Current Protein and Peptide Science - Volume 8, Issue 2, 2007

This issue of Current Protein and Peptide Science is devoted to the emerging field of likelihood of protein crystallization and is related to the seminars and lectures presented recently at the Workshop on the definition of protein domains and their likelihood of crystallization, held in Vienna at the end of June 2006 (http://www.emblhamburg. de/workshops/2006/domains/), where a number of scientists addressed these questio Read More

Efficient target selection methods are an important prerequisite for increasing the success rate and reducing the cost of high-throughput structural genomics efforts. There is a high demand for sequence-based methods capable of predicting experimentally tractable proteins and filtering out potentially difficult targets at different stages of the structural genomic pipeline. Simple empirical rules based on anecdotal evidence are Read More

In the last years there has been an increasing amount of experimental evidence pointing out that a large number of proteins are either fully or partially disordered (unstructured). Intrinsically disordered proteins are ubiquitary proteins that fulfil essential biological functions while lacking highly populated and uniform secondary and tertiary structure under physiological conditions. Despite the large abundance of disorder, Read More

The failure to produce and/or crystallize proteins is often due to their modular structure. There exists therefore considerable interest to develop strategies for tailoring proteins into crystallizable domains. In the framework of a Structural Genomics Project on soluble yeast proteins, we have tested the expression of numerous genetic constructs of our targets in order to produce and crystallize proteins and protein domains an Read More

Intrinsically disordered/unstructured proteins exist in a highly flexible conformational state largely devoid of secondary structural elements and tertiary contacts. Despite their lack of a well defined structure, these proteins often fulfill essential regulatory functions. The intrinsic lack of structure confers functional advantages on these proteins, allowing them to adopt multiple conformations and to bind to different bindin Read More

Intrinsically unstructured/disordered proteins (IUPs) and protein domains lack a well-defined three-dimensional structure under physiological conditions. Structural disorder imparts advantages in many non-conventional functions, which poses a significant challenge to our understanding of the structure-function relationship of proteins. The general appreciation of this fact, however, is hampered by the large gap in our knowl Read More

Domain prediction from sequence is a particularly challenging task, and currently, a large variety of different methodologies are employed to tackle the task. Here we try to classify these diverse approaches into a number of broad categories. Completely automatic domain prediction from sequence alone is currently fraught with problems, but this should not be so surprising since human experts currently have significant di Read More

Prediction of protein domain boundaries is an important step for the prediction of three-dimensional structure. The simple method PDP has been elaborated for prediction of the number and position of domain boundaries in multidomain proteins by use of amino acid sequence alone. The method uses an optimized scale based on the statistics of appearance of amino acid residues at domain boundaries. Our method demo Read More

Given the huge number of sequences of otherwise uncharacterized protein sequences, computer-aided prediction of posttranslational modifications (PTMs) and translocation signals from amino acid sequence becomes a necessity. We have contributed to this multi-faceted, worldwide effort with the development of predictors for GPI lipid anchor sites, for N-terminal N-myristoylation sites, for farnesyl and geranylgeranyl anchor att Read More

With recent advances in the technology and software underlying crystallographic structure solution, demands on both output and functional significance of X-ray structures are soaring. To achieve the required speed and quality also with ever larger and more difficult targets, combining HTP screening methods (robotics based or not) adopted from structural genomics initiatives with thorough expertise and dedicated char Read More