The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics

Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca2+ ions, which enables CaM to function on wide range of Ca2+ ion concentrations. EF-hand loops are 2–3 times more flexible in apo CaM whereas least flexible in Ca2+/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca2+/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca2+/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif.

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The interaction of IQGAPs with calmodulin-like proteins

Biochemical Society Transactions ◽

10.1042/bst0390694 ◽

2011 ◽

Vol 39 (2) ◽

pp. 694-699 ◽

Cited By ~ 13

Author(s):

Sevvel Pathmanathan ◽

Elaine Hamilton ◽

Erwan Atcheson ◽

David J. Timson

Keyword(s):

Protein Interactions ◽

Light Chain ◽

Protein Protein Interactions ◽

Iq Motif ◽

Calcium Dependent ◽

Essential Light Chain ◽

Cellular Processes ◽

Wide Range ◽

Related Proteins ◽

Do So

Since their identification over 15 years ago, the IQGAP (IQ-motif-containing GTPase-activating protein) family of proteins have been implicated in a wide range of cellular processes, including cytoskeletal reorganization, cell–cell adhesion, cytokinesis and apoptosis. These processes rely on protein–protein interactions, and understanding these (and how they influence one another) is critical in determining how the IQGAPs function. A key group of interactions is with calmodulin and the structurally related proteins myosin essential light chain and S100B. These interactions occur primarily through a series of IQ motifs, which are α-helical segments of the protein located towards the middle of the primary sequence. The three human IQGAP isoforms (IQGAP1, IQGAP2 and IQGAP3) all have four IQ motifs. However, these have different affinities for calmodulin, myosin light chain and S100B. Whereas all four IQ motifs of IQGAP1 interact with calmodulin in the presence of calcium, only the last two do so in the absence of calcium. IQ1 (the first IQ motif) interacts with the myosin essential light chain Mlc1sa and the first two undergo a calcium-dependent interaction with S100B. The significance of the interaction between Mlc1sa and IQGAP1 in mammals is unknown. However, a similar interaction involving the Saccharomyces cerevisiae IQGAP-like protein Iqg1p is involved in cytokinesis, leading to speculation that there may be a similar role in mammals.

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How do cells sense DNA lesions?

Biochemical Society Transactions ◽

10.1042/bst20191118 ◽

2020 ◽

Vol 48 (2) ◽

pp. 677-691 ◽

Cited By ~ 1

Author(s):

Chiara Vittoria Colombo ◽

Marco Gnugnoli ◽

Elisa Gobbini ◽

Maria Pia Longhese

Keyword(s):

Dna Damage ◽

Protein Complexes ◽

Dna Lesions ◽

Exogenous Dna ◽

Cellular Targets ◽

Cellular Processes ◽

Dna Lesion ◽

Dna Damaging Agents ◽

Wide Range ◽

Damage Response

DNA is exposed to both endogenous and exogenous DNA damaging agents that chemically modify it. To counteract the deleterious effects exerted by DNA lesions, eukaryotic cells have evolved a network of cellular pathways, termed DNA damage response (DDR). The DDR comprises both mechanisms devoted to repair DNA lesions and signal transduction pathways that sense DNA damage and transduce this information to specific cellular targets. These targets, in turn, impact a wide range of cellular processes including DNA replication, DNA repair and cell cycle transitions. The importance of the DDR is highlighted by the fact that DDR inactivation is commonly found in cancer and causes many different human diseases. The protein kinases ATM and ATR, as well as their budding yeast orthologs Tel1 and Mec1, act as master regulators of the DDR. The initiating events in the DDR entail both DNA lesion recognition and assembly of protein complexes at the damaged DNA sites. Here, we review what is known about the early steps of the DDR.

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Selectivity Determinants of RHO GTPase Binding to IQGAPs

International Journal of Molecular Sciences ◽

10.3390/ijms222212596 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12596

Author(s):

Niloufar Mosaddeghzadeh ◽

Kazem Nouri ◽

Oliver H. F. Krumbach ◽

Ehsan Amin ◽

Radovan Dvorsky ◽

...

Keyword(s):

Rho Gtpases ◽

Rho Gtpase ◽

Decisive Role ◽

Effector Proteins ◽

Iq Motif ◽

Cellular Processes ◽

Wide Range ◽

Switch Regions ◽

Protein Components ◽

Biochemical Analyses

IQ motif-containing GTPase-activating proteins (IQGAPs) modulate a wide range of cellular processes by acting as scaffolds and driving protein components into distinct signaling networks. Their functional states have been proposed to be controlled by members of the RHO family of GTPases, among other regulators. In this study, we show that IQGAP1 and IQGAP2 can associate with CDC42 and RAC1-like proteins but not with RIF, RHOD, or RHO-like proteins, including RHOA. This seems to be based on the distribution of charged surface residues, which varies significantly among RHO GTPases despite their high sequence homology. Although effector proteins bind first to the highly flexible switch regions of RHO GTPases, additional contacts outside are required for effector activation. Sequence alignment and structural, mutational, and competitive biochemical analyses revealed that RHO GTPases possess paralog-specific residues outside the two highly conserved switch regions that essentially determine the selectivity of RHO GTPase binding to IQGAPs. Amino acid substitution of these specific residues in RHOA to the corresponding residues in RAC1 resulted in RHOA association with IQGAP1. Thus, electrostatics most likely plays a decisive role in these interactions.

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Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

10.26434/chemrxiv.5496907 ◽

2017 ◽

Author(s):

Jana Shen ◽

Zhi Yue ◽

Helen Zgurskaya ◽

Wei Chen

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Transmembrane Domain ◽

Conformational Transition ◽

Conformational Dynamics ◽

Proton Release ◽

Intrinsic Resistance ◽

Constant Ph ◽

Wide Range ◽

Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

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Intracellular Ionic Strength Sensing Using NanoLuc

International Journal of Molecular Sciences ◽

10.3390/ijms22020677 ◽

2021 ◽

Vol 22 (2) ◽

pp. 677

Author(s):

Tausif Altamash ◽

Wesam Ahmed ◽

Saad Rasool ◽

Kabir H. Biswas

Keyword(s):

Thermal Stability ◽

Phase Separation ◽

Drug Discovery ◽

Ionic Strength ◽

Cellular Signaling ◽

Live Cells ◽

Protein Activity ◽

Cellular Survival ◽

Cellular Processes ◽

Wide Range

Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.

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Does uranyl-TBP complex formation happen at the aqueous-organic interface? Revelation by molecular dynamics simulations

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.115621 ◽

2021 ◽

Vol 330 ◽

pp. 115621

Author(s):

Pooja Sahu ◽

Ashish KumarSingha Deb ◽

Sk. Musharaf Ali ◽

K.T. Shenoy

Keyword(s):

Molecular Dynamics ◽

Complex Formation ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

Technology and Health Care ◽

10.3233/thc-218011 ◽

2021 ◽

pp. 1-12

Author(s):

Haiyan Li ◽

Zanxia Cao ◽

Guodong Hu ◽

Liling Zhao ◽

Chunling Wang ◽

...

Keyword(s):

Molecular Dynamics ◽

Structural Changes ◽

Binding Protein ◽

Network Models ◽

Md Simulations ◽

Protein Domain ◽

Opening Angle ◽

Conformation Changes ◽

Wide Range ◽

Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

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Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics

Molecules ◽

10.3390/molecules26030721 ◽

2021 ◽

Vol 26 (3) ◽

pp. 721

Author(s):

Srinivasaraghavan Kannan ◽

Pietro G. A. Aronica ◽

Thanh Binh Nguyen ◽

Jianguo Li ◽

Chandra S. Verma

Keyword(s):

Molecular Dynamics ◽

Computational Design ◽

Diagnostic Tools ◽

Stapled Peptides ◽

Altered Expression ◽

Cellular Processes ◽

High Affinity ◽

Limited Success ◽

Dynamics Simulations ◽

Partner Proteins

S100B(ββ) proteins are a family of multifunctional proteins that are present in several tissues and regulate a wide variety of cellular processes. Their altered expression levels have been associated with several human diseases, such as cancer, inflammatory disorders and neurodegenerative conditions, and hence are of interest as a therapeutic target and a biomarker. Small molecule inhibitors of S100B(ββ) have achieved limited success. Guided by the wealth of available experimental structures of S100B(ββ) in complex with diverse peptides from various protein interacting partners, we combine comparative structural analysis and molecular dynamics simulations to design a series of peptides and their analogues (stapled) as S100B(ββ) binders. The stapled peptides were subject to in silico mutagenesis experiments, resulting in optimized analogues that are predicted to bind to S100B(ββ) with high affinity, and were also modified with imaging agents to serve as diagnostic tools. These stapled peptides can serve as theranostics, which can be used to not only diagnose the levels of S100B(ββ) but also to disrupt the interactions of S100B(ββ) with partner proteins which drive disease progression, thus serving as novel therapeutics.

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PREDICTION OF PEEK RESIN PROPERTIES FOR PROCESSING MODELING USING MOLECULAR DYNAMICS

10.12783/asc36/35813 ◽

2021 ◽

Author(s):

KHATEREH KASHMARI ◽

PRATHAMESH DESHPANDE ◽

SAGAR PATIL ◽

SAGAR SHAH ◽

MARIANNA MAIARU ◽

...

Keyword(s):

Molecular Dynamics ◽

Residual Stresses ◽

Crystallization Kinetics ◽

Material Properties ◽

Elevated Temperatures ◽

Processing Parameters ◽

Thermomechanical Properties ◽

Volumetric Shrinkage ◽

Processing Temperature ◽

Wide Range

Polymer Matrix Composites (PMCs) have been the subject of many recent studies due to their outstanding characteristics. For the processing of PMCs, a wide range of elevated temperatures is typically applied to the material, leading to the development of internal residual stresses during the final cool-down step. These residual stresses may lead to net shape deformations or internal damage. Also, volumetric shrinkage, and thus additional residual stresses, could be created during crystallization of the semi-crystalline thermoplastic matrix. Furthermore, the thermomechanical properties of semi-crystalline polymers are susceptible to the crystallinity content, which is tightly controlled by the processing parameters (processing temperature, temperature holding time) and material properties (melting and crystallization temperatures). Hence, it is vital to have a precise understanding of crystallization kinetics and its impact on the final component's performance to accurately predict induced residual stresses during the processing of these materials. To enable multi-scale process modeling of thermoplastic composites, molecular-level material properties must be determined for a wide range of crystallinity levels. In this study, the thermomechanical properties and volumetric shrinkage of the thermoplastic Poly Ether Ether Ketone (PEEK) resin are predicted as a function of crystallinity content and temperature using molecular dynamics (MD) modeling. Using crystallization-kinetics models, the thermo-mechanical properties are directly related to processing time and temperature. This research can ultimately predict the residual stress evolution in PEEK composites as a function of processing parameters.

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