Artificial allosteric control of maltose binding protein

We demonstrate the allosteric control of a protein based on mechanical tension. When substrate binding is accompanied by a significant change of conformation of the protein, a mechanical tension favoring one or the other conformation will alter the binding affinity for the substrate. We have constructed a chimera where the two lobes of the maltose-binding protein are covalently coupled to the ends of a DNA oligomer. The mechanical tension on the protein is controlled externally by exploiting the difference in stiffness between single stranded and double stranded DNA. We report that the binding affinity of the protein for its substrates is significantly altered by the tension.     

Allosteric control through mechanical tension

Conformational changes of proteins modulate their function. In allosteric control, the conformational change is induced by the binding of a signaling molecule. Here we insert a "molecular spring" on the enzyme guanylate kinase, to control the conformation of this protein. The stiffness of the spring can be varied externally, which allows one to exert a controlled mechanical tension between the two points on the protein's surface where the spring is attached. We show that by applying and releasing the tension we can reversibly turn the enzyme off and on.     

MD studies on conformational behavior of a DNA photolyase enzyme

In this work, molecular dynamics (MD) simulations were performed on a DNA photolyase protein with two cofactors, FAD (flavin adenine dinucleotide) and MTHF (methenyltetrahydrofolate), inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane-pyrimidine dimer in damaged DNA. We were aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The conformational behavior of the FAD molecule is very important for understanding the functional and structural properties of the DNA repair protein photolyase. The photoactive FAD is an essential cofactor both for specificial binding to damaged DNA and for catalysis. The second chromophore (MTHF or 8-HDF) is not necessary for catalysis and has no effect on specific enzyme—substrate binding. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.     

Nucleic acid hydration: a volumetric perspective

Hydration represents a major force governing the conformational preferences and drug binding properties of nucleic acids. Volumetric measurements have proven useful in characterizing the hydration properties of nucleic acid structures and their complexes with other molecules. In this paper, we present an overview of recent developments in the field of volumetric investigations of nucleic acids. We discuss, in particular, the volumetric properties of nucleic acids, their molecular components and analogs, conformational transitions of DNA and RNA, and drug–DNA interactions. We emphasize the importance of hydration as a major contributor to the energetics of molecular recognition. We also emphasize the need of expanding the field of volumetric characterizations of nucleic acid structures in an effort to gain further insight into the molecular origins of various nucleic acid recognition processes, including helix-to-coil and helix-to-helix conformational transitions, as well as drug–DNA and protein–DNA interactions.     

Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins.     

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

We discuss aspects of the physics of proteins at low temperature as they are reflected in highly resolved optical spectra of molecular probes. Typical probe molecules are heme-like dyes, aromatic amino acids, but also extended molecular aggregates in light harvesting complexes. We put emphasis on the interactions of the probe with its protein environment, on the range of these interactions, on their specific behavior in external fields, as well as on the characteristic parameters of the protein which can be determined with optical techniques at low temperatures but are not easily accessible otherwise. However, the focus of the review is on spectral diffusion physics of proteins, i.e. on their motion in conformational phase space, and on how this motion is reflected in the optical spectra. These structure changing-processes reflect the non-ergodic nature of low temperature proteins. They are most clearly detected at low temperature where the resolution of the experiment is close to the ultimate limit as given by the natural linewidth and where the dynamics become slow enough to be conveniently measured. In part I we discuss aspects of ensemble experiments, in part II we focus on experiments with single protein complexes. We offer lines of reasoning which may serve as guidelines for an understanding of the phenomena.     

Model of DNA bending by cooperative binding of proteins

We present a model of nonspecific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence length, site occupancy, and cooperativity. Cooperativity leads to nonmonotonic variation of the persistence length with protein concentration, and to an unusual shape of the binding isotherm. The results are in qualitative agreement with recent single molecule experiments on nucleoid protein HU-DNA complexes.     

Theoretical study on single-molecule spectroscopy

The photon-by-photon approach for single molecule spectroscopy experiments utilizes the information carried by each detected photon and allows the measurements of conformational fluctuation with time resolution on a vast range of time scales, where each photon represents a data point. Here, we theoretically simulate the photon emission dynamics of a single molecule spectroscopy using the kinetic Monte Carlo algorithm to understand the underlying complex photon dynamic process of a single molecule. In addition, by following the molecular process in real time, the mechanism of complex biochemical reactions can be revealed. We hope that this theoretical study will serve as an introduction and a guideline into this exciting new field.     

Translational and Rotational Motions of Albumin Sensed by a Non-Covalent Associated Porphyrin Under Physiological and Acidic Conditions: A Fluorescence Correlation Spectroscopy and Time Resolved Anisotropy Study

The interaction between a free-base, anionic water-soluble porphyrin, TSPP, and the drug carrier protein, bovine serum albumin (BSA) has been studied by time-resolved fluorescence anisotropy (TRFA) and fluorescence correlation spectroscopy (FCS) at two different pH-values. Both rotational correlation times and translational diffusion times of the fluorescent species indicate that TSPP binding to albumin induces very little conformational changes in the protein under physiological conditions. By contrast, at low pH, a bi-exponential decay is obtained where a short rotational correlation time (phi (int) = 1.2 ns) is obtained, which is likely associated to wobbling movement of the porphyrin in the protein binding site. These physical changes are corroborated by circular dichroism (CD) data which show a 37% loss in the protein helicity upon acidification of the medium. In the presence of excess porphyrin formation of porphyrin J-aggregates is induced, which can be detected by time-resolved fluorescence with short characteristic times. This is also reflected in FCS data by an increase in molecular brightness together with a decrease in the number of fluorescent molecules passing through the detection volume of the sample.     

单分子荧光检测在生命科学中的应用

文章对单分子荧光检测在分子马达、离子通道、信号分子、蛋白折叠、蛋白构象变化动力学、酶活性反应、细胞过程实时观察等生命科学领域中的应用进行了介绍.这些研究结果表明,单分子荧光检测在研究生物大分子的活动规律与机制方面不但有着无法替代的优越性,而且有着广阔的发展空间.     

Field Effect Transistor Using Carbon Nanotubes and DNA as Electrical Gate

We present an electronic sensor in the molecular scale, which is very sensitive for detection and sensing of DNA characteristics and DNA activities in particular activities between DNA duplex and any protein. Here, the device shows that DNA is electronically inserted to be on the same time as an electrical device transducer and as a biological target in a carbon nanotube-DNA-carbon nanotube electronic sensor. We have performed a DNA binding through an amide group by the electron transfer through amide group. The presented device has shown an efficient and rapid procedure to bind the electrical vulnerability of DNA with the detection of enzymatic effectiveness leading to high efficient biosensor.     

Fluorescence lifetime study of ECFP/EYFP labeled MBP in Förster resonance energy transfer

This paper studies the conformational change of the binding protein by a fluorescence lifetime method. As a model protein, maltose binding protein (MBP) where enhanced cyan protein (ECFP) and enhanced yellow fluorescent protein (EYFP) were genetically fused to act as a donor and an acceptor in Förster resonance energy transfer (FRET) was used. The ECFP and the EYFP were linked to the C-terminal and N-terminal regions of the MBP, respectively. In order to investigate the conformational change of the MBP, the lifetime of the ECFP, which acts as a donor in the ECFP:MBP:EYFP fusion protein, was analyzed during the FRET process. We observed that two lifetime components exist when the ECFP is linked to the MBP and that the lifetime of the ECFP is shortened when ECFP:MBP:EYFP protein undergoes a conformational change as a result of the maltose binding. In addition, we observed that the lifetime of the donor is gradually shorter in the ECFP:MBP:EYFP fusion protein as the maltose concentration increases. By a lifetime analysis and simulation study, we found that the participant rate of the ECFP:MBP:EYFP protein in FRET is the main cause of the donor lifetime shortening in relation to the increase of the maltose concentration.     

天然同位素丰度野生型酵母细胞色素c构象变化的核磁共振检测

细胞色素c是一个重要的多功能蛋白,它在呼吸链及细胞凋亡中均发挥着重要作用.细胞色素c的构象变化与其功能密切相关,表征细胞色素c的构象变化对于明确其相关功能的分子机制至关重要.核磁共振（NMR）是近原位环境下表征蛋白构象的重要工具,但通常需要使用¹³C、¹⁵N等同位素.由于野生型细胞色素c存在翻译后修饰,故其同位素标记十分困难.本文尝试使用¹H-¹³C HSQC技术来表征提纯后的天然同位素丰度的野生型细胞色素c的构象变化.结果显示该方法能在2 h内检测到大多数甲基的信号,且化学位移变化明显的甲基与其构象变化一致.这表明该方法有助于研究天然丰度或翻译后修饰蛋白的构象变化.     

用光波导光模光谱技术研究DNA-DNA结合蛋白相互作用

探讨了应用光波导光模光谱(Optical waveguide lightmode spectroscopy,OWLS)技术研究DNA-DNA结合蛋白相互作用的可行性和灵敏性。以固定在传感器芯片表面的DNA探针为捕捉分子,溶液中同时含有探针结合序列和NF—κB结合位点序列的寡核苷酸与NF-κB亚单位p50同源二聚体形成的DNA-蛋白质复合物为检测分子,用光波导光模光谱检测技术建立非标记DNA-DNA结合蛋白相互作用检测研究体系。利用这一体系对不同样品中NF-κB p50浓度和具不同NF-κB结合位点序列的寡核苷酸与NF-κB p50亲合和力进行检测。样品中低至0．33 nmol/1的NF-κB p50被光波导光模光谱检测出,不同的NF-κB结合序列与NF-κB p50亲合力有显著的差异。研究发现,光波导光模光谱技术可以用于DNA-DNA结合蛋白相互作用研究,所建立的非标记检测研究体系可以进行样品中结合蛋白含量高灵敏检测和核酸序列与结合蛋白的亲合力的检测研究。     

Nanoscale swimmers: hydrodynamic interactions and propulsion of molecular machines

Molecular machines execute nearly regular cyclic conformational changes as a result of ligand binding and product release. This cyclic conformational dynamics is generally non-reciprocal so that under time reversal a different sequence of machine conformations is visited. Since such changes occur in a solvent, coupling to solvent hydrodynamic modes will generally result in self-propulsion of the molecular machine. These effects are investigated for a class of coarse grained models of protein machines consisting of a set of beads interacting through pair-wise additive potentials. Hydrodynamic effects are incorporated through a configuration-dependent mobility tensor, and expressions for the propulsion linear and angular velocities, as well as the stall force, are obtained. In the limit where conformational changes are small so that linear response theory is applicable, it is shown that propulsion is exponentially small; thus, propulsion is nonlinear phenomenon. The results are illustrated by computations on a simple model molecular machine.     

DNA based molecular motors

Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.     

Role of tension and twist in single-molecule DNA condensation

Using magnetic tweezers, we study in real time the condensation of single DNA molecules under tension. We find that DNA condensation occurs via discrete nucleated events. By measuring the influence of an imposed twist, we show that condensation is initiated by the formation of a plectonemic supercoil. This demonstrates a strong interplay between the condensation transition and externally imposed mechanical constraints.     

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

Understanding the processes of protein adsorption/desorption on nanoparticles’ surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.     

Quantification of Low Concentrations of DNA Using Single Molecule Detection and Velocity Measurement in a Microchannel

We present a novel method for quantifying low concentrations of DNA based on single molecule detection (SMD) for molecular counting and flow measurements inside a microchannel. A custom confocal fluorescence spectroscopic system is implemented to detect fluorescent bursts emitted from stained DNA molecules. Measurements are made one molecule at a time as they flow through a femtoliter-sized laser focal probe. Durations of single molecule fluorescent bursts, which are found to be strongly related to the molecular transit times through the detection region, are statistically analyzed to determine the in situ flow speed and subsequently the sample volume flowing through the focal probe. Therefore, the absolute concentration of a DNA sample can be quantified based on the single molecule fluorescent counts from the DNA molecules and the associated probe volume for a measured time course. To validate this method for quantifying low concentrations of biomolecules, we tested samples of pBR322 DNA ranging from 1 pM to 10 fM (∼3 ng/ml to 30 pg/ml). Besides molecular quantification, we also demonstrate this method to be a precise and non-invasive way for flow profiling within a microchannel.     

DNA localization and stretching on periodically microstructured lipid membranes

We study the conformational behavior of DNA molecules adsorbed on cationic-lipid membranes that are supported on grooved, one-dimensionally periodic microstructured surfaces. We reveal a striking ability of these periodically structured membranes to stretch DNA coils. We elucidate this DNA stretching phenomenon in terms of surface curvature dependent potential energy attained by the adsorbed DNA molecules. Because of it, DNA molecules undergo a localization transition causing them to stretch by binding to highly curved sections of the supported membranes.