Conformational ensemble of the sodium-coupled aspartate transporter

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

Download Full-text

Basic Residue Clusters in Intrinsically Disordered Regions of Peripheral Membrane Proteins: Modulating 2D Diffusion on Cell Membranes

Physchem ◽

10.3390/physchem1020010 ◽

2021 ◽

Vol 1 (2) ◽

pp. 152-162

Author(s):

Miquel Pons

Keyword(s):

Membrane Proteins ◽

Electrostatic Interactions ◽

Lipid Membrane ◽

Conformational Ensemble ◽

Basic Residue ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Peripheral Membrane Proteins ◽

Charged Residues ◽

Disordered Regions

A large number of peripheral membrane proteins transiently interact with lipids through a combination of weak interactions. Among them, electrostatic interactions of clusters of positively charged amino acid residues with negatively charged lipids play an important role. Clusters of charged residues are often found in intrinsically disordered protein regions, which are highly abundant in the vicinity of the membrane forming what has been called the disordered boundary of the cell. Beyond contributing to the stability of the lipid-bound state, the pattern of charged residues may encode specific interactions or properties that form the basis of cell signaling. The element of this code may include, among others, the recognition, clustering, and selective release of phosphatidyl inositides, lipid-mediated protein-protein interactions changing the residence time of the peripheral membrane proteins or driving their approximation to integral membrane proteins. Boundary effects include reduction of dimensionality, protein reorientation, biassing of the conformational ensemble of disordered regions or enhanced 2D diffusion in the peri-membrane region enabled by the fuzzy character of the electrostatic interactions with an extended lipid membrane.

Download Full-text

On the use of 3J-coupling NMR data to derive structural information on proteins

Journal of Biomolecular NMR ◽

10.1007/s10858-020-00355-5 ◽

2021 ◽

Vol 75 (1) ◽

pp. 39-70

Author(s):

Lorna J. Smith ◽

Wilfred F. van Gunsteren ◽

Bartosz Stankiewicz ◽

Niels Hansen

Keyword(s):

Protein Structure ◽

Structural Information ◽

Protein Structure Determination ◽

High Sensitivity ◽

Time Averaging ◽

Conformational Ensemble ◽

Torsional Angle ◽

Conformational Variability ◽

Egg White Lysozyme ◽

Coupling Time

AbstractValues of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.

Download Full-text

The Native State Conformational Ensemble of the SH3 Domain from α-Spectrin†

Biochemistry ◽

10.1021/bi990413g ◽

1999 ◽

Vol 38 (28) ◽

pp. 8899-8906 ◽

Cited By ~ 57

Author(s):

Mourad Sadqi ◽

Salvador Casares ◽

María A. Abril ◽

Obdulio López-Mayorga ◽

Francisco Conejero-Lara ◽

...

Keyword(s):

Sh3 Domain ◽

Conformational Ensemble ◽

Native State

Download Full-text

Reinforcement Learning to Boost Molecular Docking upon Protein Conformational Ensemble

Physical Chemistry Chemical Physics ◽

10.1039/d0cp06378a ◽

2021 ◽

Author(s):

Bin Chong ◽

Yingguang Yang ◽

Zi-Le Wang ◽

Han Xing ◽

Zhirong Liu

Keyword(s):

Molecular Docking ◽

Reinforcement Learning ◽

Intrinsically Disordered Proteins ◽

Therapeutic Targets ◽

Human Diseases ◽

Disordered Proteins ◽

Conformational Ensemble ◽

Intrinsically Disordered

Intrinsically disordered proteins (IDPs) widely involve in human diseases and are thus attractive therapeutic targets. In practice, however, it is computationally prohibitive to dock large ligand libraries to thousands and...

Download Full-text

4D-QSAR models applied to the study of TGF- β1 receptor inhibitors

Current Topics in Medicinal Chemistry ◽

10.2174/1568026621666210727161431 ◽

2021 ◽

Vol 21 ◽

Author(s):

Tamiris Maria de Assis ◽

Teodorico Castro Ramalho ◽

Elaine Fontes Ferreira da Cunha

Keyword(s):

External Validation ◽

Qsar Model ◽

Dynamics Simulation ◽

Conformational Ensemble ◽

Pyrimidine Derivatives ◽

Statistical Parameters ◽

Data Set ◽

Mesenchymal Transition ◽

Qsar Models ◽

Tgf Β1

Background: The quantitative structure-activity relationship is an analysis method that can be applied for designing new molecules. In 1997, Hopfinger and coworkers developed the 4D-QSAR methodology aiming to eliminate the question of which conformation to use in a QSAR study. In this work, the 4D-QSAR methodology was used to quantitatively determine the influence of structural descriptors on the activity of aryl pyrimidine derivatives as inhibitors of the TGF-β1 receptor. The members of the TGF-β subfamily are interesting molecular targets, since they play an important function in the growth and development of cell cellular including proliferation, apoptosis, differentiation, epithelial-mesenchymal transition (EMT), and migration. In late stages, TGF-β exerts tumor-promoting effects, increasing tumor invasiveness, and metastasis. Therefore, TGF-β is an attractive target for cancer therapy. Objective: The major goal of the current research is to develop 4D-QSAR models aiming to propose new structures of aryl pyrimidine derivatives. Materials and Methods: Molecular dynamics simulation was carried out to generate the conformational ensemble profile of a data set with aryl pyrimidine derivatives. The conformations were overlaid into a three-dimensional cubic box, according to the three-ordered atom alignment. The occupation of the grid cells by the interaction of pharmacophore elements provides the grid cell occupancy descriptors (GCOD), the dependent variables used to build the 4D-QSAR models. The best models were validated (internal and external validation) using several statistical parameters. Docking molecular studies were performed to better understand the binding mode of pyrimidine derivatives inside the TGF-β active site. Results : The 4D-QSAR model presented seven descriptors and acceptable statistical parameters (R2 = 0.89, q2 = 0.68, R2pred = 0.65, r2m = 0.55, R2P = 0.68 and R2rand = 0.21) besides pharmacophores groups important for the activity of these compounds. The molecular docking studies helped to understand the pharmacophoric groups and proposed substituents that increase the potency of aryl pyrimidine derivatives. Conclusion: The best QSAR model showed adequate statistical parameters that ensure their fitness, robustness, and predictivity. Structural modifications were assessed, and five new structures were proposed as candidates for a drug for cancer treatment.

Download Full-text

Can sequence specific and dynamics-based metrics representing the conformational ensemble allow us to decipher the encoded function in IDP sequences?

Biophysical Journal ◽

10.1016/j.bpj.2021.04.008 ◽

2021 ◽

Author(s):

S. Banu Ozkan

Keyword(s):

Conformational Ensemble

Download Full-text

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

Life ◽

10.3390/life10070110 ◽

2020 ◽

Vol 10 (7) ◽

pp. 110 ◽

Cited By ~ 1

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.

Download Full-text

Radiation damage effects on protein conformation at room temperature and 100K

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314096557 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C344-C344

Author(s):

Silvia Russi ◽

Shawn Kann ◽

Henry van den Bedem ◽

Ana M. González

Keyword(s):

Data Collection ◽

Radiation Damage ◽

Crystal Structures ◽

Room Temperature ◽

Relative Rate ◽

Absorbed Dose ◽

Conformational Ensemble ◽

Data Sets ◽

Cryogenic Temperatures ◽

Full Data

Protein crystallography data collection at synchrotrons today is routinely carried out at cryogenic temperatures to mitigate radiation damage to the crystal. Although damage still takes place, at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by orders of magnitude. Increasingly, experiments are carried out at room temperature. The lack of adequate cryo-protectants, the induced lattice changes or internal disorders during the cooling process, and the convenience of collecting data directly from the crystallization plates, are some of the reasons. Moreover, recent studies have shown that flash-freezing affects the conformational ensemble of crystal structures [1], and can hide important functional mechanisms from observation [2]. While there has been a considerable amount of effort in studying radiation damage at cryo-temperatures, its effects at room temperature are still not well understood. We investigated the effects of data collection temperature on secondary local damage to the side chain and main chain from different proteins. Data were collected from crystals of thaumatin and lysozyme at 100 K and room temperature. To carefully control the total absorbed dose, full data sets at room temperature were assembled from a few diffraction images per crystal. Several data sets were collected at increasing levels of absorbed dose. Our analysis shows that while at cryogenic temperatures, radiation damage increases the conformational variability, _x0004_at room temperature it has the opposite effect_x0005_. We also observed that disulfide bonds appear to break up at a different relative rate at room temperature, perhaps because of a more active repair mechanism. Our analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

Download Full-text