Time-resolved crystallography reveals allosteric communication aligned with molecular breathing

Science ◽  
2019 ◽  
Vol 365 (6458) ◽  
pp. 1167-1170 ◽  
Author(s):  
Pedram Mehrabi ◽  
Eike C. Schulz ◽  
Raison Dsouza ◽  
Henrike M. Müller-Werkmeister ◽  
Friedjof Tellkamp ◽  
...  
Keyword(s):  
Protein Function ◽  
Structural Changes ◽  
Intermediate Formation ◽  
Water Molecules ◽  
Dynamic Changes ◽  
Time Resolved ◽  
Irreversible Reaction ◽  
Allosteric Communication ◽  
Ligand Interactions ◽  
Covalent Intermediate

A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.

scholarly journals Role of Water Mediated Interactions in Calcium-Coupled Allostery of Calmodulin Domains

2019 ◽  
Author(s):  
Cheng Tan ◽  
Wenfei Li ◽  
Wei Wang ◽  
Dave Thirumalai
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Structural Response ◽  
Coordination Mechanism ◽  
Water Molecules ◽  
Hydrophobic Core ◽  
Physiological Importance ◽  
Allosteric Communication ◽  
Allosteric Transitions ◽  
Ef Hands

AbstractAllosteric communication between distant parts of protein controls many cellular functions. Binding of Ca2+ to the helix-loop-helix motifs (termed EF-hands) in calmodulin (CaM) leads to large conformational changes poising it for the binding of target proteins involved in variety of cell signaling events. Despite the physiological importance, the mechanism of Ca2+-mediated allosteric transitions in CaM remains elusive. Particularly, it is still unclear how water molecules contribute to Ca2+ coordination and the coupled conformational motions. We use all-atom molecular dynamics simulations with enhanced sampling method to investigate the coupling between the Ca2+ binding, dehydration, and the conformational change of the isolated CaM domains, each containing two EF-hands. We reveal a water-bridged coordination mechanism during Ca2+ binding and dehydration, in which the bridging water molecules reduce the entropy penalty during the coordination of liganding residues, thus contributing to efficient ligand binding in CaM domains. Exposure of hydrophobic sites occurs by calcium induced rotation of the helices of EF-hands with the hydrophobic core serving as the pivot. Interestingly, we find that despite being structurally similar, the structural response in the two EF-hands upon Ca2+ binding is highly asymmetric, which is needed for allosteric communication between them. The atomically detailed picture for the allosteric transitions of the CaM EF-hands, which are the first events in mediating a variety of intracellular processes, reveal the complex interplay between the discrete water molecules, dehydration of Ca2+, and CaM structural changes.Table of Contents graphic

scholarly journals Chemical shift imprint of intersubunit communication in a symmetric homodimer

2016 ◽  
Vol 113 (34) ◽  
pp. 9533-9538 ◽  
Author(s):  
Bradley T. Falk ◽  
Paul J. Sapienza ◽  
Andrew L. Lee
Keyword(s):  
Protein Function ◽  
Isotopic Labeling ◽  
Structural Basis ◽  
Oligomeric Proteins ◽  
Protein Ligand Interactions ◽  
Allosteric Communication ◽  
Binding Event ◽  
Ligand Interactions ◽  
Intersubunit Communication ◽  
Specific Ligand

Allosteric communication is critical for protein function and cellular homeostasis, and it can be exploited as a strategy for drug design. However, unlike many protein–ligand interactions, the structural basis for the long-range communication that underlies allostery is not well understood. This lack of understanding is most evident in the case of classical allostery, in which a binding event in one protomer is sensed by a second symmetric protomer. A primary reason why study of interdomain signaling is challenging in oligomeric proteins is the difficulty in characterizing intermediate, singly bound species. Here, we use an NMR approach to isolate and characterize a singly ligated state (“lig1”) of a homodimeric enzyme that is otherwise obscured by rapid exchange with apo and saturated forms. Mixed labeled dimers were prepared that simultaneously permit full population of the lig1 state and isotopic labeling of either protomer. Direct visualization of peaks from lig1 yielded site-specific ligand-state multiplets that provide a convenient format for assessing mechanisms of intersubunit communication from a variety of NMR measurements. We demonstrate this approach on thymidylate synthase from Escherichia coli, a homodimeric enzyme known to be half-the-sites reactive. Resolving the dUMP1 state shows that active site communication occurs not upon the first dUMP binding, but upon the second. Surprisingly, for many sites, dUMP1 peaks are found beyond the limits set by apo and dUMP2 peaks, indicating that binding the first dUMP pushes the enzyme ensemble to further conformational extremes than the apo or saturated forms. The approach used here should be generally applicable to homodimers.

scholarly journals Dynamic Community Composition Unravels Allosteric Communication in PDZ3

2020 ◽  
Author(s):  
Tandac F. Guclu ◽  
Ali Rana Atilgan ◽  
Canan Atilgan
Keyword(s):  
Community Composition ◽  
Conformational Changes ◽  
Structural Changes ◽  
Distal Segment ◽  
Allosteric Communication ◽  
C Terminus ◽  
N Terminus ◽  
Ligand Interactions ◽  
Binding Cavity ◽  
Dynamics Simulations

ABSTRACTThe third domain of PSD-95 (PDZ3) is a model for investigating allosteric communication in protein and ligand interactions. While motifs contributing to its binding specificity have been scrutinized, a conformational dynamical basis is yet to be established. Despite the miniscule structural changes due to point mutants, the observed significant binding affinity differences have previously been assessed with a focus on two α-helices located at the binding groove (α2) and the C-terminus (α3). Here, we employ a new computational approach to develop a generalized view on the molecular basis of PDZ3 binding selectivity and interaction communication for a set of point mutants of the protein (G330T, H372A, G330T-H372A) and its ligand (CRIPT named L1 and its T-2F variant L2) along with the wild type (WT). To analyze the dynamical aspects hidden in the conformations that are produced by molecular dynamics simulations, we utilize variations in community composition calculated based on the betweenness centrality measure from graph theory. We find that the highly charged N-terminus which is located far from the ligand has the propensity to share the same community with the ligand in the biologically functional complexes, indicating a distal segment might mediate the binding dynamics. N- and C-termini of PDZ3 share communities, and α3 acts as a hub for the whole protein by sustaining the communication with all structural segments, albeit being a trait not unique to the functional complexes. Moreover, α2 which lines the binding cavity frequently parts communities with the ligand and is not a controller of the binding but is rather a slave to the overall dynamics coordinated by the N-terminus. Thus, ligand binding fate in PDZ3 is traced to the population of community compositions extracted from dynamics despite the lack of significant conformational changes.

Solvent Dependence of Structural Dynamics and Spin-flip Processes in 3,4,5-tri(9H-carbazole-9-yl)benzonitrile (ortho-3CzBN)

2020 ◽  
Author(s):  
Masaki Saigo ◽  
Kiyoshi Miyata ◽  
Hajime Nakanotani ◽  
Chihaya Adachi ◽  
Ken Onda
Keyword(s):  
Dft Calculations ◽  
Excited States ◽  
Structural Changes ◽  
Photophysical Properties ◽  
Delayed Fluorescence ◽  
Time Resolved ◽  
Thermally Activated Delayed Fluorescence ◽  
Thermally Activated ◽  
Solvent Dependence ◽  
Acetonitrile Solutions

We have investigated the solvent-dependence of structural changes along with intersystem crossing of a thermally activated delayed fluorescence (TADF) molecule, 3,4,5-tri(9H-carbazole-9-yl)benzonitrile (o-3CzBN), in toluene, tetrahydrofuran, and acetonitrile solutions using time-resolved infrared (TR-IR) spectroscopy and DFT calculations. We found that the geometries of the S1 and T1 states are very similar in all solvents though the photophysical properties mostly depend on the solvent. In addition, the time-dependent DFT calculations based on these geometries suggested that the thermally activated delayed fluorescence process of o-3CzBN is governed more by the higher-lying excited states than by the structural changes in the excited states.<br>

scholarly journals Time-resolved observation of protein allosteric communication

2017 ◽  
Vol 114 (33) ◽  
pp. E6804-E6811 ◽  
Author(s):  
Sebastian Buchenberg ◽  
Florian Sittel ◽  
Gerhard Stock
Keyword(s):  
Pdz Domain ◽  
Dynamic Network ◽  
Structural Heterogeneity ◽  
Nonequilibrium Molecular Dynamics ◽  
Elastic Response ◽  
Dynamical Process ◽  
Biological Regulation ◽  
Time Resolved ◽  
Allosteric Communication ◽  
Time Resolved Infrared Spectroscopy

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response (≲0.1 ns), inelastic reorganization (∼100 ns), and structural relaxation (≳1μs). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed.

scholarly journals Selective time-dependent changes of Cu(DPPE)(DMP)·PF6on photoexcitation

2014 ◽  
Vol 70 (a1) ◽  
pp. C776-C776 ◽  
Author(s):  
Elzbieta Trzop ◽  
Bertrand Fournier ◽  
Katarzyna Jarzembska ◽  
Jesse Sokolow ◽  
Radoslaw Kaminski ◽  
...  
Keyword(s):  
Structural Changes ◽  
Dye Sensitized Solar Cells ◽  
Department Of Energy ◽  
Data Sets ◽  
Monoclinic System ◽  
Time Resolved ◽  
Pump Probe ◽  
Light Emitting Devices ◽  
Potential Applications ◽  
Photon Source

Thanks to their potential applications as light-emitting devices, chemical sensors and dye-sensitized solar cells, heteroleptic copper (I) complexes have been extensively studied. Cu(DPPE)(DMP)·PF6(dppe= 1,2-bis(diphenylphosphino)ethane; dmp = 2,9-dimethyl-1,10-phenanthroline) crystallizes in the monoclinic system, P21/c, with two independent molecules in the asymmetric unit. Previous studies on this system [1,2] show strong temperature-dependent emission. The complex was studied at 90K under 355nm laser excitation. At this temperature, the luminescence decay for Cu(DPPE)(DMP)·PF6is biexponential with lifetimes of ~3μs and ~28μs. Two time-resolved X-ray diffraction techniques were applied for studies: (1) a Laue technique at BioCARS ID-14 beamline at the Advanced Photon Source, and (2) monochromatic diffraction at a newly constructed in-house pump-probe monochromatic facility at the University at Buffalo. Structural changes determined with the two methods are in qualitative agreement; discrepancies in position of the Cu and P atoms were observed. The molecular distortions were smaller than those determined at 16K in the earlier synchrotron study by Vorontsov et al. [2]. Photodeformation maps (see Figure below), in which the increase in temperature on photoexcitation has been eliminated, clearly illustrate the photoinduced atomic shifts for both data sets. Results will be compared with those obtained for other studied heteroleptic copper (I) complexes, for instance Cu[(1,10-phenanthroline-N,N′) bis(triphenylphosphine)]·BF4[3]. The in-house pump-probe facility is discussed by Radoslaw Kaminski at this meeting. Research funded by the National Science Foundation (CHE1213223). BioCARS Sector 14 at APS is supported by NIH (RR007707). The Advanced Photon Source is funded by the Office of Basic Energy Sciences, U.S. Department of Energy, (W-31-109-ENG-38). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.

A Survey for Predicting ATP Binding Residues of Proteins Using Machine Learning Methods

2021 ◽  
Vol 28 ◽  
Author(s):  
Yu-He Yang ◽  
Jia-Shu Wang ◽  
Shi-Shi Yuan ◽  
Meng-Lu Liu ◽  
Wei Su ◽  
...  
Keyword(s):  
Machine Learning ◽  
Protein Function ◽  
Vital Role ◽  
Atp Binding ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Protein Ligand Interactions ◽  
Protein Functions ◽  
Ligand Interactions ◽  
Binding Residues

: Protein-ligand interactions are necessary for majority protein functions. Adenosine-5’-triphosphate (ATP) is one such ligand that plays vital role as a coenzyme in providing energy for cellular activities, catalyzing biological reaction and signaling. Knowing ATP binding residues of proteins is helpful for annotation of protein function and drug design. However, due to the huge amounts of protein sequences influx into databases in the post-genome era, experimentally identifying ATP binding residues is cost-ineffective and time-consuming. To address this problem, computational methods have been developed to predict ATP binding residues. In this review, we briefly summarized the application of machine learning methods in detecting ATP binding residues of proteins. We expect this review will be helpful for further research.

Sign in / Sign up

Export Citation Format

Share Document