From protein networks to biological systems

A system-level understanding of any biological process requires a map of the relationships among the various molecules involved. Technologies to detect and predict protein interactions have begun to produce very large maps of protein interactions, some including most of an organism's proteins. These maps can be used to study how proteins work together to form molecular machines and regulatory pathways. They also provide a framework for constructing predictive models of how information and energy flow through biological networks. In many respects, protein interaction maps are an entrée into systems biology.     

BIOSENSORS: BLESSING OR BANE?

Biosensor technology is changing the methodology used to detect or characterize many microorganisms and/or their metabolites of importance to food microbiologists and the food industry. Biosensors have been developed to monitor the freshness of meat and fish. ATP and glucose concentrations have been monitored as well as continuous control operations in food processing. Enzyme-substrate transformations, DNA or RNA hybridizations and antibody-antigen interactions are examples of the types of molecules used in biosensor systems. Instrumentation coupled to the biological molecules and measuring the changes that occur include reactions on simple ion-sensing electrodes, as well as complex chips, optical fibers or piezoelectric crystals. In most cases, data can be obtained within a few minutes on very small amounts of compounds. However, the long term stability of the biological molecules involved in these procedures presents a major stumbling block. Partially or completely disposable devices are under consideration.     

Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling.

Peptide-membrane interactions contribute to many important biological processes such as cellular signaling, protein trafficking and ion-channel formation. During receptor-mediated signalling, activated intracellular signalling molecules are often recruited into receptor-induced signaling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein-protein and protein-lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated cellular signalling.     

Eight-carbon volatiles in mushrooms and fungi: properties, analysis, and biosynthesis

Eight-carbon volatiles are ubiquitous among fungi and characteristic of the fungal aroma. They are the product of the oxidation and cleavage of the fatty acid linoleic acid and are classified as oxylipins, molecules taking part in a wide range of biological processes. Their involvement in the fungal aroma, interactions with pests and pathogens, and reproductive events are reviewed here, as well as the enzymic systems involved in their biosynthesis.     

Can we build synthetic,multicellular systems by controlling developmental signaling in space and time?

Using biological machinery to make new, functional molecules is an exciting area in chemical biology. Complex molecules containing both 'natural' and 'unnatural' components are made by processes ranging from enzymatic catalysis to the combination of molecular biology with chemical tools. Here, we discuss applying this approach to the next level of biological complexity -- building synthetic, functional biotic systems by manipulating biological machinery responsible for development of multicellular organisms. We describe recent advances enabling this approach, including first, recent developmental biology progress unraveling the pathways and molecules involved in development and pattern formation; second, emergence of microfluidic tools for delivering stimuli to a developing organism with exceptional control in space and time; third, the development of molecular and synthetic biology toolsets for redesigning or de novo engineering of signaling networks; and fourth, biological systems that are especially amendable to this approach.     

Towards an understating of signal transduction protein interaction networks

Protein network analysis has witnessed a number of advancements in the past for understanding molecular characteristics for important network topologies in biological systems. The signaling pathway regulates cell cycle progression and anti-apoptotic molecules. This pathway is also involved in maintaining cell survival by modulating the activity of apoptosis through RAS, P13K, AKT and BAD activities. The importance of protein-protein interactions to improve usability of the interactome by scoring and ranking interaction data for proteins in signal transduction networks is illustrated using available data and resources.     

Evidence for the Interaction of Nucleotides with Immobilized Amino-acids and its Significance for the Origin of the Genetic Code

ONE of the essential relationships between nucleic acids and amino-acids in present biological systems and perhaps in evolutionary precursors to these systems is expressed in binding and recognition interactions. Such interactions depend on the size, composition and conformation of the interacting species^1–8. When the two reacting species are simple (that is, when neither is polymeric) one cannot expect to observe “specificity” of the sort implied in the biological use of the term. Working with monomeric species in aqueous media permits the effects of individual factors to be assessed so that more complex interactions between these molecules can be understood and their evolutionary potential evaluated.     

Protein surface recognition and proteomimetics: mimics of protein surface structure and function

Due to their key roles in a number of biological processes, protein-protein interactions are attractive and important targets, typically involving areas greater than 6 nm2. The disruption of such interactions remains a challenging feat but, in recent years, there has been considerable progress in the design of proteomimetics: molecules that mimic the structure and function of extended regions of protein surfaces. In particular, porphyrins, calixarenes, alpha-helical mimetics and small molecules have successfully modulated significant protein-protein interactions, including those involved in cancer and HIV.     

Systems genetics in “-omics” era: current and future development

The systems genetics is an emerging discipline that integrates high-throughput expression profiling technology and systems biology approaches for revealing the molecular mechanism of complex traits, and will improve our understanding of gene functions in the biochemical pathway and genetic interactions between biological molecules. With the rapid advances of microarray analysis technologies, bioinformatics is extensively used in the studies of gene functions, SNP–SNP genetic interactions, LD block–block interactions, miRNA–mRNA interactions, DNA–protein interactions, protein–protein interactions, and functional mapping for LD blocks. Based on bioinformatics panel, which can integrate “-omics” datasets to extract systems knowledge and useful information for explaining the molecular mechanism of complex traits, systems genetics is all about to enhance our understanding of biological processes. Systems biology has provided systems level recognition of various biological phenomena, and constructed the scientific background for the development of systems genetics. In addition, the next-generation sequencing technology and post-genome wide association studies empower the discovery of new gene and rare variants. The integration of different strategies will help to propose novel hypothesis and perfect the theoretical framework of systems genetics, which will make contribution to the future development of systems genetics, and open up a whole new area of genetics.     

Orientation and spectral properties of two stilbazolium merocyanine dyes in stretched and unstretched polyvinyl alcohol films

Spectral properties (anisotropy coefficients calculated for absorption, emission and fluorescence decay time) of two stilbazolium merocyanine dyes have been determined to evaluate the applicability of these dyes as sensitizers in photodynamic therapy. The dyes were embedded in an anisotropic polymer matrix. Analysis of the emission decay components measured in polarized light provides information on the interactions of the dye molecules with the polymer matrix being a model of an anisotropic biological system. Different values of the emission anisotropies obtained from various polarized components of fluorescence decays have shown that the orientations of the dye molecules influence their interactions with the polymer. This means that differently oriented dye molecules located in biological systems should exhibit different interactions with membranes. The chain length and type of side groups attached as well as the salt form of the dye molecule were shown to influence the dye-polymer interactions and should be taken into account before the application of merocyanine dyes in medicine. These dyes seem to be promising optical sensors with spectral properties, including the calculated anisotropy coefficients, sensitive to the molecular environment, useful to study orientation and interaction with neighbouring molecules in biological membranes.     

Strategies for the identification and purification of ligands for orphan biomolecules

Summary The isolation of related genes with evolutionary conserved motifs by the application of polymerase chain reaction-based molecular biology techniques, or from database searching strategies, has facilitated the identification of new members of protein families. Many of these protein molecules will be involved in protein-protein interactions (e.g. growth factors, receptors, adhesion molecules), since such interactions are intrinsic to virtually every cellular process. However, the precise biological function and specific binding partners of these novel proteins are frequently unknown, hence they are known as ‘orphan’ molecules. Complementary technologies are required for the identification of the specific ligands or receptors for these and other orphan proteins (e.g., antibodies raised against crude biological extracts or whole cells). We describe herein several alternative strategies for the identification, purification and characterisation of orphan peptide and protein molecules, specifically the synergistic use of micropreparative HPLC and biosensor techniques. These authors made equivalent contributions.     

Structure-wise discrimination of cytosine,thymine, and uracil by proteins in terms of their nonbonded interactions

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein–ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue–ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.     

Differences between non-specific and bio-specific, and between equilibrium and non-equilibrium, interactions in biological systems

The interaction forces between biological molecules and surfaces are much more complex than those between non-biological molecules or surfaces, such as colloidal particle surfaces. This complexity is due to a number of factors: (i) the simultaneous involvement of many different molecules and different non-covalent forces - van der Waals, electrostatic, solvation (hydration, hydrophobic), steric, entropic and 'specific', and (ii) the flexibility of biological macromolecules and fluidity of membranes. Biological interactions are better thought of as 'processes' that evolve in space and time and, under physiological conditions, involve a continuous input of energy. Such systems are, therefore, not at thermodynamic equilibrium, or even tending towards equilibrium. Recent surface forces apparatus (SFA) and atomic force microscopy (AFM) measurements on supported model membrane systems (protein-containing lipid bilayers) illustrate these effects. It is suggested that the major theoretical challenge is to establish manageable theories or models that can describe the spatial and time evolution of systems consisting of different molecules subject to certain starting conditions or energy inputs.     

Mass spectrometry-based proteomics for systems biology

Mass spectrometry (MS)-based proteomics has significantly contributed to the development of systems biology, a new paradigm for the life sciences in which biological processes are addressed in terms of dynamic networks of interacting molecules. Because of its advanced analytical capabilities, MS-based proteomics has been used extensively to identify the components of biological systems, and it is the method of choice to consistently quantify the effects of network perturbation in time and space. Herein, we review recent contributions of MS to systems biology and discuss several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks.     

Electrostatic recognition between enzyme and inhibitor: interaction between papain and leupeptin

Electrostatic forces are involved in a wide variety of molecular interactions that are of biological interest, including, among others, DNA-Protein interactions, protein folding, and the interactions between enzymes and their substrates and inhibitors. In this work, the interaction between papain and an inhibitor, leupeptin, is analyzed from the point of view of their electrostatic interaction. The computations enable one to suggest that negatively charged amino acids located in the region of the active site are responsible for creating an environment that enables efficient binding of the inhibitor. This binding occurs despite the fact that the net global charge of both molecules is positive; an explanation for this apparent contradiction is proposed.     

Electrodynamics of Lipid Membrane Interactions in the Presence of Zwitterionic Buffers

Due to thermal motion and molecular polarizability, electrical interactions in biological systems have a dynamic character. Zwitterions are dipolar molecules that typically are highly polarizable and exhibit both a positive and a negative charge depending on the pH of the solution. We use multilamellar structures of common lipids to identify and quantify the effects of zwitterionic buffers that go beyond the control of pH. We use the fact that the repeat spacing of multilamellar lipid bilayers is a sensitive and accurate indicator of the force balance between membranes. We show that common buffers can in fact charge up neutral membranes. However, this electrostatic effect is not immediately recognized because of the concomitant modification of dispersion (van der Waals) forces. We show that although surface charging can be weak, electrostatic forces are significant even at large distances because of reduced ionic screening and reduced van der Waals attraction. The zwitterionic interactions that we identify are expected to be relevant for interfacial biological processes involving lipid bilayers, and for a wide range of biomaterials, including amino acids, detergents, and pharmaceutical drugs. An appreciation of zwitterionic electrodynamic character can lead to a better understanding of molecular interactions in biological systems and in soft materials in general.     

Protein–protein interactions and selection: yeast-based approaches that exploit guanine nucleotide-binding protein signaling

For elucidating protein–protein interactions, many methodologies have been developed during the past two decades. For investigation of interactions inside cells under physiological conditions, yeast is an attractive organism with which to quickly screen for hopeful candidates using versatile genetic technologies, and various types of approaches are now available.Among them, a variety of unique systems using the guanine nucleotide-binding protein (G-protein) signaling pathway in yeast have been established to investigate the interactions of proteins for biological study and pharmaceutical research. G-proteins involved in various cellular processes are mainly divided into two groups: small monomeric G-proteins,and heterotrimeric G-proteins. In this minireview, we summarize the basic principles and applications of yeast-based screening systems, using these two types of G-protein, which are typically used for elucidating biological protein interactions but are differentiated from traditional yeast two-hybrid systems.     

Production of useful secondary metabolites in plants: Functional genomics approaches

The paradigm of biological research has been changed by recent developments in genomics, high-throughput biology, and bioinformatics. Conventional biology often was based on empirical, labor-intensive, and time-consuming methods. In the new paradigm, biological research e is driven by a holistic approach on the basis of rational, automatic, and high-throughput methods. New functional compounds can be discovered by using high-throughput screening systems. Secondary metabolite pathways and the genes involved in those pathways are then determined by studying functional genomics in conjunction with the data-mining tools of bioinformatics. In addition, these advances in metabolic engineering enable researchers to confer new secondary metabolic pathways to crops by transferring three to five, or more, heterologous genes taken from various other species. In the future, engineering for the production of useful compounds will be designed by a set of software tools that allows the user to specify a cell’s genes, proteins, and other molecules, as well as their individual interactions.