Calcium-induced calmodulin conformational change. Electrochemical evaluation

Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field

Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.

Cell shape and tension alter focal adhesion structure

Cells are not only anchored to the extracellular matrix via the focal adhesion complex, the focal adhesion complex also serves as a sensor for force transduction. How tension influences the structure of focal adhesions is not well understood. Here, we analyse the effect of tension on the location of key focal adhesion proteins, namely vinculin, paxillin and actin. We use micropatterning on gold surfaces to manipulate the cell shape, to create focal adhesions at specific cell areas, and to perform metal-induced energy transfer (MIET) measurements on the patterned cells. MIET resolves the different protein locations with respect to the gold surface with nanometer accuracy. Further, we use drugs influencing the cellular motor protein myosin or mechanosensitive ion channels to get deeper insight into focal adhesions at different tension states. We show here that in particular actin is affected by the rationally tuned force balance. Blocking mechanosensitive ion channels has a particularly high influence on the actin and focal adhesion architecture, resulting in larger focal adhesions with elevated paxillin and vinculin and strongly lowered actin stress fibres. Our results can be explained by a balance of adhesion tension with cellular tension together with ion channel-controlled focal adhesion homeostasis, where high cellular tension leads to an elevation of vinculin and actin, while high adhesion tension lowers these proteins.

Identification of Saccharum CaM gene family and function characterization of ScCaM1 during cold and oxidant exposure in Pichia pastoris

BACKGROUND

Calmodulin (CaM) plays an essential role in binding calcium ions and mediating the interpretation of Ca²⁺ signals in plants under various stresses. However, the evolutionary relationship of CaM family proteins in Saccharum has not been elucidated.

OBJECTIVE

To deduce and explore the evolution and function of Saccharum CaM family.

METHODS

A total of 104 typical CaMs were obtained from Saccharum spontaneum and other 18 plant species. The molecular characteristics and evolution of those CaM proteins were analyzed. A typical CaM gene, ScCaM1, was subsequently cloned from sugarcane (Saccharum spp. hybrid). Its expression patterns in different tissues and under various abiotic stresses were assessed by quantitative real-time PCR. Then the green fluorescent protein was used to determine the subcellular localization of ScCaM1. Finally, the function of ScCaM1 was evaluated via heterologous yeast expression systems.

RESULTS

Three typical CaM members (SsCaM1, SsCaM2, and SsCaM3) were identified from the S. spontaneum genome database. CaMs were originated from the two last common ancestors before the origin of angiosperms. The number of CaM family members did not correlate to the genome size but correlated with allopolyploidization events. The ScCaM1 was more highly expressed in buds and roots than in other tissues. The expression patterns of ScCaM1 suggested that it was involved in responses to various abiotic stresses in sugarcane via different hormonal signaling pathways. Noteworthily, its expression levels appeared relatively stable during the cold exposure in the cold-tolerant variety but significantly suppressed in the cold-susceptible variety. Moreover, the recombinant yeast (Pichia pastoris) overexpressing ScCaM1 grew better than the wild-type yeast strain under cold and oxidative stresses. It was revealed that the ScCaM1 played a positive role in reactive oxygen species scavenging and conferred enhanced cold and oxidative stress tolerance to cells.

CONCLUSION

This study provided comprehensive information on the CaM gene family in Saccharum and would facilitate further investigation of their functional characterization.

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin

Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca²⁺), or vice versa, may provide insight into how Ca²⁺-CaM selects its target binding proteins. However, modeling of Ca²⁺-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the two lobes are relatively rigid due to tight binding of the Ca²⁺ to the calcium-binding loops where the loop forms a pentagonal bipyramidal coordination geometry with Ca²⁺. This feature that underlies the reciprocal relation between Ca²⁺ binding and target binding of CaM, however, has yet to be considered in the structural modeling. Here, we presented a coarse-grained model based on the Associative memory, Water mediated, Structure, and Energy Model (AWSEM) protein force field, to investigate the salient features of CaM. Particularly, we optimized the force field of CaM and that of Ca²⁺ ions by using its coordination chemistry in the calcium-binding loops to match with experimental observations. We presented a “community model” of CaM that is capable of sampling various conformations of CaM, incorporating various calcium-binding states, and carrying the memory of binding with various targets, which sets the foundation of the reciprocal relation of target binding and Ca²⁺ binding in future studies.

Ca2+/Calmodulin Complex Triggers CAMTA Transcriptional Machinery Under Stress in Plants: Signaling Cascade and Molecular Regulation

Calcium (Ca2+) ion is a critical ubiquitous intracellular second messenger, acting as a lead currency for several distinct signal transduction pathways. Transient perturbations in free cytosolic Ca2+ ([Ca2+]cyt) concentrations are indispensable for the translation of signals into adaptive biological responses. The transient increase in [Ca2+]cyt levels is sensed by an array of Ca2+ sensor relay proteins such as calmodulin (CaM), eventually leading to conformational changes and activation of CaM. CaM, in a Ca2+-dependent manner, regulates several transcription factors (TFs) that are implicated in various molecular, physiological, and biochemical functions in cells. CAMTA (calmodulin-binding transcription activator) is one such member of the Ca2+-loaded CaM-dependent family of TFs. The present review focuses on Ca2+ as a second messenger, its interaction with CaM, and Ca2+/CaM-mediated CAMTA transcriptional regulation in plants. The review recapitulates the molecular and physiological functions of CAMTA in model plants and various crops, confirming its probable involvement in stress signaling pathways and overall plant development. Studying Ca2+/CaM-mediated CAMTA TF will help in answering key questions concerning signaling cascades and molecular regulation under stress conditions and plant growth, thus improving our knowledge for crop improvement.

Caveolin proteins electrochemical oxidation and interaction with cholesterol

Caveolae consist in lipid raft domains composed of caveolin proteins, cholesterol, glycosphingolipids, and GPI-anchored proteins. Caveolin proteins present three different types, caveolin 1 (CAV-1), caveolin 2 (CAV-2) and caveolin 3 (CAV-3), with a very similar structure and amino acid composition. The native caveolin proteins oxidation mechanism was investigated for the first time, at a glassy carbon electrode, using cyclic, square wave and differential pulse voltammetry. The three native caveolin proteins oxidation mechanism presented only one tyrosine and tryptophan amino acid residues oxidation peak. Denatured caveolin proteins presented also the tyrosine, tryptophan and cysteine amino acid residues oxidation peaks. The reverse cholesterol transport is related to caveolae and caveolin proteins, and CAV-1 is directly connected to cholesterol transport. The influence of cholesterol on the three caveolin proteins electrochemical behaviour was evaluated. In the absence and in the presence of cholesterol, significant differences in the CAV-1 oxidation peak current were observed.

In-depth proteomic profiling of left ventricular tissues in human end-stage dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is caused by reduced left ventricular (LV) myocardial function, which is one of the most common causes of heart failure (HF). We performed iTRAQ-coupled 2D-LC-MS/MS to profile the cardiac proteome of LV tissues from healthy controls and patients with end-stage DCM. We identified 4263 proteins, of which 125 were differentially expressed in DCM tissues compared to LV controls. The majority of these were membrane proteins related to cellular junctions and neuronal metabolism. In addition, these proteins were involved in membrane organization, mitochondrial organization, translation, protein transport, and cell death process. Four key proteins involved in the cell death process were also detected by western blotting, indicated that cell death was activated in DCM tissues. Furthermore, S100A1 and eEF2 were enriched in the “cellular assembly and organization” and “cell cycle” networks, respectively. We verified decreases in these two proteins in end-stage DCM LV samples through multiple reaction monitoring (MRM). These observations demonstrate that our understanding of the mechanisms underlying DCM can be deepened through comparison of the proteomes of normal LV tissues with that from end-stage DCM in humans.

Evolutionary Cell Biology of Proteins from Protists to Humans and Plants

During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca²⁺ channels in cilia and replacement by other types during evolution. Altogether components serving Ca²⁺ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca²⁺ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H⁺ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."