scholarly journals cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach

2022 ◽  
Author(s):  
Mitchell Benton ◽  
Mercede Furr ◽  
Vivek Govind Kumar ◽  
Feng Gao ◽  
Colin D Heyes ◽  
...  
Keyword(s):  
Thylakoid Membrane ◽  
Higher Plants ◽  
Signal Recognition Particle ◽  
Dynamic Structure ◽  
Md Simulations ◽  
The Novel ◽  
External Energy ◽  
Conformational Landscape ◽  
High Flexibility ◽  
Structural Insights

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.

From bacteria to chloroplasts: evolution of the chloroplast SRP system

2017 ◽  
Vol 398 (5-6) ◽  
pp. 653-661 ◽  
Author(s):  
Dominik Ziehe ◽  
Beatrix Dünschede ◽  
Danja Schünemann
Keyword(s):  
Plasma Membrane ◽  
Thylakoid Membrane ◽  
Protein Transport ◽  
Higher Plants ◽  
Signal Recognition Particle ◽  
Great Majority ◽  
Signal Recognition ◽  
Transport Mechanisms ◽  
Thylakoid Membrane Proteins ◽  
Lower Plants

Abstract Chloroplasts derive from a prokaryotic symbiont that lost most of its genes during evolution. As a result, the great majority of chloroplast proteins are encoded in the nucleus and are posttranslationally imported into the organelle. The chloroplast genome encodes only a few proteins. These include several multispan thylakoid membrane proteins which are synthesized on thylakoid-bound ribosomes and cotranslationally inserted into the membrane. During evolution, ancient prokaryotic targeting machineries were adapted and combined with novel targeting mechanisms to facilitate post- and cotranslational protein transport in chloroplasts. This review focusses on the chloroplast signal recognition particle (cpSRP) protein transport system, which has been intensively studied in higher plants. The cpSRP system derived from the prokaryotic SRP pathway, which mediates the cotranslational protein transport to the bacterial plasma membrane. Chloroplasts contain homologs of several components of the bacterial SRP system. The function of these conserved components in post- and/or cotranslational protein transport and chloroplast-specific modifications of these transport mechanisms are described. Furthermore, recent studies of cpSRP systems in algae and lower plants are summarized and their impact on understanding the evolution of the cpSRP system are discussed.

Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling – the beginning of a wonderful friendship

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Georg Künze ◽  
Daniel Huster ◽  
Sergey A. Samsonov
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Information ◽  
Md Simulations ◽  
Specific Protein ◽  
Regulatory Proteins ◽  
Structural Constraints ◽  
Modeling Tools ◽  
Nuclear Overhauser ◽  
Nmr Methods ◽  
High Flexibility

Abstract The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.

Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19–CDC5L complex

2014 ◽  
Vol 70 (3) ◽  
pp. 780-788 ◽  
Author(s):  
Jae-Woo Ahn ◽  
Sangwoo Kim ◽  
Eun-Jung Kim ◽  
Yeo-Jin Kim ◽  
Kyung-Jin Kim
Keyword(s):  
Crystal Structure ◽  
The Novel ◽  
Molecular Architecture ◽  
Repeat Protein ◽  
Binding Partner ◽  
Catalytic Activation ◽  
Repeat Structure ◽  
Repeat Domain ◽  
Importin Α ◽  
Structural Insights

The hPrp19–CDC5L complex plays a crucial role during human pre-mRNA splicing by catalytic activation of the spliceosome. In order to elucidate the molecular architecture of the hPrp19–CDC5L complex, the crystal structure of CTNNBL1, one of the major components of this complex, was determined. Unlike canonical ARM-repeat proteins such as β-catenin and importin-α, CTNNBL1 was found to contain a twisted and extended ARM-repeat structure at the C-terminal domain and, more importantly, the protein formed a stable dimer. A highly negatively charged patch formed in the N-terminal ARM-repeat domain of CTNNBL1 provides a binding site for CDC5L, a binding partner of the protein in the hPrp19–CDC5L complex, and these two proteins form a complex with a stoichiometry of 2:2. These findings not only present the crystal structure of a novel ARM-repeat protein, CTNNBL1, but also provide insights into the detailed molecular architecture of the hPrp19–CDC5L complex.

scholarly journals Novel Pyrazolo[3,4-c]pyridine Antagonists with Nanomolar affinity for A1 / A3 Adenosine Receptors: Binding Kinetics and Exploration of their Binding Profile Using Mutagenesis Experiments, MD simulations and TI/MD calculations

2021 ◽  
Author(s):  
Margarita Stampelou ◽  
Anna Suchankova ◽  
Eva Tzortzini ◽  
Lakshiv Dhingra ◽  
Kerry Barkan ◽  
...  
Keyword(s):  
Drug Design ◽  
Transmembrane Helix ◽  
Rank Correlation ◽  
Membrane System ◽  
Md Simulations ◽  
Dissociation Rate ◽  
The Novel ◽  
Free Energies ◽  
Electronegative Group ◽  
Good Agreement

Drugs targeting the four adenosine receptor (AR) subtypes can provide “soft" treatment of various significant diseases. Even for the two experimentally resolved AR subtypes the description of the orthosteric binding area and structure-activity relationships of ligands remains a demanding task due to the high similar amino acids sequence but also the broadness and flexibility of the ARs binding area. The identification of new pharmacophoric moieties and nanomolar leads and the exploration of their binding area with mutagenesis and state-of-the-art computational methods useful also for drug design purposes remains a challenging aim for all ARs. Here, we identified several low nanomolar ligands and potent competitive antagonists against A1R / A3R, containing the novel pyrazolo[3,4-c]pyridine pharmacophore for ARs, from a screen of an in-house library of only 52 compounds, originally designed for anti-proliferative activity. We identified L2-L10, A15, A17 with 3-aryl, 7-anilino and a electronegative group at 5-position as low micromolar to low nanomolar A1R / A3R antagonists. A17 has for A1R Kd = 5.62 nM and a residence time (RT) 41.33 min and for A3R Kd = 13.5 nM, RT = 47.23 min. The kinetic data showed that compared to the not potent or mediocre congeners the active compounds have similar association, for example at A1R Kon = 13.97 x106 M-1 (A17) vs Kon = 3.36 x106 M-1 (A26) but much lower dissociation rate Koff = 0.024 min-1 (A17) vs 0.134 min-1 (A26). Using molecular dynamics (MD) simulations and mutagenesis experiments we investigated the binding site of A17 showing that it can interact with an array of residues in transmembrane helix 5 (TM5), TM6, TM7 of A1R or A3R including residues E5.30, E5.28, T7.35 in A1R instead of Q5.28, V5.30 , L7.35 in A3R. A striking observation for drug design purposes is that for L2506.51A the binding affinity of A17 significantly increased at A1R. A17 provides a lead representative of a promising series and by means of the Thermodynamics Integration coupled with MD simulations (TI/MD) method, first applied here on whole GPCR- membrane system and showing a very good agreement between calculated and experimental relative binding free energies for A1R and A3R (spearman rank correlation p = 0.82 and 0.84, respectively), and kinetic experiments can lead to ligands with improved profile against ARs.

Molecular Dynamic Structure Investigations of the Surface Stability and Adsorption of H, H2, CH3, C2H2: (100) Diamond

1992 ◽  
Vol 270 ◽  
Author(s):  
Th. Frauenheim ◽  
P. Blaudeck ◽  
D. Porezag
Keyword(s):  
Density Functional ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Minimal Basis ◽  
Surface Stability ◽  
Hydrogen Supply ◽  
Reaction Processes ◽  
Structure Investigations

ABSTRACTSurface properties - stability and reconstruction - of clean and hydrogenated diamond (100) have been studied by real temperature molecular dynarnic (MD) simulations using an approximate density functional (DF) theory expanding the total electronic wave function in a minimal basis of localized atomic valence electron orbitals (LCAO - ansatz). The clean surface is highly unstable against a spontaneous dimerization resulting in a 2×1 reconstruction. Atomic hydrogen in the gas phase above the top surface at all temperatures and H2 molecules approaching the center of the dimer bond at room temperature are reactive in breaking the dimer π-bonds forming a monohydrogenated surface which maintains a stable 2×1 structure but with elongated surface C-C dimer bonds remaining stable against continuing hydrogen supply. The dihydrogenated surface taking a 1×1 structure, because of steric overcrowding dynamically becomes unstable against forming a 1×1 (alternating) di-, monohydrogenated surface. As first elementary reaction processes which may be discussed in relation to diamond growth we studied the thermal adsorption of CH3 and C2H2 onto a clean 2×l reconstructed (100) diamond surface.

scholarly journals Conformational landscape of the epidermal growth factor receptor kinase reveals a mutant specific allosteric pocket

2018 ◽  
Vol 9 (23) ◽  
pp. 5212-5222 ◽  
Author(s):  
Srinivasaraghavan Kannan ◽  
Gireedhar Venkatachalam ◽  
Hong Hwa Lim ◽  
Uttam Surana ◽  
Chandra Verma
Keyword(s):  
Epidermal Growth Factor Receptor ◽  
Growth Factor ◽  
Epidermal Growth Factor ◽  
Growth Factor Receptor ◽  
Md Simulations ◽  
Receptor Kinase ◽  
Epidermal Growth ◽  
Conformational Landscape

An oncogenic mutant-specific druggable allosteric pocket captured by MD simulations.

scholarly journals Computational Simulations to Guide Enzyme-Mediated Prodrug Activation

2020 ◽  
Vol 21 (10) ◽  
pp. 3621 ◽  
Author(s):  
Milica Markovic ◽  
Shimon Ben-Shabat ◽  
Arik Dahan
Keyword(s):  
Molecular Docking ◽  
Hydrolytic Enzymes ◽  
Parent Drug ◽  
Md Simulations ◽  
The Novel ◽  
Computational Simulations ◽  
Prodrug Activation ◽  
Enzyme Substrate ◽  
Oxidation Reduction ◽  
Energy Perturbation

Prodrugs are designed to improve pharmaceutical/biopharmaceutical characteristics, pharmacokinetic/pharmacodynamic properties, site-specificity, and more. A crucial step in successful prodrug is its activation, which releases the active parent drug, exerting a therapeutic effect. Prodrug activation can be based on oxidation/reduction processes, or through enzyme-mediated hydrolysis, from oxidoreductases (i.e., Cytochrome P450) to hydrolytic enzymes (i.e., carboxylesterase). This study provides an overview of the novel in silico methods for the optimization of enzyme-mediated prodrug activation. Computational methods simulating enzyme-substrate binding can be simpler like molecular docking, or more complex, such as quantum mechanics (QM), molecular mechanics (MM), and free energy perturbation (FEP) methods such as molecular dynamics (MD). Examples for MD simulations used for elucidating the mechanism of prodrug (losartan, paclitaxel derivatives) metabolism via CYP450 enzyme are presented, as well as an MD simulation for optimizing linker length in phospholipid-based prodrugs. Molecular docking investigating quinazolinone prodrugs as substrates for alkaline phosphatase is also presented, as well as QM and MD simulations used for optimal fit of different prodrugs within the human carboxylesterase 1 catalytical site. Overall, high quality computational simulations may show good agreement with experimental results, and should be used early in the prodrug development process.

Unusually high flexibility of graphene–Cu nanolayered composites under bending

2019 ◽  
Vol 21 (31) ◽  
pp. 17393-17399 ◽  
Author(s):  
Yuxin Zhao ◽  
Xiaoyi Liu ◽  
Jun Zhu ◽  
Sheng-Nian Luo
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Analytical Model ◽  
Md Simulations ◽  
High Flexibility

The mechanical properties of graphene–Cu nanolayered (GCuNL) composites under bend loading are investigated via an energy-based analytical model and molecular dynamics (MD) simulations.

Structural insights into T2-cluster-containing chalcogenides with vertex-, edge- and face-sharing connection modes of NaQ6 ligands: Na3ZnMIIIQ4 (MIII = In, Ga; Q = S, Se)

2018 ◽  
Vol 47 (43) ◽  
pp. 15538-15544 ◽  
Author(s):  
Ruijiao Chen ◽  
Xiaowen Wu ◽  
Zhi Su
Keyword(s):  
The Novel ◽  
Structural Insights

New series of T2-cluster-containing chalcogenides exhibiting the novel connection mode of NaS6 ligands and torsional adjacent T2-clusters were reported.

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