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Wernersson S, Bobby R, Flavell L, Milbradt AG, Holdgate GA, Embrey KJ, Akke M. Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility. Biochemistry 2022; 61:2303-2318. [PMID: 36215732 PMCID: PMC9631989 DOI: 10.1021/acs.biochem.2c00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The bromodomain and extra-terminal (BET) protein BRD4
regulates
gene expression via recruitment of transcriptional regulatory complexes
to acetylated chromatin. Like other BET proteins, BRD4 contains two
bromodomains, BD1 and BD2, that can interact cooperatively with target
proteins and designed ligands, with important implications for drug
discovery. Here, we used nuclear magnetic resonance (NMR) spectroscopy
to study the dynamics and interactions of the isolated bromodomains,
as well as the tandem construct including both domains and the intervening
linker, and investigated the effects of binding a tetra-acetylated
peptide corresponding to the tail of histone 4. The peptide affinity
is lower for both domains in the tandem construct than for the isolated
domains. Using 15N spin relaxation, we determined the global
rotational correlation times and residue-specific order parameters
for BD1 and BD2. Isolated BD1 is monomeric in the apo state but apparently
dimerizes upon binding the tetra-acetylated peptide. Isolated BD2
partially dimerizes in both the apo and peptide-bound states. The
backbone order parameters reveal marked differences between BD1 and
BD2, primarily in the acetyl-lysine binding site where the ZA loop
is more flexible in BD2. Peptide binding reduces the order parameters
of the ZA loop in BD1 and the ZA and BC loops in BD2. The AB loop,
located distally from the binding site, shows variable dynamics that
reflect the different dimerization propensities of the domains. These
results provide a basis for understanding target recognition by BRD4.
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Affiliation(s)
- Sven Wernersson
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Romel Bobby
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Liz Flavell
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, CambridgeCB4 0WG, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Geoffrey A Holdgate
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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Bolik-Coulon N, Ferrage F. Explicit models of motions to analyze NMR relaxation data in proteins. J Chem Phys 2022; 157:125102. [DOI: 10.1063/5.0095910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nano-second motions, in particular, can be probed by nuclear spin relaxation rates which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model Free (MF) approach which makes no assumption on the nature of motions and reports on the effective amplitude and time-scale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side-chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side-chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.
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Affiliation(s)
| | - Fabien Ferrage
- Departement de chimie, Ecole Normale Superieure Departement de Chimie, France
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Ozaki Y. Recent Advances in Molecular Spectroscopy of Electronic and Vibrational Transitions in Condensed Phase and Its Application to Chemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180319] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yukihiro Ozaki
- School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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Hsu A, Ferrage F, Palmer AG. Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function. Biophys J 2018; 115:2301-2309. [PMID: 30503534 DOI: 10.1016/j.bpj.2018.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023] Open
Abstract
Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero. In this work, the inverse Gaussian probability distribution function is derived from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximal entropy. This normalized distribution function is first used to calculate the correlation function, followed by the spectral density function. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. To validate the approach, 15N spin-relaxation data for the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA, were analyzed using the inverse Gaussian probability distribution for intramolecular correlation times. The results extend previous models for the conformational dynamics of the intrinsically disordered, DNA-binding region of the bZip transcription factor domain.
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Affiliation(s)
- Andrew Hsu
- Department of Chemistry, Columbia University, New York, New York
| | - Fabien Ferrage
- Laboratoire des Biomolécules, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
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Linke M, Köfinger J, Hummer G. Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. J Phys Chem B 2018; 122:5630-5639. [DOI: 10.1021/acs.jpcb.7b11988] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Max Linke
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Department of Physics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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Palmer AG. A dynamic look backward and forward. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:73-80. [PMID: 26899226 PMCID: PMC4856014 DOI: 10.1016/j.jmr.2016.01.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 05/22/2023]
Abstract
The 2015 Gunther Laukien Prize recognized solution NMR studies of protein dynamics and thermodynamics. This Perspective surveys aspects of the development and application of NMR spin relaxation for investigations of protein flexibility and function over multiple time scales in solution. Methods highlighted include analysis of overall rotational diffusion, theoretical descriptions of R1ρ relaxation, and molecular dynamics simulations to interpret NMR spin relaxation. Applications are illustrated for the zinc-finger domain Xfin-31, the calcium-binding proteins calbindin D9k and calmodulin, and the bZip transcription factor of GCN4.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
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Gill ML, Byrd RA, Palmer AG. Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region. Phys Chem Chem Phys 2016; 18:5839-49. [PMID: 26661739 PMCID: PMC4894059 DOI: 10.1039/c5cp06197k] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways. A critical aspect of these functions is the ability of IDP/IDRs to form highly specific complexes with target molecules. However, elucidation of the contributions of conformational dynamics to function has been limited by challenges associated with structural heterogeneity of IDP/IDRs. Using NMR spin relaxation parameters ((15)N R1, (15)N R2, and {(1)H}-(15)N heteronuclear NOE) collected at four static magnetic fields ranging from 14.1 to 21.1 T, we have analyzed the backbone dynamics of the basic leucine-zipper (bZip) domain of the Saccharomyces cerevisiae transcription factor GCN4, whose DNA binding domain is intrinsically disordered in the absence of DNA substrate. We demonstrate that the extended model-free analysis can be applied to proteins with IDRs such as apo GCN4 and that these results significantly extend previous NMR studies of GCN4 dynamics performed using a single static magnetic field of 11.74 T [Bracken, et al., J. Mol. Biol., 1999, 285, 2133-2146] and correlate well with molecular dynamics simulations [Robustelli, et al., J. Chem. Theory Comput., 2013, 9, 5190-5200]. In contrast to the earlier work, data at multiple static fields allows the time scales of internal dynamics of GCN4 to be reliably quantified. Large amplitude dynamic fluctuations in the DNA-binding region have correlation times (τs ≈ 1.4-2.5 ns) consistent with a two-step mechanism in which partially ordered bZip conformations of GCN4 form initial encounter complexes with DNA and then rapidly rearrange to the high affinity state with fully formed basic region recognition helices.
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Affiliation(s)
- Michelle L Gill
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. and Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - R Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Ryabov Y. Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra. Proteins 2015; 83:1571-81. [PMID: 25900685 DOI: 10.1002/prot.24814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/23/2015] [Accepted: 04/05/2015] [Indexed: 11/08/2022]
Abstract
In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yaroslav Ryabov
- BC Portal Inc., 260 Congressional Ln. #204, Rockville, Maryland, 20852
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