Solution structure and internal dynamics of NSCP, a compact calcium-binding protein

Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation

Okadaic acid (OA) is a marine polyether cytotoxin that was first isolated from the marine sponge Halichondria okadai. OA is a potent inhibitor of protein serine/threonine phosphatases (PP) 1 and 2A, and the structural basis of phosphatase inhibition has been well investigated. However, the role and mechanism of OA retention in the marine sponge have remained elusive. We have solved the crystal structure of okadaic acid binding protein 2.1 (OABP2.1) isolated from H. okadai; it has strong affinity for OA and limited sequence homology to other proteins. The structure revealed that OABP2.1 consists of two α-helical domains, with the OA molecule deeply buried inside the protein. In addition, the global fold of OABP2.1 was unexpectedly similar to that of aequorin, a jellyfish photoprotein. The presence of structural homologues suggested that, by using similar protein scaffolds, marine invertebrates have developed diverse survival systems adapted to their living environments.

Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein

The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.

A computational investigation of allostery in the catabolite activator protein

The catabolite activator protein is a dimer that consists of two cAMP-binding subunits, each containing a C-terminus DNA-binding module and a N-terminus ligand binding domain. The system is well-known to exhibit negative cooperativity, whereby the binding of one cAMP molecule reduces the binding affinity of the other cAMP molecule by 2 orders of magnitude, despite the large separation between the cAMP binding pockets. Here we use extensive explicit-solvent molecular dynamics simulations (135 ns) to investigate the allosteric mechanism of CAP. Six trajectories were carried out for apo, singly liganded, and doubly liganded CAP, both in the presence and absence of DNA. Thorough analyses of the dynamics through the construction of dynamical cross-correlated maps, as well as essential dynamics analyses, indicated that the system experienced a switch in motion as a result of cAMP binding, in accordance with recent NMR experiments carried out on a truncated form of the protein. Analyses of conformer structures collected from the simulations revealed a remarkable event: the DNA-binding module was found to dissociate from the N-terminus ligand binding domain. An interesting aspect of this structural change is that it only occurred in unoccupied subunits, suggesting that the binding of cAMP provides additional stability to the system, consistent with the increase in entropy that was observed in our calculations and from isothermal titration calorimetry. Analysis of the distribution of intrinsic disorder propensities in CAP amino acid sequence using PONDR VLXT and VSL1 predictors revealed that the region connecting ligand-binding and DNA-binding domains of CAP have the potential to exhibit increased flexibility. We complemented these trajectories with free energy calculations following the MM-PBSA approach on more than 2000 snapshots that included 880 normal mode analysis. The resulting free energy differences between the singly liganded and doubly liganded states were in excellent agreement with isothermal titration calorimetry data. When the free energy calculations were carried out in the presence of DNA, we discovered that a switch in cooperativity occurred, so that the binding of the first cAMP promoted the binding of the other cAMP. The components of the free energy reveal that this effect is mainly entropic in nature, whereby the DNA reduces the degree of tightening that is observed in its absence, thereby promoting binding of the second cAMP. This finding prompted us to propose a new mechanism by which CAP triggers the transcription activation that is based on an order to disorder transition mediated by cAMP binding as well as DNA.

Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs

The ‘EF-hand’ Ca2+-binding motif plays an essential role in eukaryotic cellular signalling, and the proteins containing this motif constitute a large and functionally diverse family. The EF-hand is defined by its helix–loop–helix secondary structure as well as the ligands presented by the loop to bind the Ca2+ ion. The identity of these ligands is semi-conserved in the most common (the ‘canonical’) EF-hand; however, several non-canonical EF-hands exist that bind Ca2+ by a different co-ordination mechanism. EF-hands tend to occur in pairs, which form a discrete domain so that most family members have two, four or six EF-hands. This pairing also enables communication, and many EF-hands display positive co-operativity, thereby minimizing the Ca2+ signal required to reach protein saturation. The conformational effects of Ca2+ binding are varied, function-dependent and, in some cases, minimal, but can lead to the creation of a protein target interaction site or structure formation from a molten-globule apo state. EF-hand proteins exhibit various sensitivities to Ca2+, reflecting the intrinsic binding ability of the EF-hand as well as the degree of co-operativity in Ca2+ binding to paired EF-hands. Two additional factors can influence the ability of an EF-hand to bind Ca2+: selectivity over Mg2+ (a cation with very similar chemical properties to Ca2+ and with a cytoplasmic concentration several orders of magnitude higher) and interaction with a protein target. A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities.

Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection

To better understand the pathogenesis of white spot syndrome virus (WSSV) and to determine which cell pathways might be affected after WSSV infection, two-dimensional gel electrophoresis (2-DE) was used to produce protein expression profiles from samples taken at 48 h post-infection (hpi) from the stomachs of Litopenaeus vannamei (also called Penaeus vannamei) that were either specific pathogen free or else infected with WSSV. Seventy-five protein spots that consistently showed either a marked change (>50%) in accumulated levels or else were highly expressed throughout the course of WSSV infection were selected for further study. After in-gel trypsin digestion followed by LC-nanoESI-MS/MS, bioinformatics databases were searched for matches. A total of 53 proteins were identified, with functions that included energy production, calcium homeostasis, nucleic acid synthesis, signaling/communication, oxygen carrier/transportation, and SUMO-related modification. 2-DE results were shown to be consistent with relative EST database data from a previously developed EST database of two Penaeus monodon cDNA libraries. For seven selected genes, 2-DE and EST data were also compared with transcriptional time-course RT-PCR data. This study is the first global analysis of differentially expressed proteins in WSSV-infected shrimp, and in addition to increasing our understanding of the molecular pathogenesis of this virus-associated shrimp disease, the results presented here should be useful both for identifying potential biomarkers and for developing antiviral measures.

A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure

Calmodulin is a small (148 residues), ubiquitous, highly-conserved Ca(2+) binding protein serving as a modulator of many calcium-dependent processes. In this study, we followed, by means of molecular dynamics, the structural stability of the protein when one of its four bound Ca(2+) ions is removed, and compared it to a simulation of the fully Ca(2+) bound protein. We found that the removal of a single Ca(2+) ion from the N-lobe of the protein, which has a lower affinity for the ion, is sufficient to initiate a considerable structural rearrangement. Although the overall structure of the fully 4 Ca(2+) bound protein remained intact in the extended conformation, the Ca(2+)-removed protein changed its conformation into a compact state. The observation that the 3 Ca(2+) loaded protein assumes a compacted solution state is in accord with experimental observation that the NSCP protein, which binds only three Ca(2+) ions, is natively in a compact state. Examination of the folding dynamics reveals a cooperation between the C-lobe, N-lobe, and the interdomain helix that enable the conformation change. The forces driving this conformational change are discussed.