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.

Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

A fibrinogen-related protein from bay scallop Argopecten irradians involved in innate immunity as pattern recognition receptor

The family of fibrinogen-related proteins (FREPs) is a group of proteins with fibrinogen-like domains. Many members of this family play important roles as pattern recognition receptors in innate immune responses. The cDNA of bay scallop Argopecten irradians FREP (designated as AiFREP) was cloned by rapid amplification of cDNA ends (RACE) method based on the expressed sequence tag (EST). The full-length cDNA of AiFREP was of 990 bp. The open reading frame encoded a polypeptide of 251 amino acids, including a signal sequence and a 213 amino acids fibrinogen-like domain. The fibrinogen-like domain of AiFREP was highly similar to those of mammalian ficolins and other FREPs. The temporal expression of AiFREP mRNA in hemolymph was examined by fluorescent quantitative real-time PCR. The mRNA level of scallops challenged by Listonella anguillarum was significantly up-regulated, peaked to 9.39-fold at 9 h after stimulation, then dropped back to 4.37-fold at 12 h, while there was no significant change in the Micrococcus luteus challenged group in all periods of treatment. The function of AiFREP was investigated by recombination and expression of the cDNA fragment encoding its mature peptide in Escherichia coli Rosetta gami (DE3). The recombinant AiFREP (rAiFREP) agglutinated chicken erythrocytes and human A, B, O-type erythrocytes. The agglutinating activities were calcium-dependent and could be inhibited by acetyl group-containing carbohydrates. rAiFREP also agglutinated Gram-negative bacteria E. coli JM109, L anguillarum and Gram-positive bacteria M. luteus in the presence of calcium ions. These results collectively suggested that AiFREP functions as a pattern recognition receptor in the immune response of bay scallop and contributed to nonself recognition in invertebrates, which would also provide clues for elucidating the evolution of the lectin pathway of the complement system. (C) 2008 Elsevier Ltd. All rights reserved.

An ancient C-type lectin in Chlamys farreri (CfLec-2) that mediate pathogen recognition and cellular adhesion

C-type lectins are a superfamily of Ca2+ dependent carbohydrate-recognition proteins which play significant diverse roles in nonself-recognition and clearance of invaders. In the present study, a C-type lectin (CfLec-2) from Zhikong scallop Chlamys farreri was selected to investigate its functions in innate immunity. The mRNA expression of CfLec-2 in hemocytes was significantly up-regulated (P < 0.01) after scallops were stimulated by LPS. PGN or beta-glucan, and reached the highest expression level at 12h post-stimulation, which was 72.5-, 23.6- or 43.8-fold compared with blank group, respectively. The recombinant Cflec-2 (designated as rCfLec-2) could bind LPS, PGN, mannan and zymosan in vitro, but it could not bind beta-glucan. Immunofluorescence assay with polyclonal antibody specific for Cflec-2 revealed that CfLec-2 was mainly located in the mantle, kidney and gonad. Furthermore, rCfLec-2 could bind to the surface of scallop hemocytes, and then initiated cellular adhesion and recruited hemocytes to enhance their encapsulation in vitro, and this process could be specifically blocked by anti-rCfLec-2 serum. These results collectively suggested that CfLec-2 from the primitive deuterostome C. farreri could perform two distinct immune functions, pathogen recognition and cellular adhesion synchronously, while these functions were performed by collectins and selectins in vertebrates, respectively. The synchronous functions of pathogen recognition and cellular adhesion performed by CfLec-2 tempted us to suspect that CfLec-2 was an ancient form of C-type lectin, and apparently the differentiation of these two functions mediated by C-type lectins occurred after mollusk in phylogeny. (C) 2010 Elsevier Ltd. All rights reserved.

On the Gas-Liquid Two-Phase Flow Regimes and their Recognition Methods

气液两相流体系是一个复杂的多变量随机过程体系,流型的定义、流型过渡准则和判别方法等方面的研究是多相流学科目前研究的重点内容。本文就与气液两相流流型及其判别有关的研究状况进行了回顾和评述,力图反映近年来气液两相流流型及其判别问题研究的状态和趋势。

Pattern Recognition With Weighted Complex Networks

In this paper we introduce a weighted complex networks model to investigate and recognize structures of patterns. The regular treating in pattern recognition models is to describe each pattern as a high-dimensional vector which however is insufficient to express the structural information. Thus, a number of methods are developed to extract the structural information, such as different feature extraction algorithms used in pre-processing steps, or the local receptive fields in convolutional networks. In our model, each pattern is attributed to a weighted complex network, whose topology represents the structure of that pattern. Based upon the training samples, we get several prototypal complex networks which could stand for the general structural characteristics of patterns in different categories. We use these prototypal networks to recognize the unknown patterns. It is an attempt to use complex networks in pattern recognition, and our result shows the potential for real-world pattern recognition. A spatial parameter is introduced to get the optimal recognition accuracy, and it remains constant insensitive to the amount of training samples. We have discussed the interesting properties of the prototypal networks. An approximate linear relation is found between the strength and color of vertexes, in which we could compare the structural difference between each category. We have visualized these prototypal networks to show that their topology indeed represents the common characteristics of patterns. We have also shown that the asymmetric strength distribution in these prototypal networks brings high robustness for recognition. Our study may cast a light on understanding the mechanism of the biologic neuronal systems in object recognition as well.

Controllable group velocity of the probe light in a Lambda-type system with two fold levels

The group velocities of the probe laser field are studied in a A-type system where one lower state has two fold levels coupled by a control field. It is found that the interaction of double dark states leads to controllable group velocity of the probe field in this system. It can be easily realized, due to the interacting double dark resonances, that one of the group velocities at transparency positions is much slower than the other by tuning the control field to be off resonance. In particular, when the control field is on resonance. we can obtain two equal slow group velocities with a broader EIT width, which provides potential applications in quantum storage and retrieval of light. (c) 2005 Elsevier B.V. All rights reserved.

Visual pattern recognition network: Its training algorithm and its optoelectronic architecture

A visual pattern recognition network and its training algorithm are proposed. The network constructed of a one-layer morphology network and a two-layer modified Hamming net. This visual network can implement invariant pattern recognition with respect to image translation and size projection. After supervised learning takes place, the visual network extracts image features and classifies patterns much the same as living beings do. Moreover we set up its optoelectronic architecture for real-time pattern recognition. (C) 1996 Optical Society of America

Ultrafast temporal pattern generation and recognition

Ultrafast temporal pattern generation and recognition with femtosecond laser technology is presented, analyzed, and experimentally implemented. Ultrafast temporal pattern generation and recognition are realized by taking advantage of two well-known techniques: the space-time conversion technique and the ultrafast pulse measurement technique. Here the temporal pattern for the designed multiple pulses, optimized with a preassumed Gaussian spectral distribution of an ultrashort pulse, is described. With the simulation of a Gaussian spectral distribution, we realize that the uniformity of the generated multiple ultrafast temporal pulses is relevant to the repeated number of modulation periods in the mask in the spectral plane. Moreover, the change of Gaussian spectral phases with the wavelengths in the modulated phase plate is considered. Experiments of ultrafast temporal pattern recognition by the frequency-resolved optical gating (FROG) characterization technique are also given. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

Effects of morphine and its withdrawal on Y-maze spatial recognition memory in mice

Effects of morphine on acquisition and retrieval of memory have been proven in the avoidance paradigms. In present study, we used a two-trial recognition Y-maze to test the effects of acute morphine and morphine withdrawal on spatial recognition memory. T

Effect of Co-administration of Morphine and Cholinergic Antagonists on Y-maze Spatial Recognition Memory Retrieval and Locomotor Activity in Mice

吗啡和胆碱能系统的相互作用已在多项研究中提到,本实验想查明吗啡是否能和胆碱能拮抗剂、东莨菪碱以及阿托品共同作用对小鼠的Y迷宫空间识别记忆提取产生影响.采用测试前腹腔给药的方法,选用3种剂量的吗啡(5、1.5、0.5mg/kg),两种剂量的东莨菪碱(1、0.1mg/kg),以及两种剂量的阿托品(0.5、0.1mg/kg),剂量由高到低相配对作为联合给药的手段.其结果表明:1)0.5mg/kg低剂量吗啡与0.1 mg/kg低剂量的东莨菪碱,或与0.1 mg/kg低剂最的阿托品联合给药的小鼠,在记忆提取测试中, 空间探查行为(各臂停留时间百分比)对新异臂没有偏好,而新奇探索行为(各臂访问次数百分比)仍保持了对新异臂的偏好,而相应剂最药物单独给药的小鼠记忆提取均没有被损害;2)吗啡能和东莨菪碱相互作用使小鼠的活动性显著增强.暗示吗啡和胆碱能拮抗剂对小鼠空间记忆提取的破坏存在一定程度的相互作用.

Improved spatial recognition memory in mice lacking adenosine A(2A) receptors

Adenosine receptors play an important role in learning and memory as their antagonists have been found to facilitate learning and memory in various tasks in rodents. However, few studies have examined the effect of adenosine A(2A) receptor deficiency on c

Morphine and propranolol co-administration impair consolidation of Y-maze spatial recognition memory

In the present study, the interaction between morphine and the beta-adrenergic receptor antagonist, propranolol (PROP), in memory consolidation was investigated in a two-trial recognition Y-maze task. Four sets of Y-maze experiments were carried out in mi

Long-term exposure to extremely low-frequency magnetic fields impairs spatial recognition memory in mice

1. In the present study, we investigated the short- and long-term effects of extremely low-frequency (ELF) magnetic fields on spatial recognition memory in mice by using a two-trial recognition Y-maze that is based on the innate tendency of rodents to exp

Environmental enrichment and chronic restraint stress in ICR mice: Effects on prepulse inhibition of startle and Y-maze spatial recognition memory

In most studies regarding the improving or therapeutical effects induced by enriched environment (EE), EE was performed after the stress treatment or in patients with certain diseases. In the current study, the effects of chronic restraint stress (6 h/day) in mice living in an enriched environment or standard environment (SE) were tested. Mice were randomly divided into 4 groups: non-stressed or stressed mice housed in SE or EE conditions (SE, stress + SE, EE, stress + EE). Prepulse inhibition (PPI) of startle was tested after the 2 weeks or 4 weeks stress and/or EE treatment and 1 or 2 weeks withdrawal from the 4 weeks treatment. After the 4 weeks treatment, spatial recognition memory in Y-maze was also tested. The results showed that EE increased PPI in stressed and non-stressed mice after 2 weeks treatment. No effect of EE on PPI was found after the 4 weeks treatment. 4 weeks chronic restraint stress increased PPI in mice housed in standard but not EE conditions. Stressed mice showed deficits on the 1 h delay version of the Y-maze which could be prevented by living in an enriched environment. Our results indicated that living in an enriched environment reversed the impairing effects of chronic restraint stress on spatial recognition memory. However, EE did not change the effects of stress on PPI. (C) 2010 Elsevier B.V. All rights reserved.