Electron localization for a model of layered metallic structures

Several exact results are presented for a one-dimensional tight-binding model of layered binary metallic structures for the cases of arbitrary, random, incommensurate, and commensurate layer sequences.     

Exploring the chemical space of peptides for drug discovery: a focus on linear and cyclic penta-peptides

Peptide and peptide-like structures are regaining attention in drug discovery. Previous studies suggest that bioactive peptides have diverse structures and may have physicochemical properties attractive to become hit and lead compounds. However, chemoinformatic studies that characterize such diversity are limited. Herein, we report the physicochemical property profile and chemical space of four synthetic linear and cyclic combinatorial peptide libraries. As a case study, the analysis was focused on penta-peptides. The chemical space of the peptide and N-methylated peptides libraries was compared to compound data sets of pharmaceutical relevance. Results indicated that there is a major overlap in the chemical space of N-methylated cyclic peptides with inhibitors of protein–protein interactions and macrocyclic natural products available for screening. Also, there is an overlap between the chemical space of the synthetic peptides with peptides approved for clinical use (or in clinical trials), and to other approved drugs that are outside the traditional chemical space. Results further support that synthetic penta-peptides are suitable compounds to be used in drug discovery projects.     

A Bernasconi model for constructing ground-state spin systems

A Bernasconi model for a one-dimensional chain of quantum particles is considered. It is shown that searching for the ground state of such a quantum system is equivalent to searching for binary sequences with minimum energy levels of the side lobes of the aperiodic autocorrelation function (ACF). A review and new results regarding the construction of such binary sequences are presented.     

Structure‐Making Effects of Metal Nanoparticles in Amyloid Peptide Fibrillation

There is growing concern that nanoparticles (NPs) may accelerate amyloid protein aggregation and thus cause amyloid‐related diseases. Here, the potential of silver and gold NPs is explored (diameter 20 nm) on the aggregation of the amyloid peptide sequences NNFGAIL from human islet amyloid polypeptide and the yeast prion protein sequence GNNQQNY, which are both the sequences of the full systems, which are able to aggregate into characteristic amyloid cross‐beta sheet fibrillar structures. Here, it is shown that silver and gold NPs in physiological aqueous solution at ambient temperatures accelerate the aggregation kinetics of both peptides significantly (in vitro). Scanning electron microscopy and X‐ray diffraction provide solid evidence for a “structure‐making” effect of the NPs. In particular, we are able to image the initial peptide corona and measure its structural reorganization in time‐resolved kinetic experiments. After a conversion time Δt, the coated NPs appear to act as templates or seeds for rapid fibrillation. Interestingly, cross‐fibrillation experiments with different peptide‐coated NPs (pcNPs) reveal that they can efficiently induce aggregation of similar peptides once the pcNPs are structurally converted. It is discussed that these structurally converted pcNPs may display similar kinetic features as toxic and aggregation inducing oligomers/protofibrils in normal amyloid aggregation, without being transient and very low‐concentration species. Finally, we suggest and discuss a simple mechanistic picture with the biomolecule corona of NPs being central to the function of the coated NPs in amyloid fibrillation.     

Solvent effects on conformational stability of peptides: RISM analyses

We describe features of our methodology for predicting tertiary structures (i.e., conformations) of proteins in solvent just from the amino-acid sequences and molecular models for the solvent. The methodology, which is a combination of the Monte Carlo simulated annealing technique and the reference interaction site model theory, is illustrated for the small peptides, Met-enkephalin and C-peptide. Important roles played by water are discussed, and the alcohol effects on peptide conformations are newly analyzed.     

Periodicity, planarity, residual dipolar coupling, and structures

The periodic behavior of residual dipolar couplings (RDCs) arising from nucleic acid and protein secondary structures is shown to be more complex and information-rich than previously believed. We have developed a theoretical framework which allows the bond vector orientation of nucleic acids and the peptide plane orientations of protein secondary structures to be extracted from their Dipolar waves. In this article, we focus on utilizing "Dipolar waves" of peptides to extract structure information, and describe in more detail the fundamental principles of the relationship between the periodicities in structure and RDCs, the practical procedure to extract peptide plane orientation information from RDC data, and assessment of errors using Monte-Carlo simulations. We demonstrate the utility of our method for two model alpha-helices, one kinked and one curved, and as well as an irregular beta-strand.     

Detection and Location of Multi-Period Phenomena in Chaotic Binary Sequences

Due to the influence of finite calculation accuracy and binary quantization method, the performance of chaotic binary sequences has been degraded in varying degrees, and some sequences emerge as multi-period phenomena. Aiming at the problem that it is difficult to accurately detect this phenomenon, this paper proposes a multi-period positioning algorithm (MPPA), which can accurately detect and locate the accurate period and local period phenomena contained in chaotic binary sequences. In order to test the effectiveness and correctness of the algorithm, the multi-period characteristics of logistic binary sequences with different calculation accuracy are analyzed. MPPA evaluates the randomness of binary sequences from a new perspective, which provides a new idea for the analysis of cryptographic security of chaotic sequences.     

Various Auto-Correlation Functions of m-Bit Random Numbers Generated from Chaotic Binary Sequences

This paper discusses the auto-correlation functions of m-bit random numbers obtained from m chaotic binary sequences generated by one-dimensional nonlinear maps. First, we provide the theoretical auto-correlation function of an m-bit sequence obtained by m binary sequences that are assumed to be uncorrelated to each other. The auto-correlation function is expressed by a simple form using the auto-correlation functions of the binary sequences. This implies that the auto-correlation properties of the m-bit sequences can be easily controlled by the auto-correlation functions of the original binary sequences. In numerical experiments using a computer, we generated m-bit random sequences using some chaotic binary sequences with prescribed auto-correlations generated by one-dimensional chaotic maps. The numerical experiments show that the numerical auto-correlation values are almost equal to the corresponding theoretical ones, and we can generate m-bit sequences with a variety of auto-correlation properties. Furthermore, we also show that the distributions of the generated m-bit sequences are uniform if all of the original binary sequences are balanced (i.e., the probability of 1 (or 0) is equal to 1/2) and independent of one another.     

一类位于加周期分岔中的貌似混沌的随机神经放电节律的识别

识别非周期神经放电节律是混沌还是随机一直是一个重要的科学问题. 在神经起步点实验中发现了一类介于周期k和周期k+1(k=1,2)节律之间非周期自发放电节律, 其行为是长串的周期k簇和周期k+1簇的交替. 确定性理论模型Chay模型展示出了周期k和周期k+1节律的共存行为. 噪声在共存区诱发出了与实验结果类似的非周期节律, 说明该类节律是噪声引起的两类簇的跃迁. 非线性预报及其回归映射揭示该节律具有确定性机理; 将两类簇分别转换为0和1得到一个二进制序列, 对该序列进行概率分析获得了两类簇跃迁的随机机理. 这不仅说明该节律是具有确定性结构的随机节律而不是混沌, 还为深入识别现实神经系统的混沌和随机节律提供了典型示例和有效方法.     

Protein Sequence and Structure: Is One More Fundamental than the Other?

We argue that protein native state structures reside in a novel “phase” of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a sequence-independent free energy landscape with relatively few low energy minima with funnel-like character. The choice of a sequence that fits well into one of these predetermined structures facilitates rapid and cooperative folding. Our model calculations show that this novel phase facilitates the formation of an efficient route for sequence design starting from random peptides.     

Adsorption of neurotensin‐family peptides on SERS‐active Ag substrates

Kinetensin (KN) and its amino acids 1–8 fragment ([des‐Leu⁹]KN), neuromedin N (NMN), and xenopsin (XP) and its two analogs (XP‐1 and XP‐2) belong to the neurotensin family of peptides and are known to stimulate the growth of human tumors. In this work, we report Fourier transform‐Raman and surface‐enhanced Raman scattering (SERS) studies of these peptides and discuss their structures, orientation, and mode of adsorption onto a highly specific, electrochemically roughened SERS‐active Ag electrode that is characterized by the formation of a 50–150 nm Ag island on its surface. We show that the investigated peptides bind preferentially to this surface by substantial electronic overlap between the metal surface and the π‐orbitals of the benzene rings of the Phe, Tyr, and Trp residues, which forces them to take parallel or almost parallel orientations with respect to the surface. In addition, the –CH₂–, –CNH₂, and –COO^‐ molecular fragments are involved in interactions with (binding to or in close proximity with) the Ag surface. The SERS data show that the adsorption modes in each of these cases are very similar. In addition, we show that the specific differences in the amino acid sequences do not significantly affect the orientation of the investigated peptides on the Ag substrate. This result implies that the N‐termini of the neurotensin‐family peptides do not influence the mode for adsorption onto the Ag substrates. Copyright © 2012 John Wiley & Sons, Ltd.     

A specialized fast cross-correlation for acoustical measurements using coded sequences

In acoustics applications, binary maximal-length sequences and related sequences are increasingly used for acoustics system identification tasks. A number of coded sequences, such as binary maximal-length related sequences and ternary sequences possess two-valued or pulselike autocorrelation functions. It is this correlation property that is exploited in most of acoustical applications. However, the length of some of these sequences is not directly suitable for FFT-based cross-correlation algorithms. This paper explores using standard FFTs to calculate the cross-correlation between two periodic finite-length sequences of equal length, where the lengths of the sequences are not a power of 2. We apply our specialized correlation algorithm to analyze data collected in a room-acoustic environment to simultaneously obtain impulse responses between multiple sources and multiple receivers.     

Coarse-graining protein energetics in sequence variables

We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility of a sequence with a given structure, by many orders of magnitude. The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. We show, as example, that good prediction accuracy is obtained with up to pairwise interactions for a coiled-coil backbone, and that triplet interactions are important in the energetics of a more globular zinc-finger backbone.     

Utilization of multiple phage display libraries for the identification of dissimilar peptide motifs that bind to a B7-1 monoclonal antibody

Summary Seven random peptide libraries (two displaying linear peptides and five displaying cysteine-constrained peptides) were constructed as gene III fusion proteins of the bacteriophage fd-tet. These libraries were used to screen a blocking monoclonal antibody raised against B7-1 (CD80), a human cell surface antigen that binds two T cell receptors, CD28 and CTLA-4. After three rounds of screening against the immobilized antibody, 1000-fold enrichment was observed in libraries displaying both linear and cysteineconstrained peptides. DNA sequencing of the enriched phage revealed two distinct consensus sequences: HXG(A/Y)XH and DVCXXGGPGC. Phage expressing these consensus sequences bound to L307.4 but not to an isotype matched antibody, indicating that binding was antibody specific. Synthetic peptides corresponding to both motifs inhibited phage binding to L307.4, indicating that the gene III protein is not required for peptide binding. In addition, the cyclized forms of synthetic peptides containing the DVCXXGGPGC motif were capable of inhibiting L307.4 binding to soluble B7-1/Fc fusion. Moreover, phage expressing only the HXG(A/Y)XH consensus sequence were inhibited from binding to L307.4 by the presence of chelating agents. These results indicate that the framework within which the peptide is presented on the surface of the phage may allow the identification of unique peptide motifs with distinct binding characteristics. These peptide motifs could be used for the design of peptidomimetics with therapeutic applications if they inhibit the binding of B7-1 to its T cell receptors.     

Peptide arrays with designed α-helical structures for characterization of proteins from FRET fingerprint patterns

A practical high-throughput protein detection system is described, based on synthetic peptide arrays consisting of designed alpha-helical peptides, detected by fluorescence resonance energy transfer (FRET). Initially a model alpha-helical peptide known to interact with a structured protein, calmodulin, was selected to establish the strategy for high-throughput detection. In comparison to peptides with a single probe, a much higher FRET response has been observed with two fluorescent probes (7-diethylaminocoumarin-3-carboxylic acid and 5(6)-carboxy-fluorescein) at both termini of the synthetic peptides. To establish a reproducible high-throughput detection system, peptides were also immobilized onto a solid surface for detection of the target proteins. A small library of 112 different peptides was constructed, based on a model of the alpha-helical peptide with systematic replacement of residues carrying specific charges and/or hydrophobicities. The library was used to effectively characterize various proteins, giving their own 'protein fingerprint' patterns. The resulting 'protein fingerprints' correlate with the recognition properties of the proteins. The present microarray with designed synthetic peptides as the capturing agents is promising for the development of protein detection chips.     

Structural study on the crystallization behavior of Sb3Te2 alloy for phase change memory

The atomic crystal structure of the Sb₃Te₂ binary alloy has been investigated with high‐resolution transmission electron microscopy (HR‐TEM) and fast Fourier transform patterns. As a result, there is inconsistency between the previous theoretical model and the experimental result. But, from the calculations of lattice parameters and the number of layers in the unit cell, it is found that the Sb₃Te₂ alloy can be crystallized into the Sb₂Te structure with P m1 space group and the difference between stacking sequences of the Sb₃Te₂ and the Sb₂Te structures has been discussed with the proposed atomic arrangement model of unit cells. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Symbolic Analysis of NMR-Laser Chaos

For the extended Bloch-type model of the NMR laser, a binary partition is determined directly from tangencies between forward and backward foliations of the Poincar6 map. Both forward and backward foliations are well ordered according to their symbolic sequences as those of the H6non map with a positive Jacobian. Based on the symbolic dynamics of the H6non map the admissibility condition for allowed sequences is derived and admissible periods are obtained, among which some were formally regarded as forbidden. The allowed periodic orbits are numerically verified. Allowed chaotic sequences are also constructed.     

Structural aspects of antibody-antigen interaction revealed through small random peptide libraries

Summary Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 10⁷ hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems.Abbreviations ABTS 2,2-azino-di-3-ethylbenzthiazoline sulfonate - EGF epidermal growth factor - Mab monoclonal antibody - OD_ccd optical density obtained using CCD camera - RAMPO rabbit-antimouse peroxidase - SDS sodium dodecylsulfate - TGEV transmissible gastroenteritis virus     

Intermolecular (1)H[(19)F] NOEs in studies of fluoroalcohol-induced conformations of peptides and proteins

Mixtures of fluorinated alcohols and water can selectively stabilize certain secondary structures of peptides and proteins. Such mixtures may also be of use in solubilizing hydrophobic or membrane-bound proteins. We show that intermolecular dipolar interactions between the fluorine nuclei of such solvents and the protons of a dissolved protein lead to readily detected (1)H[(19)F] nuclear Overhauser effects. These NOEs can potentially provide information about solvent exposure of particular groups as well as indicate the formation of long-lived fluoroalcohol-solute complexes. Results obtained with HEW lysozyme in solutions containing trifluoroethanol illustrate these possibilities.     

New efficient five-input majority gate for quantum-dot cellular automata

Zinc oxide (ZnO) is a semiconductor compound with a potential for wide use in various applications, including biomaterials and biosensors, particularly as nanoparticles (the size range of ZnO nanoparticles is from 2 to 100?nm, with an average of about 35?nm). Here, we report isolation of novel ZnO-binding peptides, by screening of a phage display library. Interestingly, amino acid sequences of the ZnO-binding peptides reported in this paper and those described previously are significantly different. This suggests that there is a high variability in sequences of peptides which can bind particular inorganic molecules, indicating that different approaches may lead to discovery of different peptides of generally the same activity (e.g., binding of ZnO) but having various detailed properties, perhaps crucial under specific conditions of different applications.