Helix coil mixing in twist-storing polymers

Twist-storing polymers respond with elastic energy penalty to coherent or random twisting along the local chain axis away from its equilibrium, which can be straight (as in “ribbons”) or helical (as in DNA and other biopolymers). Here we study the equilibrium conformation of such polymers, focusing on the thermodynamic balance between twist and writhe, resulting from the competition between the random coil entropy and the potential energy stored in superhelical portions of the polymer chain. Two macroscopic variables characterise such a chain, the end-to-end distance R and the link number Lk, which is a topological invariant of a given polymer with clamped ends. We find that with increasing link number Lk, the chain accommodates its excess twist in growing plectonemes, unless forced out of this state by stretching its end-to-end distance R. We calculate the force-extension relation, which exhibits crossovers between different deformation regimes. Received 16 November 2000 and Received in final form 6 February 2001     

Direct measurement of electron transport features in cytochrome c via V–I characteristics of STM currents

The morphology of and electron tunneling through single and cluster cytochrome c molecules deposited on self-assembled dodecanthiol monolayer film on a gold substrate have been studied experimentally using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy. STM images of a single cytochrome c molecule revealed a globular structure with a diameter of 4 nm and height of 1.5 nm. A spectroscopic study obtained by recording tunneling current–bias voltage (V–I) curves revealed that the STM current increases stepwise at asymmetric threshold sample bias voltages of +100 mV and –200 mV.     

冷冻电镜技术应用于生物分子高分辨结构解析——2017年诺贝尔化学奖浅谈

The 2017 Nobel Prize in chemistry was awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for their contribution to developing the cryo-electron microscopy (cryo-EM) method for high-resolution structure determination of biomolecules in solution. In recent years, cryo-EM is leading a revolution in structural biology, and becoming a major tool in studying the structure and function of biomolecular machines. Here, we briefly describe the method development of cryo-EM and the personal contributions of the three Nobel Laureates.     

Force mode atomic force microscopy as a tool for protein folding studies

The advent of a new class of force microscopes designed specifically to “pull” biomolecules has allowed non-specialists to use force microscopy as a tool to study single-molecule protein unfolding. This powerful new technique has the potential to explore regions of the protein energy landscape that are not accessible in conventional bulk studies. It has the added advantage of allowing direct comparison with single-molecule simulation experiments. However, as with any new technique, there is currently no well described consensus for carrying out these experiments. Adoption of standard schemes of data selection and analysis will facilitate comparison of data from different laboratories and on different proteins. In this review, some guidelines and principles, which have been adopted by our laboratories, are suggested. The issues associated with collecting sufficient high quality data and the analysis of those data are discussed. In single-molecule studies, there is an added complication since an element of judgement has to be applied in selecting data to analyse; we propose criteria to make this process more objective. The principal sources of error are identified and standardised methods of selecting and analysing the data are proposed. The errors associated with the kinetic parameters obtained from such experiments are evaluated. The information that can be obtained from dynamic force experiments is compared, both quantitatively and qualitatively to that derived from conventional protein folding studies.     

A study on the production of PMMA/P(MMA-AAm) composite polymer particles and the effect of acrylamide content on the adsorption behaviors of biomolecules

 A series of poly(methyl methacrylate)/poly(methyl methacrylate-acrylamide) composite polymer particles was prepared with varying proportions of acrylamide in the copolymer shell layer. Adsorption behaviors of some biomolecules and specific activity of adsorbed trypsin were studied. The hydrophobic interaction between the composite polymer particle surfaces and biomolecules decreased with increasing acrylamide content. Received: 7 February 2001 Accepted: 16 May 2001     

Integration of microcolumns and microfluidic fractionators on multitasking centrifugal microfluidic platforms for the analysis of biomolecules

This work demonstrates the development of microfluidic compact discs (CDs) for protein purification and fractionation integrating a series of microfluidic features, such as microreservoirs, microchannels, and microfluidic fractionators. The CDs were fabricated with polydimethylsiloxane (PDMS), and each device contained multiple identical microfluidic patterns. Each pattern employed a microfluidic fractionation feature with operation that was based on the redirection of fluid into an isolation chamber as a result of an overflow. This feature offers the advantage of automated operation without the need for any external manipulation, which is independent of the size and the charge of the fractionated molecules. The performance of the microfluidic fractionator was evaluated by its integration into a protein purification microfluidic architecture. The microfluidic architecture employed a microchamber that accommodated a monolithic microcolumn, the fractionator, and an isolation chamber, which was also utilized for the optical detection of the purified protein. The monolithic microcolumn was polymerized “in situ” on the CD from a monolith precursor solution by microwave-initiated polymerization. This technique enabled the fast, efficient, and simultaneous polymerization of monoliths on disposable CD microfluidic platforms. The design of the CD employed allows the integration of various processes on a single microfluidic device, including protein purification, fractionation, isolation, and detection.      

Characterization of gold nanoparticle bioconjugation by resonance light scattering correlation spectroscopy

<正>Gold nanoparticles(GNPs) have been widely used as probes and nanomaterials in certain biological and biomedical fields thanks to its special physical and chemical properties.However,it is still difficult to characterize GNPs-bioconjugates in solution,which has greatly limited further bioapplications of GNPs.In this study,we reported a single particle method for characterizing GNPsbiomolecules in solution using resonance light scattering correlation spectroscopy(RLSCS).The interaction of GNPs with bovine serum albumin(BSA) and thiol-modified oligonucletides were investigated.     

A new numerical method for nonlocal electrostatics in biomolecular simulations

The electrostatic behavior of biomolecules solved in water can be described by an elliptic system of partial differential equations for the potential. In previous studies, this system has been solved by the Boundary Element Method (BEM).     

SURFACE MODIFICATION OF POLYMERS

The principal objectives and methods of surface modification of polymers are reviewed inthis paper. The methods covered include physical, chemical, mechanical and biological.     

Self-assembly and structure transformations in living polymers forming fibrils

The classical isodesmic one-dimensional model for equilibrium polymerization is generalized in order to describe self-assembly in systems forming fibrils. The model was applied to peptide solutions forming -sheet tapes which can further aggregate into stacks of various thickness: double tapes and fibrils (several double tapes stacked together). We found that in some cases the model yields several step-like transitions as the concentration increases: first from monomers to single or double tapes, and then to fibrils. The abruptness of the first transition is controlled by the free energy penalty for transformation of a peptide from random coil to a straight -strand conformation (the latter is characteristic for tapes). If both single and double tapes are allowed, the length of the aggregates after the first transition can be very large with high scission energies. For very low energies of attraction between double tapes, the transition from double tapes to fibrils happens separately (above the first transition), and it is even more abrupt and produces extremely long fibrils. The theoretical findings are used to extract the characteristic molecular parameters for the self-assembly of the de novo peptide DN1 forming polymeric -sheets in water. Received 28 June 1999