Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

High-dimensional assembly depending on polyoxoanion templates, metal ion coordination geometries, and a flexible bis(imidazole) ligand

By introducing the flexible 1,1'-(1,4-butanediyl)bis(imidazole) (bbi) ligand into the polyoxovanadate system, five novel polyoxoanion-templated architectures based on [As8V14O42](4-) and [V16O38Cl](6-) building blocks were obtained: [M(bbi)(2)](2)[As8V14O42(H2O)] [M = Co (1), Ni (2), and Zn (3)], [Cu(bbi)](4)[As8V14O42(H2O)] (4), and [Cu(bbi)](6)[V16O38Cl] (5). Compounds 1-3 are isostructural, and they exhibit a binodal (4,6)-connected 2D structure with Schlafli symbol (3(4)center dot 4(2))(3(4)center dot 4(4)center dot 5(4)center dot 6(3))(2), in which the polyoxoanion induces a closed four-membered circuit of M-4(bbi)(4). Compound 4 exhibits an interesting 3D framework constructed from tetradentate [As8V14O42](4-) cluster anions and cationic ladderlike double chains. There exists a bigger M-8(bbi)(6)O-2 circuit in 4. The 3D extended structure of 5 is composed of heptadentate [V16O38Cl](6-) anions and flexural cationic chains; the latter consists of six Cu(bbi) segments arranged alternately. It presents the largest 24-membered circuit of M-24(bbi)(24) so far observed made of bbi molecules and transition-metal cations. Investigation of their structural relations shows the important template role of the polyoxoanions and the synergetic interactions among the polyoxoanions, transition-metal ions, and flexible ligand in the assembly process.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Monte Carlo simulation of the aggregation of rod-flexible triblock copolymers in a thin film

The aggregation of rod-flexible ABA and BAB triblock (A was rod block and repulsive with block B) copolymers in a thin film was studied as a function of varying the rigidity (eta) and the length of the rod block by Monte Carlo simulation. The rigidity of block A was defined as eta = R-c/R-max in this study. R-c, was the end-to-end distance below which the conformation of the block was not allowed, whereas R-max, was the longest end-to-end distance that the block could be. If eta = 0 the block was flexible, whereas if eta = 1 the block was a straight rod. The simulation results showed that the ABA triblock copolymer film were likely to form lamella structure with increasing the rigidity (eta) of block A. The lamellas were parallel each other and perpendicular to the film surface. However, the aggregation of BAB triblock copolymers tended to change from lamella to cylinder structure with increasing the rigidity (eta) of block A. Typical lamella and cylinder co-exist structure was obtained at eta = 0.504 for the BAB copolymer film. On the other hand, the simulation results indicated that the film changed from disorder to order, then to disorder structure with increasing the relative length of B block for both ABA and BAB copolymer films.

Lanthanide coordination polymers with dicarboxylate-like ligands: crystal structures of polymeric lanthanum(III) and terbium(III) complexes with flexible double betaines

Four novel polymeric lanthanide(III) complexes of two new double betaine derivatives have been synthesized and structurally determined. In [{La-2(L-1)(2)(H2O)(9)}(n)]Cl-6n. 2nH(2)O (1) and [{Tb(L-1)(H2O)(4)}(n)]Cl-3n. nH(2)O (2) (L-1 =4,4'-trimethylenedipyridinio-N,N'-diacetate), the lanthanide(III) ions form a two-dimensional layer in which each pair of lanthanide(III) ions is bridged by two syn-anti mu-carboxylato-O,O' groups. Adjacent layers are cross-linked through hydrogen bonds among aqua ligands, lattice water molecules and chloride ions, to form a three-dimensional network. Isomorphous [{Ln(L-1)(H2O)(4)}(n)]Cl-3n. 5nH(2)O (Ln=La, 3; Ln=Tb, 4; L-2=1,3 bis(pyridinio-4-carboxylato)-propane) each contain a centrosymmetric paddle-wheel-like dimeric unit in which each pair of adjacent metal atoms is bridged by four syn-syn mu-carboxylato-O,O' groups that are oriented nearly perpendicular to each other about the metal-metal axis. Neighboring dimeric subunits are bridged by a pair of flexible LL ligands into a polymeric chain. Adjacent chains are inter-linked by hydrogen bonds among aqua ligands, lattice water molecules and chloride ions into a three-dimensional network. (C) 1999 Elsevier Science Ltd. All rights reserved.

Synthesis and structural characterization of a novel polymeric praseodymium(III) complex with a new flexible double betaine

A novel polymeric Pr(III) complex with a new double betaine, namely [{Pr(L-1)(1.5)(H2O)(2)}(n)] [ClOli4]3(n). nH(2)O (1) (L-1= 1,4-diazoniobicyclo[2,2,2]octane- 1,4-dipropionate), has been synthesized and characterized by X-ray analysis. In the title complex, the Pr(III) atom is nine-coordinated by seven oxygen atoms from five L-1 ligands and two aqua ligands. Each pair of adjacent praseodymium(III) atoms is linked by a pair of mu(3) chelating and bridging carboxylate groups, thus forming an infinite metal metal chain running parallel to the a direction, and such chains are cross-linked by flexible backbones of L-1 ligands into a three-dimensional network with the perchlorate anions and lattice water molecules accommodated in the interstitial space. The title complex crystallizes in the monoclinic space group P2(1)/n with a = 8.085(2), b = 14.316(3), c = 29.775(6) Angstrom, beta = 103.04(3)degrees and Z = 4.

Optical anisotropy of flexible polyimide thin films

Optical anisotropy of thin films of an organo-soluble flexible polyimide based on 1,4-bis(3,4-dicarboxyphenoxy) benzene dianhydride (HQDPA) and 2,2-dimethyl-4,4'-methylene dianiline (DMMDA) was detected by a prism-coupler technique. A mechanism is proposed, based on the model of gel film collapse. The degrees of optical anisotropy of the thin films were evaluated via the level of negative birefringence. The residual solvent in the films lessens the levels of negative birefringence so that the residual solvent must be evacuated. The levels of negative birefringence are independent on the solid content of the initial solution, but dependent on the thickness of the films. For a film of 16 mu m thick, zero birefringence was achieved, postulated from the dependence of negative birefringence on the thickness of thin films. The relationship between the optical anisotropy and solution properties shows that the degrees of optical anisotropy of thin films on the same scale of thickness depend on macromolecular sizes in their dilute solutions.

Synthesis and miscibility studies of rodlike flexible polyimide molecular composites via para-para linked aromatic poly(amic ester) precursors

Para-para linked aromatic poly(amic ester) precursors of rodlike polyimide (PI) BPDA-PDA and polyetherimide (PEI) HQDPA-ODA were synthesized. The para-para linked poly(amic ester)s were employed in this work to obtain, in theory, full-imidized polyimides. The two precursors were mixed by dissolving them in N, N'-dimethyl acetamide and subsequently coagulating in methanol. After thermal imidization, the miscibility behaviour of the resulting composites has been studied by means of dynamic mechanical analysis (d.m.a.) and differential scanning calorimetry (d.s.c.). The composites show a single glass transition temperature (T-g) at both d.m.a. and d.s.c. in which the T-g increases with increasing PI content. These Tg values are reproducible in repeated heating cycles, suggesting the true miscibility of the blends. (C) 1997 Elsevier Science Ltd.

SPECTROPHOTOMETRIC DETERMINATION OF LANTHANUM AND SUM OF OTHER LIGHT RARE-EARTHS BY FLEXIBLE TOLERANCE SIMPLEX-METHOD

The absorptivities of color elements in a mixture can be obtained by using Gauas' elimination with selection of principal element in matrix to the standards. These values can be applied to flexible tolerance simplex method to give the composition of samples. In the exprimental design and data treatment, an effort was made to minimize the errors of results according the principal of optimization. When the difference of absorptivities of color material is significant to the exprimental error, the pr...

A Scheduling Algorithm for Flexible Manufacturing Cell

In this paper, a new scheduling algorithm for the flexible manufacturing cell is presented, which is a discrete time control method with fixed length control period combining with event interruption. At the flow control level we determine simultaneously the production mix and the proportion of parts to be processed through each route. The simulation results for a hypothetical manufacturing cell are presented.

Minimizing Residual Vibrations in Flexible Systems

Residual vibrations degrade the performance of many systems. Due to the lightweight and flexible nature of space structures, controlling residual vibrations is especially difficult. Also, systems such as the Space Shuttle remote Manipulator System have frequencies that vary significantly based upon configuration and loading. Recently, a technique of minimizing vibrations in flexible structures by command input shaping was developed. This document presents research completed in developing a simple, closed- form method of calculating input shaping sequences for two-mode systems and a system to adapt the command input shaping technique to known changes in system frequency about the workspace. The new techniques were tested on a three-link, flexible manipulator.

Shaping Inputs to Reduce Vibration in Flexible Space Structures

Future NASA plans to launch large space strucutres solicit the need for effective vibration control schemes which can solve the unique problems associated with unwanted residual vibration in flexible spacecraft. In this work, a unique method of input command shaping called impulse shaping is examined. A theoretical background is presented along with some insight into the methdos of calculating multiple mode sequences. The Middeck Active Control Experiment (MACE) is then described as the testbed for hardware experiments. These results are shown and some of the difficulties of dealing with nonlinearities are discussed. The paper is concluded with some conclusions about calculating and implementing impulse shaping in complex nonlinear systems.