic phase in concentrated solutions of these peptides is also examined briefy.
Thermodynamic examination of the ordering of lipid hydrocarbon chains in the presence of protein
Authors: Chen Chang‐Hwei , Guard‐Friar Deborah
Published: May 2005

Thermodynamic relationships have been derived to describe the change in the entropy (ΔS) of lipid vesicles in the presence of a protein in terms of experimental quantities, the concentration of protein (C), the temperature (tm), and the enthalpy (ΔH) of the main lipid phase transition. Knowledge of the change in ΔS can provide an insight into the effect of a protein on the ordering of the lipid hydrocarbon chains. For a general case, evaluation of the entropy change requires information on the changes of ΔH and tm with respect to C. In a special cae where tm remains inchanged and (ΔH) varies, the change in ΔS can be represented simply as (ΔHc − ΔHo)/Tm, where the subscripts c and o denote the presence and absence of a protein, respectively. Data for 1,2‐dimyristoyl phosphatidylcholone in the presence of lysozyme was used to illustrate a thermodynamic analysis.
Selective fluorescent labeling at the α‐amino group of bovine pancreatic trypsin inhibitor
Authors: Amir Dan , Varshavski Lidya , Haas Elisha
Published: May 2005

Experimental investigation of protein structure and dynamics by spectroscopic methods using external probes requires attachment of a probe to a well‐defined site and preparation of pure samples. Measurements of efficiency of nonradiative excitation energy transfer can yield very detailed information about the structure of proteins, provided that two different probes are selectively attached to well‐defined sites. We have used specific protection of ε‐amino groups using tert‐butylazidoformate at high pH for covalent attachment of the fluorescent probe 2‐naphthoxyacetic acid at the α‐amino group of bovine pancreatic trypsin inhibitor (BPTI). The product is a chromatoraphically homogenous protein derivative that contains the probe at a dye to protein ratio of 1:1, specifically located at the N‐terminus, and and that retains its full biological activity. The HPLC tryptic peptide map of BPTI has been analyzed, and all the peptide fragments have been identified. Analysis of tryptic fragments of the labled BPTI derivative showed that it was selectively labeled at the N‐terminal amino acid. The probe absorbs in the 310–325‐nm range, which is spectrally distinct from the absorption of the protein, and has a monoexponetial fluorescence decay. These and other charactristics make this probe a good energy donor in transfer‐efficiency measurements.
Sequence and conformational effects on imino proton exchange in A · T‐ and A · U‐containing DNA and RNA duplexes
Authors: Mirau Peter A. , Kearns David R.
Published: May 2005

1H‐nmr relaxation has been used to study the effect of sequence and conformation on imino proton exchange in adenine–thymine (A · T) and adenine–uracil (A · U) containing DNA and RNA duplexes. At low temperature, relaxation is caused by dipolar interactions between the imino and the adenine amino and AH2 protons, and at higher temperature, by exchange with the solvent protons. Although room temperature exchange rates vary between 3 and 12s−1, the exchange activation energies (Eα) are insensitive to changes in the duplex sequence (alternating vs homopolymer duplexes), the conformation (B‐form DNA vs A‐form RNA), and the identity of the pyrimidine base (thymine vs uracil). The average value of the activation energy for the five duplexes studied, poly[d(A‐T)], poly[d(A) · d(T)], poly[d(A‐U)], Poly[d(A) · d(U)], and poly[r(A) · r(U)], was 16.8 ± 1.3 kcal/mol. In addition, we find that the average Eα for the A.T base pairs in a 43‐base‐pair restriction fragment is 16.4 ± 1.0 kcal/mol. This result is to be contrasted with the observation that the Eα of cytosine‐containing duplexes depends on the sequence, conformation, and substituent groups on the purine and pyrimidine bases. Taken together, the data indicate that there is a common low‐energy pathway for the escape of the thymine (uracil) imino protons from the double helix. The absolute values of the exchange rates in the simple sequence polymers are typically 3–10 times faster than in DNAs containing both A · T and G · C base pairs.
Model computations on the differential scattering of circularly polarized light (CIDS) by dense macromolecular particles
Authors: Keller David , Bustamante Carlos , Maestre Marcos F. , Tinoco Ignacio
Published: May 2005

Circular intensity differential scattering (CIDS) patterns have been calculated for two general types of chiral arrangements. The calculations were done using the second Born approximation. The geometries considered are (a) a linear array of anisotropic scattering groups with a spiraling orientation (a twisted ladder) and (b) a helical array of scattering groups with arbitrary anisotropy and orientation. The CIDS expressions for the first of these models (twisted ladder) reduces to a simple analytical form and clearly illustrates many properties of CIDS patterns. The second geometry (helix) is more general. Calculations were done for oriented scatterers and for rotationally averaged scatterers as would be found in solution.
Vibrational circular dichroism in amino acids and peptides. 10. Fourier transform VCD and Fourier self‐deconvolution of the amide I region of poly(γ‐benzyl‐L‐glutamate)
Authors: Lipp Elmer D. , Nafie Laurence A.
Published: May 2005

Vibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamate), using a Fourier transform ir VCD spectrometer operating at 4‐cm−1 resolution. These results reveal a new negative VCD band at 1650 cm−1 in addition to the previously observed negative positive VCD couplet centered at 1660 cm−1. Fourier self‐deconvolution (FSD) of the VCD spectrum reveals three strong VCD component bands, rather than just two, as originally supposed. FSD also resolves the absorbance spectrum into two components corresponding to the parallel polarized A mode at lower frequency, and an unresolved perpendicular polarized E1 mode at higher frequency. The VCD spectrum is reassigned on the basis of this new spectral data and the FSD‐VCD results are analyzed for the Moffitt contribution and the so‐called helical contribution. Comparison with theory shows the VCD to be more intense than expected, particularly for the helical term. Charge flow between subunits is suggested as an additional source of VCD intensity that is presently not included in theoretical exciton descriptions. The splitting of the E1 mode and the large VCD contribution attributed to the helical term implies a deviation of the polypeptide structure from perfect helical symmetry and, as a result, a mixing of the A and E1 vibrational modes.
Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
Authors: Brooks C. L. , Brünger Axel , Karplus M.
Published: May 2005

The stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are discussed.
Thermotropic behavior of dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase
Authors: Chen Chang‐Hwei , Guard‐Friar Deborah , Yu Chang‐An
Published: May 2005

The thermotropic behavior of lipid vesicles prepared from dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase has been studied by highly sensitive differential scanning microcalorimetry. This protein has a remarkable effect on the gel–liquid crystalline transition of dimyristoylphosphatidylcholine. In the presence of cytochrome c oxidase, the thermogram of the lipid vesicles exhibits a second endothermic peak, which is adjacent to the main lipid phase‐transition peak and appears at a higher temperature. As the concentration of added protein increases, the two endothermic peaks become further separated, and the transition temperatures and the heats of transition corresponding to both endothermic peaks decrease. A greater decrease in the transition temperature at the lower‐temperature peak with added protein suggests that the lower‐temperature peak is more perturbed than the higher‐temperature peak. The higher‐temperature peak is not thermally reversible. Treatment of sample well above the transition temperature results in a reduction of the magnitude of the higher‐temperature peak. The lipid–protein interaction contributing to the higher‐temperature peak is discussed.
Quasielastic light scattering from long rigid rods
Authors: Hallett F. R. , Nickel B. , Craig T.
Published: May 2005

The purpose of this work was to improve our understanding of quasielastic light scattering from long rigid rods (QL >> 1). For these scatterers, only small angular displacements are required to produce dephasing of the scattering light. This plus the fact that only rods lying perpendicular to Q contribute to the scattered light allow one to simplify the intermediate scattering function to an analytic form. This form is shown to be nonexponential, exhibiting (t)−½ behavior at long delay times. This new scattering function can then be fit to experimental functions using standard methods.
Use of buildup and energy‐minimization procedures to compute low‐energy structures of the backbone of enkephalin
Authors: Vásquez Max , Scheraga Harold A.
Published: May 2005

A method for the conformational analysis of a polypeptide, using buildup and energy‐minimization procedures, is presented. It has been tested by computing the conformation of the backbone of Met‐enkephalin, a pentapeptide, and comparing the results with those obtained by a Monte Carlo procedure. The agreement between the results of the two different methods indicates that the multiple‐minima problem has been overcome for the enkephalin molecule (with fixed side‐chain conformations). The buildup procedure uses objective criteria, which should be applicable to the conformational analysis of polypeptides much larger than enkephalin. With anticipated advances in supercomputers, the methodology should be applicable to proteins.
Quaternary structure of elastin: Characterization of multichain peptide fragments obtained by elastase digestion
Authors: Serafini‐Fracassini A. , Field J. M. , Campbell A. M. , Hunter J. C.
Published: May 2005

Enzyme‐purified elastin from bovine ligamentum nuchae was digested with elastase in the presence of sodium dodecyl sulfate. Chromatographic fractionation of the digest, after removal of the detergent, resulted in the high‐yield isolation of two peptide fractions (F2 and F3) that differed in size and composition. The larger, F2, which accounted for about 55% of the starting material, was subjected to sedimentation‐equilibrium analysis in three chaotropic solvents. Comparison of the distribution of point‐average molecular weights (Mw and Mz) with protein concentration in the three systems lead to the conclusion that significant self‐association of peptides occurred in the absence of 6M guanidinium hydrochloride. In this solvent, the molecular‐weight distribution was between 25,000 and 34,000, a range of values in agreement with an intrinisic viscosity of 13.1 cc g−1 determined in the same solvent. Assessment of chain weight by N‐ and C‐terminal analysis was consistent with F2 being a multichain molecule comprising four polypeptide chains linked by three polyfunctional amino acids. Results are interpreted in terms of an anisotropic ultrastructural model of the protein, in which four polypeptide chains constitute the primary filament visualized by electron microscopy in the intact fiber.
Binding of ethidium to bacteriophage T7 and T7 deletion mutants
Authors: Griess Gary A. , Serwer Philip , Horowitz Paul M.
Published: May 2005

Equilibrium binding of ethidium, quantitated by fluorescence enhancement, to DNA packaged in bacteriophage T7 and T7 deletion mutants has been compared with the binding of this dye to DNA released from its capsid (free DNA). During achievement of apparent equilibrium binding, no change in bacteriophage T7 structure occurred, by the criterion of agarose gel electrophoresis. However, excessive incubation with ethidium bromide caused detectable changes in bacteriophage structure, a possible explanation of disagreements in similar studies previously performed with T‐even bacteriophages. Scatchard plots for packaged DNA had a curvature greater than the previously demonstrated [Bresloff, J. L. & Crothers, D. M. (1981) Biochemistry 20, 3547–3553] curvature for free DNA. By treating plots for packaged DNA as though they were biphasic, it was found that binding to most sites occurred with an apparent association constant (Kap) 3.3–4.3 times lower than the Kap of free DNA. The number of these sites increased significantly as the density of packaged DNA was decreased by use of the deletion mutants. Values of ΔH° for these sites were negative and equal to the ΔH° for free DNA; values of ΔS° were positive and about half the ΔS° for free DNA. A second class of sites, roughly 1.2% of the total, had a significantly higher Kap and more negative ΔH° than those of the majority of sites.
The role of hydrophobic bonding in collagen fibril formation: A quantitative model
Authors: Wallace Donald
Published: May 2005

A model has been developed for approximating the free energy of collagen fibril formation (ΔFf) and the equilibrium solubility of collagen under physiological conditions. The model utilizes an expression of Flory for rodlike polymers, with the modification that the “pure” anisotropic phase is defined as a collagen fibril containing about 0.3 g water/g collagen. The model also assumes that χ1, the polymer–solvent interaction term, is entirely due to hydrophobic effects. χ1 is estimated from hydrophobic bond energies of amino acid side chains, using the results of Némethy and Scheraga. The temperature dependence of χ1 is utilized to calculate equilibrium solubilities and ΔFf as a function of temperature.
Conformational behavior of α,α‐dialkylated peptides
Authors: Barone Vincenzo , Lelj Francesco , Bavoso Alfonso , Di Blasio Benedetto , Grimaldi Patrizio , Pavone Vincenzo , Pedone Carlo
Published: May 2005

The preferred conformations of N‐acetyl‐N′‐methyl amides of some dialkylglycines have been determined by empirical conformational‐energy calculations; minimum‐energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low‐energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the Cα, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the Cα atom: In particular, helical structures are favored by standard values (111°) of the N‐Cα‐C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α‐di‐n‐propylglycine.
Unified representation of helical parameters: Application to polysaccharides
Authors: Perez Serge , Vergelati Caroll
Published: May 2005

A unified representation of helical parameters (n,h) based on a polar mapping is proposed. Its application to the case of polysaccharides allows a straightforward comparison of all secondary structures displayed by this class of biopolymers in the solid state. Based on the concept that a disordered state of a polymer may be described by a succession of local helical parameters, the application of this unified representation has been extended to the simulation of chain behavior in solution.
Molecular mechanical calculations on the interaction of ethidium cation with double‐helical DNA
Authors: Lybrand Terry , Kollman Peter
Published: May 2005

Molecular mechanical calculations were done on complexes of ethidium cation with various base‐paired deoxydinucleoside monophosphates [(ApT)2, (TpA)2, (A2 · T2), (GpC)2, (CpG)2, and (G2 · C2)] and deoxyhexanucleoside pentaphosphates [(ATATAT)2, (TATATA)2, (A6 · T6), (GCGCGC)2, (CGCGCG)2, and G6 · C6]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all‐atom force field) gave results in good agreement with previous calculations and experimental work. Less‐sophisticated models did not perform as well.
Noncooperative temperature melting of a globular protein without specific tertiary structure: Acid form of bovine carbonic anhydrase B
Authors: Brazhnikov E. V. , Chirgadze Yu. N. , Dolgikh D. A. , Ptitsyn O. B.
Published: May 2005

Heat denaturation of native globular proteins is a cooperative process usually connected with the melting of the main part of their regular secondary structure. In this paper, a noncooperative temperature‐induced melting of the regular secondary structure in the carbonic anhydrase B at pH 2.6 in heavy water is observed by ir spectroscopy. The molecules of carbonic anhydrase B in an acid medium, unlike the native ones, do not have a specific tertiary structure. Nevertheless, the β‐structure content is about the same in both of these states. A temperature‐induced noncooperative melting process takes place from 10 to 67°C with a decrease of the antiparallel β‐form content by about one third. The remaining part of the β‐form melts with a more intensive heat absorption, with a maximum at 87°C. The whole melting process is practically reversible. We assume that the observed noncooperative process displays a general property of a new type of structural state of the globular protein—the “molten globule state.”