Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users

Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank

About 5% of the disulfide bonds (DBs) observed in the Protein Data Bank bridge two protein chains. Several of their features were comprehensively analyzed, resulting in a structural atlas of the intermolecular DBs. The analysis was performed on a very large set of data extracted from the Protein Data Bank, according to the RaSPDB procedure. It was observed that the two chains tend to have different sequences and belong to the same structural class. Intermolecular DBs tend to be more solvent accessible and less distorted from the most stable conformation than intermolecular DBs while showing similar B-factors. They tend to occur in beta strands and in mainly-beta structures. These and other data should prove useful in protein modelling and design.

Random sampling of the Protein Data Bank: RaSPDB

A novel and simple procedure (RaSPDB) for Protein Data Bank mining is described. 10 PDB subsets, each containing 7000 randomly selected protein chains, are built and used to make 10 estimations of the average value of a generic feature F—the length of the protein chain, the amino acid composition, the crystallographic resolution, and the secondary structure composition. These 10 estimations are then used to compute an average estimation of F together with its standard error. It is heuristically verified that the dimension of these 10 subsets—7000 protein chains—is sufficiently small to avoid redundancy within each subset and sufficiently large to guarantee stable estimations amongst different subsets. RaSPDB has two major advantages over classical procedures aimed to build a single, non-redundant PDB subset: a larger fraction of the information stored in the PDB is used and an estimation of the standard error of F is possible.

Chalcogen Bonds Involving Selenium in Protein Structures

Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.

Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions

Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88-90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction.

Packing topology in crystals of proteins and small molecules: a comparison

We compared the topologies of protein and small molecule crystals, which have many common features - both are molecular crystals with intermolecular interactions much weaker than intramolecular interactions. They also have different features - a considerably large fraction of the volume of protein crystals is occupied by liquid water while no room is available to other molecules in small molecule crystals. We analyzed the overall and local topology and performed multilevel topological analyses (with the software package ToposPro) of carefully selected high quality sets of protein and small molecule crystal structures. Given the suboptimal packing of protein crystals, which is due the special shape and size of proteins, it would be reasonable to expect that the topology of protein crystals is different from the topology of small molecule crystals. Surprisingly, we discovered that these two types of crystalline compounds have strikingly similar topologies. This might suggest that molecular crystal formations share symmetry rules independent of molecular dimension.

Waters in room temperature and cryo protein crystal structures

Since it has been observed that low temperature protein crystal structures may differ from room temperature structures, it is necessary to compare systematically the protein hydration structure in low and room protein crystal structures. High quality data sets of protein structures were built in an extremely rigorous manner and crystal symmetry was included in the identification of four types of water molecules (buried in the protein core, deeply inserted into crevices at the protein surface, first and second hydration layers). More water molecules are observed at low temperature only if the resolution is better than 2.1–2.3 Å. At worse resolution, temperature does not play any role. The numerous water molecules that become detectable at low temperature and at higher resolution are more mobile, relative to the protein average flexibility. Despite that, the occupancy does not depend on temperature. It can be hypothesized that water structure and around proteins and hydrogen bond network do not depend on the temperature, at least in the temperature range examined here. At low temperature more water molecules are detected because the average flexibility of all the atoms decreases, so that also water molecules that are considerably more mobile than the average atoms become observable in the electron density maps.