Single chain force spectroscopy - Reading the sequence of HP protein models

We study the elastic properties of single A/B random copolymer chains, with a specific sequence and use them as theoretical model for so called HP proteins. HP proteins carry hydrophilic (P) and hydrophobic (H) monomers. We predict a rich structure in the force-extension relations which can be attributed to the information in the sequence. The variational method is used to probe local minima on the path of stretching and releasing for the chain molecules. At a given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, the unfolding path shows a stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain, resulting in a different path of collapse. The long-range interactions and stiffness of the chain simplify the potential landscape given by the disorder in sequence. Received 5 March 2002 / Received in final form 16 May 2002 Published online 13 August 2002     

Synthesis of temperature-sensitive micron-sized monodispersed composite polymer particles and its application as a carrier for biomolecules

 Temperature-sensitive micron-sized monodispersed composite polymer particles were prepared by seeded copolymerization of dimethylaminoethyl methacrylate and ethylene glycol dimethacrylate with 1.77 μm-sized monodispersed polystyrene seed particles. The change in surface property at temperature above and below 35 °C was examined by differential scanning calorimetry, trypsin activity and the adsorption/ desorption behaviors of low molecular weight cationic emulsifier as well as biomolecules. Received: 6 August 1997 Accepted: 16 January 1998     

Magnetic Resonance Access to Transiently Formed Protein Complexes

Protein–protein interactions are of utmost importance to an understanding of biological phenomena since non-covalent and therefore reversible couplings between basic proteins leads to the formation of complex regulatory and adaptive molecular systems. Such systems are capable of maintaining their integrity and respond to external stimuli, processes intimately related to living organisms. These interactions, however, span a wide range of dissociation constants, from sub-nanomolar affinities in tight complexes to high-micromolar or even millimolar affinities in weak, transiently formed protein complexes. Herein, we demonstrate how novel NMR and EPR techniques can be used for the characterization of weak protein–protein (ligand) complexes. Applications to intrinsically disordered proteins and transiently formed protein complexes illustrate the potential of these novel techniques to study hitherto unobserved (and unobservable) higher-order structures of proteins.     

Multivalent ions and biomolecules: Attempting a comprehensive perspective

Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca²⁺, to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the “atomistic/molecular” local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.     

活细胞内单个大分子的行为

以往细胞内大分子活动的研究,多数是许多分子活动的一个平均结果,即一种集群平均（ensemble averaging）的结果,随着各种技术,特别是光学及荧光检测技术的成熟,实时视见活细胞内单个大分子的时代已经到来.在现时条件下,有许多方法可供选择,如荧光共振能量转移、原子力显微镜、全内反射显微技术、荧光相关光谱法等等.“活细胞内单个大分子的行为”的研究有可能为了解活细胞内单个分子的活动带来完全新的认识,但目前还存在不少方法学上的局限性,有待进一步提高,如有效的特异标记物、细胞深部荧光的检测、新型显微镜的开发等.     

Heteroleptic ruthenium bioflavonoid complexes: from synthesis to in vitro biological activity

Heteroleptic ruthenium(II) bioflavonoid complexes of quercetin, morin, chrysin, and 3-hydroxyflavone were prepared and their interaction with CT DNA and BSA along with antioxidant and in vitro anticancer and antimicrobial activities was investigated. The formulation and characterization of complexes were achieved through elemental and thermal analysis, mass spectrometry, ¹H NMR spectroscopy along with infrared, electronic absorption, and emission spectroscopy as well as square-wave voltammetry, and magnetic and conductivity measurements. Ruthenium(II) is octahedrally coordinated in cationic complex species to two bidentate diimine ligands (2,2′-bipyridine or 1,10-phenanthroline) and one bidentate monobasic flavonoid ligand through 3,4-site of quercetin, morin, and 3-hydroxyflavone or 4,5-site of chrysin. Complexes bind CT DNA by intercalation and binding constants comparable to ethidium bromide or 10 times higher. Binding constants of complexes to BSA were several times higher compared to ibuprofen and diazepam, and suggest that the complexes have a strong affinity to BSA. Antioxidant activity tests showed that the complexes are more potent in terms of radical inhibition compared to the parent flavonoids. Cytotoxic testing revealed that the Ru(II) complex of quercetin with 2,2′-bipyridine co-ligand has good selectivity to breast adenocarcinoma, while the complex of 3-hydroxyflavone with 2,2′-bipyridine co-ligand showed strong cytotoxicity toward all tested cell lines with IC₅₀ ～ 1 μM. All complexes showed moderate activity toward Acinetobacter baumannii, while the Ru(II) complex of 3-hydroxyflavone with 2,2′-bipyridine showed excellent activity toward MRSA and Candida albicans.     

Elucidating the Structure of Chiral Molecules by using Amplified Vibrational Circular Dichroism: From Theory to Experimental Realization

Recent experimental observations of enhanced vibrational circular dichroism (VCD) in molecular systems with low‐lying electronically excited states suggest interesting new applications of VCD spectroscopy. The theory describing VCD enhancement through vibronic coupling schemes was derived by Nafie in 1983, but only recently experimental evidence of VCD amplification has demonstrated the extent to which this effect can be exploited as a structure elucidation tool to probe local structure. In this Concept paper, we give an overview of the physics behind vibrational circular dichroism, in particular the equations governing the VCD amplification effect, and review the latest experimental developments with a prospective view on the application of amplified VCD to locally probe biomolecular structure.