1
|
Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
Collapse
Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| |
Collapse
|
2
|
Abstract
Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.
Collapse
|
3
|
Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophys J 2019. [PMID: 29539393 DOI: 10.1016/j.bpj.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.
Collapse
Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon.
| | | |
Collapse
|
4
|
Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J 2019; 116:205-214. [PMID: 30606449 PMCID: PMC6349996 DOI: 10.1016/j.bpj.2018.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/23/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
The atomic-level mechanisms that coordinate ligand release from protein pockets are only known for a handful of proteins. Here, we report results from accelerated molecular dynamics simulations for benzene dissociation from the buried cavity of the T4 lysozyme Leu99Ala mutant (L99A). In these simulations, benzene is released through a previously characterized, sparsely populated room-temperature excited state of the mutant, explaining the coincidence for experimentally measured benzene off rate and apo protein slow-timescale NMR relaxation rates between ground and excited states. The path observed for benzene egress is a multistep ligand migration from the buried cavity to ultimate release through an opening between the F/G-, H-, and I-helices and requires a number of cooperative multiresidue and secondary-structure rearrangements within the C-terminal domain of L99A. These rearrangements are identical to those observed along the ground state to excited state transitions characterized by molecular dynamic simulations run on the Anton supercomputer. Analyses of the molecular properties of the residues lining the egress path suggest that protein surface electrostatic potential may play a role in the release mechanism. Simulations of wild-type T4 lysozyme also reveal that benzene-egress-associated dynamics in the L99A mutant are potentially exaggerations of the substrate-processivity-related dynamics of the wild type.
Collapse
Affiliation(s)
| | | | - Daniel J Mermelstein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Nathan Mih
- Department of Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California
| | | | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
| |
Collapse
|
5
|
On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLoS Comput Biol 2019; 15:e1006665. [PMID: 30645590 PMCID: PMC6333327 DOI: 10.1371/journal.pcbi.1006665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023] Open
Abstract
Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450. Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry. In recent times, in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs. Even so, discovery of binding pathways of small molecules both at the primary binding site, as well as sites for allosteric control, is time consuming and often fortuitous. We provide here a framework within which critical conformational changes likely to occur during binding are quantified from statistical analysis of configurations of proteins in their apo, or inactive form, greatly simplifying identification of target residues. We illustrate this idea by analysing ligand binding pathways for three proteins T4- Lysozyme, P450 and Src kinase, which are active respectively in the immune system, metabolism and cancer.
Collapse
|
6
|
Saleem-Batcha R, Teufel R. Structural methods for probing the interaction of flavoenzymes with dioxygen and its surrogates. Methods Enzymol 2019; 620:349-363. [DOI: 10.1016/bs.mie.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
7
|
Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme. PLoS Comput Biol 2018; 14:e1006180. [PMID: 29775455 PMCID: PMC5979041 DOI: 10.1371/journal.pcbi.1006180] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/31/2018] [Accepted: 05/06/2018] [Indexed: 12/22/2022] Open
Abstract
Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition in a solvent-inaccessible cavity, contrary to the common perception of a single dominant pathway for ligand binding.
Collapse
|
8
|
Kitahara R, Sakuraba S, Kameda T, Okuda S, Xue M, Mulder FAA. Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein Sci 2018; 27:769-779. [PMID: 29271012 DOI: 10.1002/pro.3371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/28/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022]
Abstract
The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O2 gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O2 in solvent to 8.9 mM, O2 -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O2 binding sites and their atomic coordinates from the 1/r6 distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O2 -accessible sites were identified in internal cavities: One site was consistent with the xenon-binding site in the protein in crystal, and the other site was established to be a novel ligand-binding site. MD simulations performed at 10 and 100 mM O2 revealed dioxygen ingress and egress as well as rotational and translational motions of O2 in the cavities. It is therefore suggested that conformational fluctuations within the ground-state ensemble transiently develop channels for O2 association with the internal protein cavities.
Collapse
Affiliation(s)
- Ryo Kitahara
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tomoshi Kameda
- Computational Omics Research Team, Artificial Intelligence Research Center, Advanced Industrial Science and Technology, Koto, Tokyo, 135-0064, Japan
| | - Sanshiro Okuda
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Mengjun Xue
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
| |
Collapse
|
9
|
Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prangé T. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure. Biophys J 2017; 113:2199-2206. [PMID: 29108649 DOI: 10.1016/j.bpj.2017.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 10/06/2017] [Indexed: 01/27/2023] Open
Abstract
Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.
Collapse
Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie University, CERVOxy Team, Centre Cyceron, Caen, France.
| | - Philippe Carpentier
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, Grenoble, France; European Synchrotron Radiation Facility, Grenoble, France
| | - Laura C Montemiglio
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France
| |
Collapse
|
10
|
Wang Y, Martins JM, Lindorff-Larsen K. Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics. Chem Sci 2017; 8:6466-6473. [PMID: 29619200 PMCID: PMC5859887 DOI: 10.1039/c7sc01627a] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
The behaviour of biomolecular systems is governed by their thermodynamic and kinetic properties. It is thus important to be able to calculate, for example, both the affinity and rate of binding and dissociation of a protein-ligand complex, or the populations and exchange rates between distinct conformational states. Because these are typically rare events, calculating these properties from long molecular dynamics simulations remains extremely difficult. Instead, one often adopts a divide-and-conquer strategy in which equilibrium free-energy differences and the fastest state-to-state transition (e.g. ligand association or minor-to-major state conversion) are combined to estimate the slow rate (e.g. ligand dissociation) using a two-state assumption. Here we instead address these problems by using a previously developed method to calculate both the forward and backward rates directly from simulations. We then estimate the thermodynamics from the rates, and validate these values by independent means. We applied the approach to three systems of increasing complexity, including the association and dissociation of benzene to a fully buried cavity inside the L99A mutant variant of T4 lysozyme. In particular, we were able to determine both millisecond association and dissociation rates, and the affinity, of the protein-ligand system by directly observing dozens of rare events in atomic detail. Our approach both sheds light on the precision of methods for calculating kinetics and further provides a generally useful test for the internal consistency of kinetics and thermodynamics. We also expect our route to be useful for obtaining both the kinetics and thermodynamics at the same time in more challenging cases.
Collapse
Affiliation(s)
- Yong Wang
- Structural Biology and NMR Laboratory , Linderstrøm-Lang Centre for Protein Science , Department of Biology , University of Copenhagen , Ole Maaløes Vej 5 , DK-2200 Copenhagen N , Denmark .
| | - João Miguel Martins
- Structural Biology and NMR Laboratory , Linderstrøm-Lang Centre for Protein Science , Department of Biology , University of Copenhagen , Ole Maaløes Vej 5 , DK-2200 Copenhagen N , Denmark .
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory , Linderstrøm-Lang Centre for Protein Science , Department of Biology , University of Copenhagen , Ole Maaløes Vej 5 , DK-2200 Copenhagen N , Denmark .
| |
Collapse
|
11
|
Analysis of O 2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A. Biophys J 2017; 112:1820-1828. [PMID: 28494953 DOI: 10.1016/j.bpj.2017.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 11/22/2022] Open
Abstract
Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O2-binding sites by O2-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer surface protein A contains a nonglobular single-layer β-sheet that connects the N- and C-terminal globular domains. Several cavities have been observed in both domains of the crystallized protein structure. The receptor-binding sites are occluded and line the largest cavity of the C-terminal domain. We observed significant O2-induced PREs for amide protons located around the largest cavity and at the central β-sheet. We suggested three potential O2-accessible sites in the protein based on the 1/r6 distance dependence of the PRE. Two sites were in or close to the largest cavity and the third site was in the surface crevice of the central β-sheet. These results provide, to our knowledge, the first evidence of ligand binding to the surface crevice and cavity of the protein in solution. Because O2 generally binds more specifically to hydrophobic rather than hydrophilic cavities within a protein, the results also indicated that the receptor-binding sites lining the largest cavity were in the hydrophobic environment in the ground-state conformation. Molecular dynamics simulations permitted the visualization of the rotational and translational motions of O2 within the largest cavity, egress of O2 from the cavity, and ingress of O2 in the surface crevice of the β-sheet. These molecular dynamics simulation results qualitatively explained the O2-induced changes in NMR observations. Exploring cavities that are sufficiently dynamic to enable access by small molecules can be a useful strategy for the design of stable proteins and their ligands.
Collapse
|
12
|
Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J 2017; 111:1631-1640. [PMID: 27760351 DOI: 10.1016/j.bpj.2016.08.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 01/07/2023] Open
Abstract
Proteins commonly sample a number of conformational states to carry out their biological function, often requiring transitions from the ground state to higher-energy states. Characterizing the mechanisms that guide these transitions at the atomic level promises to impact our understanding of functional protein dynamics and energy landscapes. The leucine-99-to-alanine (L99A) mutant of T4 lysozyme is a model system that has an experimentally well characterized excited sparsely populated state as well as a ground state. Despite the exhaustive study of L99A protein dynamics, the conformational changes that permit transitioning to the experimentally detected excited state (∼3%, ΔG ∼2 kcal/mol) remain unclear. Here, we describe the transitions from the ground state to this sparsely populated excited state of L99A as observed through a single molecular dynamics (MD) trajectory on the Anton supercomputer. Aside from detailing the ground-to-excited-state transition, the trajectory samples multiple metastates and an intermediate state en route to the excited state. Dynamic motions between these states enable cavity surface openings large enough to admit benzene on timescales congruent with known rates for benzene binding. Thus, these fluctuations between rare protein states provide an atomic description of the concerted motions that illuminate potential path(s) for ligand binding. These results reveal, to our knowledge, a new level of complexity in the dynamics of buried cavities and their role in creating mobile defects that affect protein dynamics and ligand binding.
Collapse
Affiliation(s)
- Jamie M Schiffer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Victoria A Feher
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; Drug Design Data Resource, University of California, San Diego, La Jolla, California.
| | - Robert D Malmstrom
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; National Biomedical Computation Resource, University of California, San Diego, La Jolla, California
| | - Roxana Sida
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; Centro de Enseñanza Técnica y Superior (CETYS) Campus Ensenada, Camino a Microondas Trinidad, Ensenada, Baja Califiornia, Mexico
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; National Biomedical Computation Resource, University of California, San Diego, La Jolla, California; Drug Design Data Resource, University of California, San Diego, La Jolla, California.
| |
Collapse
|
13
|
Genheden S, Essex JW, Lee AG. G protein coupled receptor interactions with cholesterol deep in the membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:268-281. [DOI: 10.1016/j.bbamem.2016.12.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/28/2016] [Accepted: 12/01/2016] [Indexed: 01/20/2023]
|
14
|
Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria. Biochim Biophys Acta Gen Subj 2017; 1861:323-334. [DOI: 10.1016/j.bbagen.2016.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/09/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
|