Effect of secondary structure on the conformations and folding behaviors of protein-like chains

We present a new model considering the effects of secondary structure on the conformations and folding process of protein-like chains in three-dimensional simple cubic lattice in this paper. The properties such as chain dimensions, shape, average contacts and chain average energy with different helical energy of a helix (ε_hel=0, −0.75, −1.5, and −3 in the unit of kT) are discussed here. Unlike conventional polymers, protein-like chains are much compact. We also find that the ability to form helix of residue is different under the condition of different helical energy of a helix. The energy distribution for protein-like chains with different length and the conformation changes in the process of folding of proteins are discussed. Comparisons with real protein chains are also made.     

Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

GPS中新的P码直接捕获算法的提出与分析

目前P码的捕获通常是利用C/A码来完成.为保证扩频信号具有更高的扩频增益、更强的抗模仿和抗欺骗能力,必须实现P码的直接捕获,而不依赖于其他短码来捕获.本文从研究信号直接捕获算法角度出发,提出了一种新的P码快速直接捕获算法.仿真结果表明:该算法能够达到有效的P码捕获.     

铝箔合卷机多电机系统的速度控制

对铝箔合卷机多电机系统的速度控制进行了阐述，认为定期、定时调整传送辊转速是确保合卷机各传送辊线速度误差不超过2％的关键，从而使铝箔的产量和表面质量稳步提高，取得了较好的效果。     

棉型服装面料服用性能测试分析

通过使用悬垂仪、耐磨仪、撕裂仪、透气仪以及折皱弹性仪对棉及棉型织物的各主要服用性能指标进行测试，采用灰色关联的方法分析织物的悬垂性能、透气性能、折皱弹性性能、撕裂性能、耐磨性能等服用性能与主要影响因素(织物的规格，结构)之间的关联程度，分析最终对纺织品面料外观、舒适性、耐用性和保养性的影响。     

Inductively Verifying Invariant Properties of Parameterized Systems

Verification of distributed algorithms can be naturally cast as verifying parameterized systems, the parameter being the number of processes. In general, a parameterized concurrent system represents an infinite family (of finite state systems) parameterized by a recursively defined type such as chains, trees. It is therefore natural to verify parameterized systems by inducting over this type. However, construction of such proofs require combination of model checking with deductive capability. In this paper, we develop a logic program transformation based proof methodology which achieves this combination. One of our transformations (unfolding) represents a single resolution step. Thus model checking can be achieved by repeated application of unfolding. Other transformations (such as folding) represent deductive reasoning and help recognize the induction hypothesis in an inductive proof. Moreover the unfolding and folding transformations can be arbitrarily interleaved in a proof, resulting in a tight integration of decision procedures (such as model checking) with deductive verification.Based on this technique, we have designed and implemented an invariant prover for parameterized systems. Our proof technique is geared to automate nested induction proofs which do not involve strengthening of induction hypothesis. The prover has been used to automatically verify invariant properties of parameterized cache coherence protocols, including broadcast protocols and protocols with global conditions. Furthermore, we have employed the prover for automatic verification of mutual exclusion in the Java Meta-Locking Algorithm. Meta-Locking is a distributed algorithm developed recently by designers in Sun Microsystems for ensuring secure access of Java objects by an arbitrary number of Java threads.     

Identification of the Primary Factors Determining the Specificity of Human VKORC1 Recognition by Thioredoxin-Fold Proteins

Redox (reduction–oxidation) reactions control many important biological processes in all organisms, both prokaryotes and eukaryotes. This reaction is usually accomplished by canonical disulphide-based pathways involving a donor enzyme that reduces the oxidised cysteine residues of a target protein, resulting in the cleavage of its disulphide bonds. Focusing on human vitamin K epoxide reductase (hVKORC1) as a target and on four redoxins (protein disulphide isomerase (PDI), endoplasmic reticulum oxidoreductase (ERp18), thioredoxin-related transmembrane protein 1 (Tmx1) and thioredoxin-related transmembrane protein 4 (Tmx4)) as the most probable reducers of VKORC1, a comparative in-silico analysis that concentrates on the similarity and divergence of redoxins in their sequence, secondary and tertiary structure, dynamics, intraprotein interactions and composition of the surface exposed to the target is provided. Similarly, hVKORC1 is analysed in its native state, where two pairs of cysteine residues are covalently linked, forming two disulphide bridges, as a target for Trx-fold proteins. Such analysis is used to derive the putative recognition/binding sites on each isolated protein, and PDI is suggested as the most probable hVKORC1 partner. By probing the alternative orientation of PDI with respect to hVKORC1, the functionally related noncovalent complex formed by hVKORC1 and PDI was found, which is proposed to be a first precursor to probe thiol–disulphide exchange reactions between PDI and hVKORC1.     

移动式定子铁芯叠压模具设计

为了使模具定子冲片(散片)在模具中能得到正确的定位、可靠的预压紧和确保顺利脱模。运用一面二销定位解决了散片装夹和定位时可能产生的片间参差不齐和垂直度误差;通过采用小斜度斜楔确保了散片间的紧密度,通过轴向限位的方式防止压入支架后定子铁芯端面呈蝶形翻翘状;采用哈夫压板成功解决了支架套筒压入后的脱模问题。经批量生产证明,该叠压模结构简单,定位准确,操作安全、简便,造价低廉,产品质量稳定。     

A Conditionally Fluorescent Peptide Reporter of Secondary Structure Modulation

Proteins containing intrinsic disorder often form secondary structure upon interaction with a binding partner. Modulating such structures presents an approach for manipulating the resultant functional outcomes. Translational repressor protein 4E-BP1 is an example of an intrinsically disordered protein that forms an α-helix upon binding to its protein ligand, eIF4E. Current biophysical methods for analyzing binding-induced structural changes are low-throughput, require large amounts of sample, or are extremely sensitive to signal interference by the ligand itself. Herein, we describe the discovery and development of a conditionally fluorescent 4E-BP1 peptide that reports structural changes of its helix in high-throughput format. This reporter peptide is based on conditional quenching of fluorescein by thioamides. In this case, fluorescence signal increases as the peptide becomes more ordered. Conversely, destabilization of the α-helix results in decreased fluorescence signal. The low concentration and low volume of peptide required make this approach amenable for high-throughput screening to discover ligands that alter peptide secondary structure.     

Probing Protein Folding with Sequence-Reversed α-Helical Bundles

Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.