scholarly journals Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS

2020 ◽  
Author(s):  
Maximilia F. de Souza Degenhardt ◽  
Phelipe A. M. Vitale ◽  
Layara A. Abiko ◽  
Martin Zacharias ◽  
Michael Sattler ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Md Simulations ◽  
Bound State ◽  
Conformational Ensemble ◽  
Regulation Mechanism ◽  
Multiple Sources ◽  
Intracellular Loop ◽  
Saxs Data ◽  
Structure Information ◽  
Apo State

ABSTRACTNa+/Ca2+ exchangers (NCX) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+-sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the Na+/Ca2+ exchanger of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant inter-domain flexibility in the Apo state, but assume rigid inter-domain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the Apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the Apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N RDCs) and Small-Angle X-Ray Scattering (SAXS) data in a combined modelling strategy that generated atomistic information on the most representative conformations. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, while the wide-open inter-domain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble towards extended conformers, which could be a key step in the Na+/Ca2+ exchangers’ allosteric regulation mechanism. The present strategy, combining MD with NMR and SAXS, provides a powerful approach to select representative structures from ensembles of conformations, which could be applied to other flexible multi-domain systems.SIGNIFICANCEThe conformational ensemble of CALX-CBD12, the main Ca2+-sensor of Drosophila’s Na+/Ca2+ exchanger, was characterized by a combination of MD simulations with SAXS and NMR data using the EOM approach. This analysis showed that this two-domain construct experiences opening-closing motions, providing molecular information about CALX-CBD12 in the Apo state. Ca2+-binding shifts the conformational ensemble towards extended conformers. These findings are consistent with a model according to which Ca2+ modulation of CBD12 plasticity is a key step in the Ca2+-regulation mechanism of the full-length exchanger.

scholarly journals NMR-Based Structural Characterization of a Two-Disulfide-Bonded Analogue of the FXIIIa Inhibitor Tridegin: New Insights into Structure–Activity Relationships

2021 ◽  
Vol 22 (2) ◽  
pp. 880
Author(s):  
Thomas Schmitz ◽  
Ajay Abisheck Paul George ◽  
Britta Nubbemeyer ◽  
Charlotte A. Bäuml ◽  
Torsten Steinmetzer ◽  
...  
Keyword(s):  
Structural Information ◽  
Coagulation Factor ◽  
Md Simulations ◽  
2D Nmr ◽  
Label Free ◽  
2D Nmr Spectroscopy ◽  
Structure Information ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Blood Sucking

The saliva of blood-sucking leeches contains a plethora of anticoagulant substances. One of these compounds derived from Haementeria ghilianii, the 66mer three-disulfide-bonded peptide tridegin, specifically inhibits the blood coagulation factor FXIIIa. Tridegin represents a potential tool for antithrombotic and thrombolytic therapy. We recently synthesized two-disulfide-bonded tridegin variants, which retained their inhibitory potential. For further lead optimization, however, structure information is required. We thus analyzed the structure of a two-disulfide-bonded tridegin isomer by solution 2D NMR spectroscopy in a combinatory approach with subsequent MD simulations. The isomer was studied using two fragments, i.e., the disulfide-bonded N-terminal (Lys1–Cys37) and the flexible C-terminal part (Arg38–Glu66), which allowed for a simplified, label-free NMR-structure elucidation of the 66mer peptide. The structural information was subsequently used in molecular modeling and docking studies to provide insights into the structure–activity relationships. The present study will prospectively support the development of anticoagulant-therapy-relevant compounds targeting FXIIIa.

scholarly journals Cryo-EM structure of the human histamine H1 receptor/Gq complex

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ruixue Xia ◽  
Na Wang ◽  
Zhenmei Xu ◽  
Yang Lu ◽  
Jing Song ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Intracellular Loop ◽  
Cryo Electron Microscopy ◽  
Allergy Treatment ◽  
Domain 3 ◽  
Extracellular Side ◽  
Key Residues ◽  
Loop 2

AbstractHistamine receptors play important roles in various pathophysiological conditions and are effective targets for anti-allergy treatment, however the mechanism of receptor activation remain elusive. Here, we present the cryo-electron microscopy (cryo-EM) structure of the human H1R in complex with a Gq protein in an active conformation via a NanoBiT tethering strategy. The structure reveals that histamine activates receptor via interacting with the key residues of both transmembrane domain 3 (TM3) and TM6 to squash the binding pocket on the extracellular side and to open the cavity on the intracellular side for Gq engagement in a model of “squash to activate and expand to deactivate”. The structure also reveals features for Gq coupling, including the interaction between intracellular loop 2 (ICL2) and the αN-β junction of Gq/11 protein. The detailed analysis of our structure will provide a framework for understanding G-protein coupling selectivity and clues for designing novel antihistamines.

scholarly journals Dynamical Behavior and Conformational Selection Mechanism of the Intrinsically Disordered Sic1 Kinase-Inhibitor Domain

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 110 ◽  
Author(s):  
Davide Sala ◽  
Ugo Cosentino ◽  
Anna Ranaudo ◽  
Claudio Greco ◽  
Giorgio Moro
Keyword(s):  
Kinase Inhibitor ◽  
Dynamical Behavior ◽  
Md Simulations ◽  
Molecular Shape ◽  
Conformational Space ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Selection Mechanism ◽  
Conformational Selection ◽  
Intrinsically Disordered

Intrinsically Disordered Peptides and Proteins (IDPs) in solution can span a broad range of conformations that often are hard to characterize by both experimental and computational methods. However, obtaining a significant representation of the conformational space is important to understand mechanisms underlying protein functions such as partner recognition. In this work, we investigated the behavior of the Sic1 Kinase-Inhibitor Domain (KID) in solution by Molecular Dynamics (MD) simulations. Our results point out that application of common descriptors of molecular shape such as Solvent Accessible Surface (SAS) area can lead to misleading outcomes. Instead, more appropriate molecular descriptors can be used to define 3D structures. In particular, we exploited Weighted Holistic Invariant Molecular (WHIM) descriptors to get a coarse-grained but accurate definition of the variegated Sic1 KID conformational ensemble. We found that Sic1 is able to form a variable amount of folded structures even in absence of partners. Among them, there were some conformations very close to the structure that Sic1 is supposed to assume in the binding with its physiological complexes. Therefore, our results support the hypothesis that this protein relies on the conformational selection mechanism to recognize the correct molecular partners.

scholarly journals Biophysical and functional characterization of Norrin signaling through Frizzled4

2018 ◽  
Vol 115 (35) ◽  
pp. 8787-8792 ◽  
Author(s):  
Injin Bang ◽  
Hee Ryung Kim ◽  
Andrew H. Beaven ◽  
Jinuk Kim ◽  
Seung-Bum Ko ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Wnt Signaling ◽  
Conformational Changes ◽  
Cellular Response ◽  
Transmembrane Domain ◽  
Functional Characterization ◽  
Intracellular Loop ◽  
Ligand Interaction ◽  
Rich Domain ◽  
Linker Domain

Wnt signaling is initiated by Wnt ligand binding to the extracellular ligand binding domain, called the cysteine-rich domain (CRD), of a Frizzled (Fzd) receptor. Norrin, an atypical Fzd ligand, specifically interacts with Fzd4 to activate β-catenin–dependent canonical Wnt signaling. Much of the molecular basis that confers Norrin selectivity in binding to Fzd4 was revealed through the structural study of the Fzd4CRD–Norrin complex. However, how the ligand interaction, seemingly localized at the CRD, is transmitted across full-length Fzd4 to the cytoplasm remains largely unknown. Here, we show that a flexible linker domain, which connects the CRD to the transmembrane domain, plays an important role in Norrin signaling. The linker domain directly contributes to the high-affinity interaction between Fzd4 and Norrin as shown by ∼10-fold higher binding affinity of Fzd4CRD to Norrin in the presence of the linker. Swapping the Fzd4 linker with the Fzd5 linker resulted in the loss of Norrin signaling, suggesting the importance of the linker in ligand-specific cellular response. In addition, structural dynamics of Fzd4 associated with Norrin binding investigated by hydrogen/deuterium exchange MS revealed Norrin-induced conformational changes on the linker domain and the intracellular loop 3 (ICL3) region of Fzd4. Cell-based functional assays showed that linker deletion, L430A and L433A mutations at ICL3, and C-terminal tail truncation displayed reduced β-catenin–dependent signaling activity, indicating the functional significance of these sites. Together, our results provide functional and biochemical dissection of Fzd4 in Norrin signaling.

scholarly journals Microsecond-timescale simulations suggest 5-HT–mediated preactivation of the 5-HT3Aserotonin receptor

2019 ◽  
Vol 117 (1) ◽  
pp. 405-414 ◽  
Author(s):  
Nicholas B. Guros ◽  
Arvind Balijepalli ◽  
Jeffery B. Klauda
Keyword(s):  
Serotonin Receptor ◽  
Molecular Mechanisms ◽  
Transmembrane Domain ◽  
Allosteric Regulation ◽  
Md Simulations ◽  
Binding Pocket ◽  
Careful Examination ◽  
Dynamic Binding ◽  
Order Of Magnitude ◽  
Membrane Bound

Aided by efforts to improve their speed and efficiency, molecular dynamics (MD) simulations provide an increasingly powerful tool to study the structure–function relationship of pentameric ligand-gated ion channels (pLGICs). However, accurate reporting of the channel state and observation of allosteric regulation by agonist binding with MD remains difficult due to the timescales necessary to equilibrate pLGICs from their artificial and crystalized conformation to a more native, membrane-bound conformation in silico. Here, we perform multiple all-atom MD simulations of the homomeric 5-hydroxytryptamine 3A (5-HT3A) serotonin receptor for 15 to 20 μs to demonstrate that such timescales are critical to observe the equilibration of a pLGIC from its crystalized conformation to a membrane-bound conformation. These timescales, which are an order of magnitude longer than any previous simulation of 5-HT3A, allow us to observe the dynamic binding and unbinding of 5-hydroxytryptamine (5-HT) (i.e., serotonin) to the binding pocket located on the extracellular domain (ECD) and allosteric regulation of the transmembrane domain (TMD) from synergistic 5-HT binding. While these timescales are not long enough to observe complete activation of 5-HT3A, the allosteric regulation of ion gating elements by 5-HT binding is indicative of a preactive state, which provides insight into molecular mechanisms that regulate channel activation from a resting state. This mechanistic insight, enabled by microsecond-timescale MD simulations, will allow a careful examination of the regulation of pLGICs at a molecular level, expanding our understanding of their function and elucidating key structural motifs that can be targeted for therapeutic regulation.

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

scholarly journals In Silico Study of the Mechanism of Binding of the N-Terminal Region of α Synuclein to Synaptic-Like Membranes

Life ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 98 ◽  
Author(s):  
Carlos Navarro-Paya ◽  
Maximo Sanz-Hernandez ◽  
Alfonso De Simone
Keyword(s):  
Lipid Bilayers ◽  
Conformational Transition ◽  
Md Simulations ◽  
Bound State ◽  
Terminal Region ◽  
Coarse Grained ◽  
Biological Behavior ◽  
In Silico Study ◽  
Membrane Bound ◽  
Presynaptic Protein

The membrane binding by α-synuclein (αS), a presynaptic protein whose aggregation is strongly linked with Parkinson’s disease, influences its biological behavior under functional and pathological conditions. This interaction requires a conformational transition from a disordered-unbound to a partially helical membrane-bound state of the protein. In the present study, we used enhanced coarse-grained MD simulations to characterize the sequence and conformational determinants of the binding to synaptic-like vesicles by the N-terminal region of αS. This region is the membrane anchor and is of crucial importance for the properties of the physiological monomeric state of αS as well as for its aberrant aggregates. These results identify the key factors that play a role in the binding of αS with synaptic lipid bilayers in both membrane-tethered and membrane-locked conformational states.

TMEM16A–TMEM16B chimaeras to investigate the structure–function relationship of calcium-activated chloride channels

2013 ◽  
Vol 452 (3) ◽  
pp. 443-455 ◽  
Author(s):  
Paolo Scudieri ◽  
Elvira Sondo ◽  
Emanuela Caci ◽  
Roberto Ravazzolo ◽  
Luis J. V. Galietta
Keyword(s):  
Chloride Channels ◽  
Transmembrane Domain ◽  
Amino Acid Residues ◽  
Intracellular Loop ◽  
Transmembrane Segments ◽  
C Terminus ◽  
Third Intracellular Loop ◽  
Cl Channels ◽  
Function Relationship ◽  
Relationship Of

TMEM16A and TMEM16B proteins are CaCCs (Ca2+-activated Cl− channels) with eight putative transmembrane segments. As shown previously, expression of TMEM16B generates CaCCs characterized by a 10-fold lower Ca2+ affinity and by faster activation and deactivation kinetics with respect to TMEM16A. To investigate the basis of the different properties, we generated chimaeric proteins in which different domains of the TMEM16A protein were replaced by the equivalent domains of TMEM16B. Replacement of the N-terminus, TMD (transmembrane domain) 1–2, the first intracellular loop and TMD3–4 did not change the channel's properties. Instead, replacement of intracellular loop 3 decreased the apparent Ca2+ affinity by nearly 8-fold with respect to wild-type TMEM16A. In contrast, the membrane currents derived from chimaeras containing TMD7–8 or the C-terminus of TMEM16B showed higher activation and deactivation rates without a change in Ca2+ sensitivity. Significantly accelerated kinetics were also found when the entire C-terminus of the TMEM16A protein (77 amino acid residues) was deleted. Our findings indicate that the third intracellular loop of TMEM16A and TMEM16B is the site involved in Ca2+-sensitivity, whereas the C-terminal part, including TMD7–8, affect the rate of transition between the open and the closed state.

scholarly journals Resistance of Hypogonadic Patients with Mutated GnRH Receptor Genes to Pulsatile GnRH Administration

1999 ◽  
Vol 84 (3) ◽  
pp. 990-996 ◽  
Author(s):  
Philippe Caron ◽  
Stéphanie Chauvin ◽  
Sophie Christin-Maitre ◽  
Antoine Bennet ◽  
Najiba Lahlou ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Receptor Gene ◽  
Hypogonadotropic Hypogonadism ◽  
Chinese Hamster ◽  
Gnrh Receptor ◽  
Primary Amenorrhea ◽  
Recessive Trait ◽  
Intracellular Loop ◽  
Α Subunit ◽  
Pulsatile Gnrh

We have studied a kindred with three siblings with isolated hypogonadotropic hypogonadism caused by compound heterozygote mutations in the GnRH receptor gene. The disorder was transmitted as an autosomal recessive trait. The R262Q mutation in intracellular loop 3 of the receptor was associated with a mutation in the third transmembrane domain of the receptor, A129D, that has never been described before. This A129D mutation results in a complete loss of function, indicated by the lack of inositol triphosphate (TP3) 3 production by transfected Chinese hamster ovary (CHO) cells after GnRH stimulation. The two brothers had microphallus and bilateral cryptorchidism and were referred for lack of puberty, whereas their sister had primary amenorrhea and a complete lack of puberty. Their basal gonadotropin concentrations were below the reference range, and their endogenous LH secretory patterns were abnormal, with a low-normal frequency of small pulses or no apparent LH pulse. Pulsatile GnRH administration (10 μg/pulse every 90 min for 40 h) resulted in increased mean LH without any significant changes in testosterone levels in the two brothers, whereas the LH secretory profile of their sister remained apulsatile. Larger pulses of exogenous GnRH (20 μg every 90 min for 24 h) caused the sister to produce recognizable low amplitude LH pulses. The concentrations of free α-subunit significantly increased in all patients during the pulsatile GnRH administration. Thus, these hypogonadal patients are partially resistant to pulsatile GnRH administration, suggesting that they should be treated with gonadotropins to induce spermatogenesis or ovulation rather than with pulsatile GnRH.

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