A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study

Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling

The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.

Association of Alpha-Crystallin with Fiber Cell Plasma Membrane of the Eye Lens Accompanied by Light Scattering and Cataract Formation

α-crystallin is a major protein found in the mammalian eye lens that works as a molecular chaperone by preventing the aggregation of proteins and providing tolerance to stress in the eye lens. These functions of α-crystallin are significant for maintaining lens transparency. However, with age and cataract formation, the concentration of α-crystallin in the eye lens cytoplasm decreases with a corresponding increase in the membrane-bound α-crystallin, accompanied by increased light scattering. The purpose of this review is to summarize previous and recent findings of the role of the: (1) lens membrane components, i.e., the major phospholipids (PLs) and sphingolipids, cholesterol (Chol), cholesterol bilayer domains (CBDs), and the integral membrane proteins aquaporin-0 (AQP0; formally MIP26) and connexins, and (2) α-crystallin mutations and post-translational modifications (PTMs) in the association of α-crystallin to the eye lens's fiber cell plasma membrane, providing thorough insights into a molecular basis of such an association. Furthermore, this review highlights the current knowledge and need for further studies to understand the fundamental molecular processes involved in the association of α-crystallin to the lens membrane, potentially leading to new avenues for preventing cataract formation and progression.

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

Proteins are a diverse set of biological molecules responsible for numerous functions within cells, such as obtaining energy from food or transport of small molecules, and many processes rely on interactions of specific proteins. Moreover, a single protein may acquire different roles depending on cellular requirements and as a response to changes in the environment. A commonly used way to quickly change protein’s function or activity is by introducing small chemical modifications on specific locations within the protein. These modifications can cause the protein to interact in a more or less stable way with other proteins. We have previously developed a computational pipeline for predicting the effect of modifications on interactions of proteins, and in this work we apply it to all yeast proteins with known structures. We find differences in effects on the binding for different types of modifications. Importantly, we demonstrate that the modifications far from the interaction interface also significantly contribute to binding due to their impact on protein’s shape, which is often neglected by other methods. This work contributes to our understanding of the modulation of protein interactions in yeast due to modifications, while our widely applicable method will allow similar investigations in other organisms.

Dimeric phosphorylation of glyoxalase I alters its symmetry and substrate binding mechanism: simulation studies

Glyoxalase I (GLO1) is a dimeric esterase of the glyoxalase system. Phosphorylation of the residue T106 has been found to inhibit GLO1 activity, and contribute to the onset of oxidative stress and cellular damage. This research uses multiple molecular dynamics simulations and automated docking of both GLO1 and dimerically phosphorylated GLO1 (p2-GLO1) to predict the initial structural differences induced by phosphorylation, and their interaction with the intermediate substrate Hemimercaptal. This research indicates that immediately following phosphorylation, GLO1 exhibits reduced sphericity, partly caused by outward splaying of the loop region surrounding T106. Phosphorylation induces enhanced concerted motions in the loop composed of residues immediately surrounding T106, which are correlated with motions at the active site pocket at the distant, opposite end of the dimer. These T106 region loop motions result in the distortion of the shape of the active site, and potentially alter its accessibility. Phosphorylation alters the manner in which GLO1 interacts with Hemimercaptal. For GLO1, Hemimercaptal is predicted to bind to T106, which we propose constitutes a novel, highly accessible 'capture site' responsible for initial contact with the substrate. In contrast, for p2-GLO1, Hemimercaptal is unable to bind favourably to (phosphorylated) position T106, suggesting that this proposed transient 'capture site' is abolished upon phosphorylation of GLO1. Hence, a novel physiological role is here proposed for the known essential GLO1 residue T106. These results may further contribute to understanding the inhibition mechanism of GLO1 upon phosphorylation.Communicated by Ramaswamy H. Sarma.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

BACKGROUND

Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process.

OBJECTIVE

The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design.

METHOD

This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained.

RESULTS

This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations.

CONCLUSION

The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus

The assembly of human cytomegalovirus (HCMV) virions is an orchestrated process that requires, as an essential prerequisite, the complex crosstalk between viral structural proteins. Currently, however, the mechanisms governing the successive steps in the constitution of virion protein complexes remain elusive. Protein phosphorylation is a key regulator determining the sequential changes in the conformation, binding, dynamics, and stability of proteins in the course of multiprotein assembly. In this review, we present a comprehensive map of the HCMV virion proteome, including a refined view on the virion phosphoproteome, based on previous publications supplemented by new results. Thus, a novel dataset of viral and cellular proteins contained in HCMV virions is generated, providing a basis for future analyses of individual phosphorylation steps and sites involved in the orchestrated assembly of HCMV virion-specific multiprotein complexes. Finally, we present the current knowledge on the activity of pUL97, the HCMV-encoded and virion-associated kinase, in phosphorylating viral and host proteins.

Advances in distributed computing with modern drug discovery

INTRODUCTION

Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms. Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD). Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.

How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study

Pyruvate (PYR) dehydrogenase complex (PDC) is an enzymatic system that plays a crucial role in cellular metabolism as it controls the entry of carbon into the Krebs cycle. From a structural point of view, PDC is formed by three different subunits (E1, E2 and E3) capable of catalyzing the three reaction steps necessary for the full conversion of pyruvate to acetyl-CoA. Recent investigations pointed out the crucial role of this enzyme in the replication and survival of specific cancer cell lines, renewing the interest of the scientific community. Here, we report the results of our molecular dynamics studies on the mechanism by which posttranslational modifications, in particular the phosphorylation of three serine residues (Ser-264-α, Ser-271-α, and Ser-203-α), influence the enzymatic function of the protein. Our results support the hypothesis that the phosphorylation of Ser-264-α and Ser-271-α leads to (1) a perturbation of the catalytic site structure and dynamics and, especially in the case of Ser-264-α, to (2) a reduction in the affinity of E1 for the substrate. Additionally, an analysis of the channels connecting the external environment with the catalytic site indicates that the inhibitory effect should not be due to the occlusion of the access/egress pathways to/from the active site.

Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes

Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.

Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations

ADP-ribosylhydrolases (ARH1, ARH2 and ARH3) are a family of enzymes to catalyze ADP-ribosylation, a reversible and covalent post-translational modification (PTM). There are four phosphorylated sites (Tyr-4, Tyr-19, Tyr-20, and Tyr-205) in ARH1. To explore the structural changes and functional impact induced by phosphorylation, molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations were performed for the phosphorylated and non-phosphorylated ARH1 with the ligands. MD simulations results indicate that: (1) Glu-25 is more frequently in the α helix group in the phosphorylated state with the adenosine-5-diphosphate-ribosylarginine (ADP-RA) complex (51.56%) than that of the non-phosphorylated state(2.12%); (2) Ser-124 and Ser-264 become less flexible in the phosphorylated state with ADP-RA complex, which helps two residues form hydrogen bonds with ADP-RA; and (3) Tyr-211 is also less flexible in the phosphorylated state with ADP-RA complex, which helps stabilize the cation-π interaction of Y211-R119. All these changes facilitate ADP-RA to bind ARH1. In addition, according to the crystal structure of adenosine-5-diphosphate-ribose (ADP-ribose) in complex with non-phosphorylated and phosphorylated ARH1, the possible unbinding pathways of ADP-ribose from non-phosphorylated and phosphorylated ARH1 were explored respectively using SMD simulations. Our results show that phosphorylated ARH1 has more ordered structures than the non-phosphorylated type.

Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations

Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (Egap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design.

The function of small heat-shock proteins and their implication in proteostasis

All organisms rely on a conserved cellular machinery supporting and controlling the life cycle of proteins: the proteostasis network. Within this network, the main players that determine the fate of proteins are molecular chaperones, the ubiquitin–proteasome and the lysosome–autophagy systems. sHsps (small heat-shock proteins) represent one family of molecular chaperones found in all domains of life. They prevent irreversible aggregation of unfolded proteins and maintain proteostasis by stabilizing promiscuously a variety of non-native proteins in an ATP-independent manner. In the cellular chaperone network, sHsps act as the first line of defence and keep their substrates in a folding-competent state until they are refolded by downstream ATP-dependent chaperone systems. Besides this interaction with unfolding substrates upon stress, sHsps show a different mode of binding for specific clients which are also recognized under physiological conditions. In vertebrates, sHsps are especially needed to maintain the refractive index of the eye lens. Additionally, sHsps are linked to a broad variety of diseases such as myopathies and neuropathies. The most striking feature of sHsps is their ability to form dynamic ensembles of higher oligomers. The activity of sHsps is regulated by changes in the composition of the ensembles.