Backbone Design Research Articles

Hierarchical Approach for Survivable Network Design

A central design challenge facing network planners is how to select a cost-effective network configuration that can provide uninterrupted service despite edge failures. In this paper, we study the Survivable Network Design (SND) problem, a core model underlying the design of such resilient networks that incorporates complex cost and connectivity trade-offs. Given an undirected graph with specified edge costs and (integer) connectivity requirements between pairs of nodes, the SND problem seeks the minimum cost set of edges that interconnects each node pair with at least as many edge-disjoint paths as the connectivity requirement of the nodes. We develop a hierarchical approach for solving the problem that integrates ideas from decomposition, tabu search, randomization and optimization. The approach decomposes the SND problem into two subproblems, Backbone design and Access design, and uses an iterative multi-stage method for solving the SND problem in a hierarchical fashion. Since both subproblems are NP-hard, we develop effective, optimization-based tabu search strategies that balance intensification and diversification to identify near-optimal solutions. To initiate this method, we develop two heuristic procedures that can yield good starting points. We test the combined approach on large-scale SND instances, and empirically assess the quality of the solutions vis-a-vis optimal values or lower bounds. On average, our hierarchical solution approach generates solutions within 2.7% of optimality even for very large problems (that cannot be solved using exact methods), and our results demonstrate that the performance of the method is robust for a variety of problems with different size and connectivity characteristics.

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Reliable IPTV Service Delivery Using PIM-SSM Routing

Internet Protocol Television (IPTV) is a service where digital TV signal data is delivered by using Internet protocol (IP). Telecom and network operators focus on IPTV service for its fastest growth, lower price for operators and market economy. With the improvement of broadband connection and technology, IPTV will get more and more importance. Main challenge for IPTV service is resiliency and Quality of Service (QoS) to meet the users Service Level Agreement (SLA). The design space for IPTV service in terms of resilient backbone design, routing algorithms and fast failure restoration shall be explored. It is described from DSL FORUM and leading IPTV service-providing companies. In the context of this work, the PIM-SSM was configured and QoS was implemented for tagged VLAN of multicast traffic. IPTV traffic is analysed in ACREO testbed and Norrksen network.Keywords: IPTV; QoS; Multicast; PIM; PIM-SM; PIM-SSM; VLAN.© 2009 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v1i3.2633 J. Sci. Res. 1 (3), 495-507 (2009)

Motif‐directed flexible backbone design of functional interactions

Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse-grained sampling of possible side-chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side-chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side-chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movements that can give rise to any specified set of desired side-chain atomic placements and interactions, using protein-DNA interfaces as a model system. We use a library of previously observed protein-DNA interactions (motifs) and a rotamer-based description of side-chain conformation freedom to identify placements for the protein backbone that can give rise to a favorable side-chain interaction with DNA. We describe a tree-search algorithm for identifying those combinations of interactions from the library that can be realized with minimal perturbation of the protein backbone. We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations.

Computational De Novo Peptide and Protein Design: Rigid Templates versus Flexible Templates

Both rigid and flexible backbone design templates have been used in the numerous computational de novo peptide and protein design efforts reported so far. In this review paper, we use the type of templates (i.e., rigid or flexible) as a criterion to classify and review examples of successes in de novo protein design. For both cases of rigid and flexible templates, we briefly outline the different search methods for exploring the sequence space and quote some notable success examples for each search method. In particular, we divide the case of flexible templates into three subcategories, according to their approaches for incorporating backbone flexibility: (i) discrete rotamers on multiple backbones with fixed backbone assumption for each, (ii) discrete rotamers on a continuum backbone through algebraic parametrization, and (iii) continuum backbone template with continuous ranges of backbone angles.

Solid-phase peptide synthesis and circular dichroism study of chiral β-peptoid homooligomers

N-alkyl-beta-alanine oligomers (beta-peptoids) with alpha-chiral side chains [(R)- or (S)-1-(phenylethyl)amino groups] were synthesized and analyzed by CD spectroscopy. These chiral beta-peptoid homomers exhibited chain-length-dependent and solvent-dependent ellipticity, strongly indicating the presence of a secondary structure in solution. The CD behaviour was only slightly temperature-dependent upon heating, as also previously observed for stable alpha-peptoid helices containing the same type of side chains. Thus, the data presented here comprise the first evidence for a chain length-dependent secondary folding of compounds with this novel peptidomimetic backbone design. In addition, applicability of a novel hyphenated technique, HPLC-SPE-NMR/MS, for analysis of crude SPPS reaction products was demonstrated.

Recapitulation and Design of Protein Binding Peptide Structures and Sequences

An important objective of computational protein design is the generation of high affinity peptide inhibitors of protein-peptide interactions, both as a precursor to the development of therapeutics aimed at disrupting disease causing complexes, and as a tool to aid investigators in understanding the role of specific complexes in the cell. We have developed a computational approach to increase the affinity of a protein-peptide complex by designing N or C-terminal extensions which interact with the protein outside the canonical peptide binding pocket. In a first in silico test, we show that by simultaneously optimizing the sequence and structure of three to nine residue peptide extensions starting from short (1-6 residue) peptide stubs in the binding pocket of a peptide binding protein, the approach can recover both the conformations and the sequences of known binding peptides. Comparison with phage display and other experimental data suggests that the peptide extension approach recapitulates naturally occurring peptide binding specificity better than fixed backbone design, and that it should be useful for predicting peptide binding specificities from crystal structures. We then experimentally test the approach by designing extensions for p53 and dystroglycan-based peptides predicted to bind with increased affinity to the Mdm2 oncoprotein and to dystrophin, respectively. The measured increases in affinity are modest, revealing some limitations of the method. Based on these in silico and experimental results, we discuss future applications of the approach to the prediction and design of protein-peptide interactions.

Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design

We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for a fixed amino acid sequence using atomic-resolution structure prediction. We find that such a flexible backbone design method better recapitulates protein family sequence variation than sequence optimization on fixed backbones or randomly perturbed backbone ensembles for ten diverse protein structures. For the SH3 domain, the backbone structure variation in the family is also better recapitulated than in randomly perturbed backbones. The potential application of this method as a model of protein family evolution is highlighted by a concerted transition to the amino acid sequence in the structural core of one SH3 domain starting from the backbone coordinates of an homologous structure.

A Bioinorganic Perspective on Matrix Metalloproteinase Inhibition

The zinc-dependent enzymes known as matrix metalloproteinases (MMPs) are medicinal targets due to the activity of these enzymes associated with diseases such as cancer, heart disease, and arthritis. The development of most MMP inhibitors (MPIs) has followed a basic design formula: a peptidomimetic backbone is attached to a zinc-binding group (ZBG). MPI backbones have varied enormously and improved with increased knowledge of MMP structure and function while hydroxamic acids have been used as the ZBG in most inhibitors. The problems associated with hydroxamic acid and other current ZBGs have been identified; the incorporation of more potent and selective ZBGs for the active site zinc(II) ion is necessary to improve the development of second-generation inhibitors. Herein, we highlight ZBGs that have been proposed as alternatives to hydroxamic acids. In addition, techniques used to identify new ZBGs are also discussed. New insights from a bioinorganic approach using model complexes of the MMP active site are presented as tools in examining the mode of binding for various known and novel ZBGs. Novel computational methods are highlighted that allow for modeling the drug-protein interactions with non-hydroxamate inhibitors of MMPs. We suggest that significant efforts to augment ZBGs combined with the available information on inhibitor backbone design will accelerate the discovery of improved MPIs. Newly devised drug design methods will help to realize this proposal.

De novo Backbone and Sequence Design of an Idealized α/β-barrel Protein: Evidence of Stable Tertiary Structure

We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized α/β-barrel protein. The design was elaborated in two steps. First, the idealized backbone was defined with geometric parameters representing our target fold: a central eight parallel-stranded β-sheet surrounded by eight parallel α-helices, connected together with short structural turns on both sides of the barrel. An automated sequence selection algorithm, based on the dead-end elimination theorem, was used to find the optimal amino acid sequence fitting the target structure. A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. Far-UV CD spectra with prominent bands at 222 nm and 208 nm revealed the presence of α-helix secondary structures (50%) in fairly good agreement with the model. A pronounced absorption band in the near-UV CD region, arising from immobilized aromatic side-chains, showed that the artificial protein is folded in solution. Chemical unfolding monitored by tryptophan fluorescence revealed a conformational stability (Δ G H2O) of 35 kJ/mol. Thermal unfolding monitored by near-UV CD revealed a cooperative transition with an apparent T m of 65 °C. Moreover, the artificial protein did not exhibit any affinity for the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid (ANS), providing additional evidence that the artificial barrel is not in the molten globule state, contrary to previously designed artificial α/β-barrels. Finally, 1H NMR spectra of the folded and unfolded proteins provided evidence for specific interactions in the folded protein. Taken together, the results indicate that the de novo designed α/β-barrel protein adopts a stable three-dimensional structure in solution. These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm.

The Precursor Polymer Approach to Electrodeposition and Patterning of Conjugated Polymer Ultrathin Films

ABSTRACTIn this paper, we report strategies for electrodepositing and patterning ultrathin films of conjugated polymers on flat electrode surfaces using the precursor polymer approach. This involves a rational synthesis design of the precursor polymer followed by careful electrodeposition and characterization of ultrathin films on conducting substrates. This has resulted in the preparation of smooth, high optical quality films, which should be important for applications involving flat electrode surfaces in devices. Characterization was made using surface sensitive spectroscopic and microscopic techniques. Copolymerization with monomers, polymer backbone design, and grafting on modified surfaces are key points in this strategy. Novel methods of in-situ characterization techniques have also been developed combing electrochemistry and surface plasmon resonance techniques.

Long-Range Electron Transfer in Rigid 310-Helical Oligopeptides Containing Redox Cyclic a-Amino Acids

Intrahelical photoinduced electron transfer processes (ET) in conformationally restricted oligopeptides have been studied by nanosecond time-resolved transient spectroscopy. The helical peptides were constructed from sterically hindered alpha-aminoisobutyric acid (Aib) and two cyclic alpha-amino acids (Aib class) bearing electron acceptor and donor side chains (DkNap, ThQx). This helical backbone design provides high conformation stability, as previously demonstrated, and yields reliable 3(10)-helical architectures in solution. The forward ET between ThQx and 3DkNap is followed by a slow back ET thus giving rise to an accumulation of the charge-separated ion pairs for hundreds of nanoseconds. We demonstrate the modulation of electronic interactions by the number of intervening Aib residues separating acceptor-donor side chains and propose modifications of the peptide framework by inclusion of a non-Aib amino acid residue. These well-defined and sterically stable frameworks are suited for the precise evaluation of intrahelical electron transfer processes mediated by peptides.

Long-Range Electron Transfer in Rigid 310-Helical Oligopeptides Containing Redox Cyclic α-Amino Acids

Intrahelical photoinduced electron transfer processes (ET) in conformationally restricted oligopeptides have been studied by nanosecond time-resolved transient spectroscopy. The helical peptides were constructed from sterically hindered alpha-aminoisobutyric acid (Aib) and two cyclic alpha-amino acids (Aib class) bearing electron acceptor and donor side chains (DkNap, ThQx). This helical backbone design provides high conformation stability, as previously demonstrated, and yields reliable 3(10)-helical architectures in solution. The forward ET between ThQx and 3DkNap is followed by a slow back ET thus giving rise to an accumulation of the charge-separated ion pairs for hundreds of nanoseconds. We demonstrate the modulation of electronic interactions by the number of intervening Aib residues separating acceptor-donor side chains and propose modifications of the peptide framework by inclusion of a non-Aib amino acid residue. These well-defined and sterically stable frameworks are suited for the precise evaluation of intrahelical electron transfer processes mediated by peptides.

Hub location in backbone/tributary network design: a review

A common architecture for a communications network consists of tributary networks, which connect nodes to hubs, and a backbone network, which interconnects the hubs. Often, because of the size of the problem or the nature of the application, the design of the backbone network and the tributary networks are considered independently. However, in many cases, it is desirable or necessary to treat backbone and tributary design as an integrated problem, in which a key decision is the choice of hub locations. We provide a review of earlier algorithmic work on this integrated problem, drawing from the literature on facility location, network design, telecommunications, computer systems and transportation. Certain key issues in modeling hub location problems in the particular context of communications networks are discussed, and possible avenues for future work are proposed.

A new optimal algorithm for backbone topology design in communications networks

In this paper, we present an exact algorithm (OPTNET) to design an optimal backbone network. We consider the classical backbone design problem under discrete constraints imposed on the transmission lines and traffic routing. That is, we assume that the node and circuit requirements are given. The objective is to find the minimum cost link topology that satisfies all circuit requirements. This problem is related to the discrete multicommodity flow problem in mathematics. We show that OPTNET is practical in designing small and medium size networks.