Aminonet-a tool to construct and visualize amino acid networks, and to calculate topological parameters

The self-assembly, aggregation and phase transitions of food protein systems in one, two and three dimensions

Abstract: The aggregation of proteins is of fundamental relevance in a number of daily phenomena, as important and diverse as blood coagulation, medical diseases, or cooking an egg in the kitchen. Colloidal food systems, in particular, are examples that have great significance for protein aggregation, not only for their importance and implications, which touches on everyday life, but also because they allow the limits of the colloidal science analogy to be tested in a much broader window of conditions, such as pH, ionic strength, concentration and temperature. Thus, studying the aggregation and self-assembly of proteins in foods challenges our understanding of these complex systems from both the molecular and statistical physics perspectives. Last but not least, food offers a unique playground to study the aggregation of proteins in three, two and one dimensions, that is to say, in the bulk, at air/water and oil/water interfaces and in protein fibrillation phenomena. In this review we will tackle this very ambitious task in order to discuss the current understanding of protein aggregation in the framework of foods, which is possibly one of the broadest contexts, yet is of tremendous daily relevance.

NAPS: Network Analysis of Protein Structures.

Abstract: Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in A) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/.

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization.

Abstract: The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues’ cliques. The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. The thermophiles do not only have the higher number of long-range interactions; they also have larger cluster of connected residues at higher interaction strengths among amino acids, than their mesophilic counterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding and stabilization; at the same time, it shed light on the higher communication ability of hydrophobic subnetworks over the others. The results give an indication of the controlling role of hydrophobic subclusters in determining protein’s folding rate. The occurrences of higher perimeters of hydrophobic and charged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distant part of primary structure of a protein through London van der Waals interaction.

The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory

Abstract: Intra–molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein– ligand and protein–nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra–protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web–based resources for protein complexes, as well as protein network servers and related bioinformatics tools.

Inferring Ancestral Pueblo Social Networks from Simulation in the Central Mesa Verde

Abstract: Understanding exchange is essential for understanding past societies. The exchange of knowledge and goods undeniably influenced the development of Pueblo culture. Previous studies within Southwestern archaeology have mostly focused on the exchange of material goods such as ceramics or prestige items since these items do not decay, while other day-to-day exchanges, such as the exchange of food items, are relatively undetectable in archaeology. Sahlins (1972) notes that in small-scale societies, food exchange is essential for the survival of individuals in patchy landscapes. Moreover, Sahlins’s research shows that cross-culturally in small-scale societies, the exchange of food is one of the fundamental structuring mechanisms for alliances. With this knowledge, we may want to study the exchange of food within societies, but without being able to see the actual exchange, how can archaeologists explore the impact of food exchange given the relatively sparse archaeological record? In this paper, I use computer simulation to explore the extent to which food-sharing practices would have been instrumental for the survival of Ancestral Pueblo people across the patchy landscape of the Prehispanic American Southwest and suggest that we can see direct evidence of exchange through the aggregation of households into clustered settlements. Social networks would have created stable bonds among these exchanging individuals, further helping the survival of those individuals and their progeny. Specifically, I engage Sahlins’s notion of balanced reciprocal exchange networks (BRN; when unrelated individuals rely upon reputation building to inform exchange relationships) within the experimental test-bed of the Village Ecodynamics Project’s agent-based simulation.

The Protein Data Bank

Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

Inference of macromolecular assemblies from crystalline state.

Abstract: We discuss basic physical-chemical principles underlying the formation of stable macromolecular complexes, which in many cases are likely to be the biological units performing a certain physiological function We also consider available theoretical approaches to the calculation of macromolecular affinity and entropy of complexation The latter is shown to play an important role and make a major effect on complex size and symmetry We develop a new method, based on chemical thermodynamics, for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments As found, biological units may be recovered at 80-90% success rate, which makes X-ray crystallography an important source of experimental data on macromolecular complexes and protein-protein interactions The method is implemented as a public WWW service

Network biology: understanding the cell's functional organization

Abstract: A key aim of postgenomic biomedical research is to systematically catalogue all molecules and their interactions within a living cell. There is a clear need to understand how these molecules and the interactions between them determine the function of this enormously complex machinery, both in isolation and when surrounded by other cells. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century.

Evolution of Networks: From Biological Nets to the Internet and WWW

Abstract: Only recently did mankind realise that it resides in a world of networks. The Internet and World Wide Web are changing our life. Our physical existence is based on various biological networks. We have recently learned that the term "network" turns out to be a central notion in our time, and the consequent explosion of interest in networks is a social and cultural phenomenon. The principles of the complex organization and evolution of networks, natural and artificial, are the topic of this book, which is written by physicists and is addressed to all involved researchers and students. The aim of the text is to understand networks and the basic principles of their structural organization and evolution. The ideas are presented in a clear and a pedagogical way, with minimal mathematics, so even students without a deep knowledge of mathematics and statistical physics will be able to rely on this as a reference. Special attention is given to real networks, both natural and artifical. Collected empirical data and numerous real applications of existing theories are discussed in detail, as well as the topical problems of communication networks. Available in OSO: http://www.oxfordscholarship.com/oso/public/content/physics/9780198515906/toc.html