A Study of Protein Structure Using Amino Acid Interaction Networks

In this chapter we represent proteins by amino acid interaction networks. The nodes in these networks correspond to amino acids. Two nodes are linked if the distance between the corresponding amino acids in the folded protein is below a certain threshold. Ignoring details, such as the type and the exact position of each amino acid, this abstract and compact description allows to focus on the interactions' structure and organization. Interaction networks for proteins of known structure can be easily obtained using the information available in Protein Data Bank. We study amino acid interaction networks using graph theory tools in order to determine their main characteristics, such as mean degree, degree distribution, mean node distances, etc. Some of these characteristics are common to all proteins while others are different for different classes of proteins

Modelling a Multi-Modal Logistic Network with Agents and Dynamic Graphs

International audienceThis paper presents a model of a logistic system. Our goal is to understand how such a system (with numerous stakeholders) behaves and evolves according to different constraints or scenarios. We adopted a complex system approach which leads us to propose an agent-based model coupled with dynamic graphs. It allows us to represent the properties, constraints and behaviours at a local level of a logistic system in order to reproduce the global behaviours thanks to the simulation in a dynamic context. The simulation (which uses data about the Seine axis) allows to test different scenarios in order to understand how local decisions impact the whole system. For example, this work presents the evolution of the system at the opening of the Seine-Nord Europe Canal. Indeed, this canal is a real major project for Europe, and has numerous economical stakes. So, we first describe the traffic evolution on the multi-modal transportation network (see figures 1 to 4). Then, we observe different other measures (evolution of costs, transportation mode share). Thanks to these analyses, we show that the Seine-Nord Europe Canal should promote the use of the river barges and reduce financial costs. In the same time, it could modify the respective shares of the northern European ports

Lipolytic and oxidative changes in acoustically assisted frozen fattened duck liver

The delicate structure of the fattened duck liver requires rapid freezing as quickly as possible. Acoustically assisted freezing meets both the requirement for quick freezing and energy efficiency. For the purpose of the experiment, a fattened duck liver “foie gras” was used. The degree of lipolysis (acid value) and primary (peroxide value) and secondary (2-thiobarbituric acid value) products of lipid oxidization were examined at 2 h post mortem. The oxidative changes were evaluated after conventional (CF) and acoustically assisted freezing (AAF) and at the 6-th and 12-th month of storage at -18°C. Both time storage and type of freezing affect the degree of lipolysis. The duck liver after AAF had higher degree of lipolysis at the 12-th month of storage at -18°C. The peroxide value increased almost 2 times in both fattened duck livers (CF and AAF) during the 6 months of storage at -18°C and stabilizes until the 12-th month. A conclusion was made that the acoustically assisted freezing of the fattened duck liver did not promote higher lipid oxidation compared to the conventional type of freezing

Quality, Microstructure, and Technological Properties of Sheep

The objective of this study was to explore the effect of 24 and 48 h alkaline (2% pentasodium tripolyphosphate), acid (2% sodium lactate), and water-oil marinating (water : sun flavor oil = 1 : 1 and 2% salt) as well as brine soaking (2% salt) on microstructure, changes in protein, and lipid fractions and technological properties of sheep (m. Longissimus dorsi). Strong myofibrillar fragmentation after 48 h alkaline marinating was observed. Significant swelling and increasing of spaces between myofibrils were found after 24 h brine soaking. Marinating in water-oil emulsions did not show a significant impact on the muscle microstructure. Alkaline and acid marinating as well as salt soaking promote the myofibrillar protein solubility and increased the free amino nitrogen content. After 24 h acid and 48 h alkaline marinating SDS-PAGE electrophoresis showed increasing of 25–30 kDa protein bands. The results obtained for the lipid and protein oxidation confirm prooxidant action of the sodium lactate (2%) and antioxidant effect of polyphosphates (2%) in marinated sheep

A General Model for Amino Acid Interaction Networks.

5 pagesInternational audienceIn this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure

Reconstructing Amino Acid Interaction Networks by an Ant Colony Approach

Summary. In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. We consider the problem of reconstructing protein’s interaction network from its amino acid sequence. We rely on a probability that two amino acids interact as a function of their physico-chemical properties coupled to an ant colony system to solve this problem. Key words: ant algorithm, interaction network, protein structure

Proteins : From Structural Classification to Amino Acid Interaction Networks.

7 pagesInternational audienceIn this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. Some of them are common to all proteins, while others depend on the structure arrangement. The last group of properties allows to characterize structural classes, defined by CATH or SCOP, in the terms of interaction network properties

Characterization of amino acid interaction networks in proteins

National audienceA protein interaction network is a graph whose vertices are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we study the properties of these networks. In particular, we are interested in the degree distribution and mean degree of the vertices. The results presented in this paper constitute the first steps of a new network approach to the protein folding problem

Node Degree Distribution in Amino Acid Interaction Networks

6 pagesInternational audienceA protein interaction network is a graph whose vertices are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we study the properties of these networks. In particular, we are interested in the degree distribution and mean degree of the vertices. The results presented in this paper constitute the first steps of a new network approach to the protein folding problem