A structural study for the optimisation of functional motifs encoded in protein sequences

BACKGROUND: A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. RESULTS: Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. CONCLUSION: Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available

Query3d: a new method for high-throughput analysis of functional residues in protein structures

BACKGROUND: The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. RESULTS: Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. CONCLUSION: With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface

pdbFun: mass selection and fast comparison of annotated PDB residues

pdbFun () is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide–domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites

Phosphorylation is the most common protein post-translational modification. Phosphorylated residues (serine, threonine and tyrosine) play critical roles in the regulation of many cellular processes. Since the amount of data produced by screening assays is growing continuously, the development of computational tools for collecting and analysing experimental data has become a pivotal task for unravelling the complex network of interactions regulating eukaryotic cell life. Here we present Phospho3D, , a database of 3D structures of phosphorylation sites, which stores information retrieved from the phospho.ELM database and is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites

Dietary Iron Intake Has Long-Term Effects on the Fecal Metabolome and Microbiome

Iron is essential for life, but its imbalances can lead to severe health implications. Iron deficiency is the most common nutrient disorder worldwide, and iron disregulation in early life has been found to cause long-lasting behavioral, cognitive, and neural effects. However, little is known about the effects of dietary iron on gut microbiome function and metabolism. In this study, we sought to investigate the impact of dietary iron on the fecal metabolome and microbiome by using mice fed with three diets with different iron content: an iron deficient, an iron sufficient (standard), and an iron overload diet for seven weeks. Additionally, we sought to understand whether any observed changes would persist past the 7-week period of diet intervention. To assess this, all feeding groups were switched to a standard diet, and this feeding continued for an additional 7 weeks. Analysis of the fecal metabolome revealed that iron overload and deficiency significantly alter levels of peptides, nucleic acids, and lipids, including di- and tri-peptides containing branched-chain amino acids, inosine and guanosine, and several microbial conjugated bile acids. The observed changes in the fecal metabolome persist long after the switch back to a standard diet, with the cecal gut microbiota composition and function of each group distinct after the 7-week standard diet wash-out. Our results highlight the enduring metabolic consequences of nutritional imbalances, mediated by both host and gut microbiome, which persist after returning to original standard diets

3dLOGO:a web server for the identification, analysis and use of conserved protein substructures

3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it

Owner motivation in small size family farms: insights from an exploratory study on the ornamental plant industry

Owner motivations are a relatively new area of investigation, which has seen over the last fifteen years the succession of numerous articles and studies.Therefore an in-depth study of the owner motivation can become an useful and strategic tool for improving strategies of small firm success. This case study particularly aims to analyse this phenomenon in the context of the ornamental plant sector, considering that the characteristics of this sector may be indicative of the ongoing dynamics for modern agricultural productions. The analysis was designed and planned in order to identify the owners motivations within family farm and it was conducted by segmenting the sample into two sub-samples according to a range of different production (short or long productive cycle) and economic size farm.Results allow to highlight how emotion item is particularly relevant for owners in both groups. Affective motivation is a key factors influencing the actions and business approaches of respondents. In addition inheritance is another predominant motivation among respondents that prompted the decision to become an owner. The findings also show interesting questions that could have on the potential impact about the owner’s decision-making. In fact, we have identified two aspects of owner action, which can be exclusively the competence of the individual (Group A), or well distinct among managerial responsible management and commitment to operational management skills and more knowledge of human resources (Group B). Despite the limit of the research, this study contributes to report the results for a specific region and a specific sector, its empirical applications could reasonably be extensible and also applicable to other similar agricultural sectors of the Mediterranean, with a high level of technological innovation and a high level of owners’ know-how where there remains a strong link between businesses and socio-familiar context.\ud \ud \ud Keywords: micro size farms, innovation, ownership, organization training management

Development of Computational Tools for the Inference of Protein Interaction Specificity Rules and Functional Annotation Using Structural Information

Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry). Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods