scholarly journals Structural basis of client specificity in mitochondrial membrane-protein chaperones

2020 ◽  
Vol 6 (51) ◽  
pp. eabd0263
Author(s):  
Iva Sučec ◽  
Yong Wang ◽  
Ons Dakhlaoui ◽  
Katharina Weinhäupl ◽  
Tobias Jores ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Integral Membrane Proteins ◽  
Structural Basis ◽  
Salt Bridges ◽  
Mitochondrial Carrier ◽  
Poorly Soluble ◽  
Dynamics Simulations ◽  
Fine Tune ◽  
Mitochondrial Membrane Protein ◽  
Hydrophilic Domain

Chaperones are essential for assisting protein folding and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone-client binding, but our understanding of how additional interactions enable client specificity is sparse. Here, we decipher what determines binding of two chaperones (TIM8·13 and TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1 and Tim23, which has an additional disordered hydrophilic domain. Combining NMR, SAXS, and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity versus specificity.

scholarly journals Structural basis of client specificity in mitochondrial membrane-protein chaperones

2020 ◽  
Author(s):  
Iva Sučec ◽  
Yong Wang ◽  
Ons Dakhlaoui ◽  
Katharina Weinhäupl ◽  
Tobias Jores ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Integral Membrane Proteins ◽  
Structural Basis ◽  
Salt Bridges ◽  
Mitochondrial Carrier ◽  
Poorly Soluble ◽  
Dynamics Simulations ◽  
Fine Tune ◽  
Mitochondrial Membrane Protein ◽  
Hydrophilic Domain

Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the alltransmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the trans-membrane part are weaker than in TIM9·10. Consequently, TIM9·10 is outcompeting TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity vs. specificity.

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

2015 ◽  
Vol 71 (4) ◽  
pp. 779-789 ◽  
Author(s):  
Zhiming Wang ◽  
Zhu Qiao ◽  
Sheng Ye ◽  
Rongguang Zhang
Keyword(s):  
Bound States ◽  
Hydrophobic Interactions ◽  
Crystal Packing ◽  
Protein Structures ◽  
Structural Basis ◽  
Phosphagen Kinase ◽  
Domain Arrangement ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Shaped Domain

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

scholarly journals Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol

2016 ◽  
Vol 114 (2) ◽  
pp. 206-214 ◽  
Author(s):  
Rameshwar U. Kadam ◽  
Ian A. Wilson
Keyword(s):  
Influenza Virus ◽  
Broad Spectrum ◽  
Hydrophobic Interactions ◽  
Antiviral Drug ◽  
Binding Mode ◽  
Influenza Viruses ◽  
Structural Basis ◽  
Salt Bridges ◽  
Fusion Inhibition ◽  
Conformational Rearrangements

The broad-spectrum antiviral drug Arbidol shows efficacy against influenza viruses by targeting the hemagglutinin (HA) fusion machinery. However, the structural basis of the mechanism underlying fusion inhibition by Arbidol has remained obscure, thereby hindering its further development as a specific and optimized influenza therapeutic. We determined crystal structures of Arbidol in complex with influenza virus HA from pandemic 1968 H3N2 and recent 2013 H7N9 viruses. Arbidol binds in a hydrophobic cavity in the HA trimer stem at the interface between two protomers. This cavity is distal to the conserved epitope targeted by broadly neutralizing stem antibodies and is ∼16 Å from the fusion peptide. Arbidol primarily makes hydrophobic interactions with the binding site but also induces some conformational rearrangements to form a network of inter- and intraprotomer salt bridges. By functioning as molecular glue, Arbidol stabilizes the prefusion conformation of HA that inhibits the large conformational rearrangements associated with membrane fusion in the low pH of the endosome. This unique binding mode compared with the small-molecule inhibitors of other class I fusion proteins enhances our understanding of how small molecules can function as fusion inhibitors and guides the development of broad-spectrum therapeutics against influenza virus.

scholarly journals Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45

2005 ◽  
Vol 201 (3) ◽  
pp. 441-452 ◽  
Author(s):  
Hyun-Joo Nam ◽  
Florence Poy ◽  
Haruo Saito ◽  
Christin A. Frederick
Keyword(s):  
Crystal Structure ◽  
Protein Tyrosine Phosphatase ◽  
Active Site ◽  
Active Sites ◽  
Hydrophobic Interactions ◽  
Tyrosine Phosphatase ◽  
Receptor Protein ◽  
Structural Basis ◽  
Salt Bridges ◽  
Protein Tyrosine

CD45 is the prototypic member of transmembrane receptor-like protein tyrosine phosphatases (RPTPs) and has essential roles in immune functions. The cytoplasmic region of CD45, like many other RPTPs, contains two homologous protein tyrosine phosphatase domains, active domain 1 (D1) and catalytically impaired domain 2 (D2). Here, we report crystal structure of the cytoplasmic D1D2 segment of human CD45 in native and phosphotyrosyl peptide-bound forms. The tertiary structures of D1 and D2 are very similar, but doubly phosphorylated CD3ζ immunoreceptor tyrosine-based activation motif peptide binds only the D1 active site. The D2 “active site” deviates from the other active sites significantly to the extent that excludes any possibility of catalytic activity. The relative orientation of D1 and D2 is very similar to that observed in leukocyte common antigen–related protein with both active sites in an open conformation and is restrained through an extensive network of hydrophobic interactions, hydrogen bonds, and salt bridges. This crystal structure is incompatible with the wedge model previously suggested for CD45 regulation.

scholarly journals Interdimer “zipping” in the chemoreceptor signaling domain revealed by molecular dynamics simulations

2019 ◽  
Author(s):  
Marharyta G. Petukh ◽  
Davi R. Ortega ◽  
Jerome Baudry ◽  
Igor B. Zhulin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Salt Bridges ◽  
Compact Structure ◽  
Flagellar Motors ◽  
Signaling Domain ◽  
Dynamics Simulations

ABSTRACTChemoreceptors are principal components of the bacterial sensory system that modulates cellular motility. They detect changes in the environment and transmit information to CheA histidine kinase, which ultimately controls cellular flagellar motors. The prototypical Tsr chemoreceptor in E. coli is a homodimer containing two principal functional modules: (i) a periplasmic ligand-binding domain and (ii) a cytoplasmic signaling domain. Chemoreceptor dimers are arranged into a trimer of dimers at the tip of the signaling domain comprising a minimal physical unit essential for enhancing the CheA activity several hundredfold. Trimers of dimers are arranged into highly ordered hexagon arrays at the cell pole; however, the mechanism underlying the trimer-of-dimer and higher order array formation remains unclear. Furthermore, molecular mechanisms of signal transduction that are likely to involve inter-dimer interactions are not fully understood. Here we apply all-atom, microsecond-time scale molecular dynamics simulations of the Tsr trimer of dimers atomic model in order to obtain further insight into potential interactions within the chemoreceptor signaling unit. We show extensive interactions between homodimers at the hairpin tip of the signaling domain, where strong hydrophobic interactions maintain binding. A subsequent zipping of homodimers is facilitated by electrostatic interactions, in particular by polar solvation energy and salt bridges that stabilize the final compact structure, which extends beyond the kinase interacting subdomain. Our study provides evidence that interdimer interactions within the chemoreceptor signaling domain are more complex than previously thought.

3D-QSAR, Docking, and Molecular Dynamics Simulations Studies on Quinazoline Derivatives as PAK4 Inhibitors

2021 ◽  
Vol 18 ◽  
Author(s):  
Xiao-Zhong Chen ◽  
Dai Chen ◽  
Yan Shen ◽  
Juan Wang ◽  
Yong Hu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Interactions ◽  
3D Qsar ◽  
Structural Basis ◽  
High Biological Activity ◽  
Promising Target ◽  
Wide Range ◽  
Dynamics Simulations

Background: The p21-activated kinases 4 (PAK4) refer to a promising target for cancer treatment. Currently, a wide range of PAK4 inhibitors has been reported. Objective: To study the structural requirements of quinoline derivatives as PAK4 inhibitors and design novel PAK4 inhibitors. Method: In the present study, a set of quinazoline PAK4 inhibitors underwent CoMFA, CoMSIA, molecular docking, as well as molecular dynamics simulations. Results: The built CoMFA (q2=0.792, r2=0.994, r2pred =0.74) and CoMSIA (q2=0.873, r2=0.994, r2pred=0.81) models exhibited high robustness and prominent predicting ability. As revealed from the results of molecular docking and molecular dynamics simulations, hydrogen bond and hydrophobic interactions primarily impact the affinity of PAK4 inhibitors, and Leu398 acts as an amino acid that leads to significant stabilization of the mentioned inhibitors. Moreover, the present study developed five novel molecules exhibiting high biological activity predicted and satisfactory ADME properties. Conclusion: The structural basis of PAK4 with respect to the activities of its inhibitors was revealed, which may be conducive to designing novel PAK4 inhibitors.

scholarly journals Structural influence of the conserved Hsp40 HPD tripeptide on Hsp70 chaperone function

2020 ◽  
Author(s):  
OO Mallapre ◽  
NAD Bascos
Keyword(s):  
Atp Hydrolysis ◽  
Hydrophobic Interactions ◽  
Computational Cost ◽  
Interaction Network ◽  
Salt Bridges ◽  
Hsp70 Chaperone ◽  
Functional Control ◽  
Individual Bond ◽  
Dynamics Simulations ◽  
Key Residues

ABSTRACTThe control of Hsp70 functions has been related to the modulation of ATP hydrolysis and substrate capture by Hsp40. Structural and biophysical analyses of Hsp40 variants and their interactions with Hsp70 have identified key residues for this functional control mechanism. Conserved residues in both Hsp40 and Hsp70 have revealed conserved interactions that link Hsp40 binding to the catalytic residues within Hsp70. The current work investigates the effect of documented J-domain dysfunctional mutations (i.e. D35N, H33Q) on the described interaction linkage. Molecular dynamics simulations were used to compare the persistence of individual bond types (i.e. H-bonds, salt bridges, hydrophobic interactions) between Hsp70 and the bound forms of functional and dysfunctional Hsp40 variants. The generated data suggests the involvement of both direct and allosteric effects for the tested mutations. The observed changes relate mutations in the conserved HPD tripeptide of Hsp40 to alterations in the interaction network that induces Hsp70 chaperone functions.STATEMENT OF SIGNIFICANCEThe significance of the work may be summarized as follows. First, the interaction network for the simulated systems were observed to be different from one previously proposed for a disulfide linked complex (9). This may be attributed to altered residue movement and interactions without the restrictions set by the disulfide link. These results support the use of in silico methods to refine investigations of molecular contacts, particularly for systems, whose in vitro structural elucidation are difficult to achieve without modifications.Second, key interactions for intermolecular and intramolecular contacts were observed within a short simulation time (0.1 ns) matched those from much longer runs (500 ns) (4). This result highlights the possibility of identifying key interactions with relatively low computational cost.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

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