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Yang L, Guo S, Liao C, Hou C, Jiang S, Li J, Ma X, Shi L, Ye L, He X. Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300022. [PMID: 37483413 PMCID: PMC10362119 DOI: 10.1002/gch2.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Indexed: 07/25/2023]
Abstract
Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- School of AerospaceMechanical and Mechatronic EngineeringThe University of SydneyNSW2006Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chenchen Liao
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chengyu Hou
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Lin Ye
- School of System Design and Intelligent ManufacturingSouthern University of Science and TechnologyShenzhen518055P. R. China
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- Shenzhen STRONG Advanced Materials Research Institute Co., LtdShenzhen518035P. R. China
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2
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Clabbers MT, Martynowycz MW, Hattne J, Gonen T. Hydrogens and hydrogen-bond networks in macromolecular MicroED data. J Struct Biol X 2022; 6:100078. [PMID: 36507068 PMCID: PMC9731847 DOI: 10.1016/j.yjsbx.2022.100078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.
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Affiliation(s)
- Max T.B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Michael W. Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States,Department of Physiology, University of California, Los Angeles, CA 90095, United States,Corresponding author at: Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
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3
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Sequeira JN, Rodrigues FEP, Silva TGD, Reis PBPS, Machuqueiro M. Extending the Stochastic Titration CpHMD to CHARMM36m. J Phys Chem B 2022; 126:7870-7882. [PMID: 36190807 PMCID: PMC9776569 DOI: 10.1021/acs.jpcb.2c04529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The impact of pH on proteins is significant but often neglected in molecular dynamics simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology to deal with these effects. However, it still lacks widespread adoption by the scientific community. The stochastic titration CpHMD is one of such methods that, until now, only supported the GROMOS force field family. Here, we extend this method's implementation to include the CHARMM36m force field available in the GROMACS software package. We test this new implementation with a diverse group of proteins, namely, lysozyme, Staphylococcal nuclease, and human and E. coli thioredoxins. All proteins were conformationally stable in the simulations, even at extreme pH values. The RMSE values (pKa prediction vs experimental) obtained were very encouraging, in particular for lysozyme and human thioredoxin. We have also identified a few residues that challenged the CpHMD simulations, highlighting scenarios where the method still needs improvement independently of the force field. The CHARMM36m all-atom implementation was more computationally efficient when compared with the GROMOS 54A7, taking advantage of a shorter nonbonded interaction cutoff and a less frequent neighboring list update. The new extension will allow the study of pH effects in many systems for which this force field is particularly suited, i.e., proteins, membrane proteins, lipid bilayers, and nucleic acids.
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4
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Khaniya U, Mao J, Wei RJ, Gunner MR. Characterizing Protein Protonation Microstates Using Monte Carlo Sampling. J Phys Chem B 2022; 126:2476-2485. [PMID: 35344367 PMCID: PMC8997239 DOI: 10.1021/acs.jpcb.2c00139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The ΔG, ΔH, and ΔS between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. At pH 7 the lysozyme charge ranges from 6 to 10, with 24 accepted protonation microstates, while RCs have ≈50,000. A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and how they change when the quinone in the QB site is reduced. Protonation microstates can be used to define input MD parameters and provide insight into the motion of protons coupled to reactions.
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Affiliation(s)
- Umesh Khaniya
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Junjun Mao
- Department of Physics, City College of New York, New York, New York 10031, United States
| | - Rongmei Judy Wei
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - M R Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
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5
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Gray JG, Giambaşu GM, Case DA, Luchko T. Integral equation models for solvent in macromolecular crystals. J Chem Phys 2022; 156:014801. [PMID: 34998331 PMCID: PMC8889494 DOI: 10.1063/5.0070869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvent can occupy up to ∼70% of macromolecular crystals, and hence, having models that predict solvent distributions in periodic systems could improve the interpretation of crystallographic data. Yet, there are few implicit solvent models applicable to periodic solutes, and crystallographic structures are commonly solved assuming a flat solvent model. Here, we present a newly developed periodic version of the 3D-reference interaction site model (RISM) integral equation method that is able to solve efficiently and describe accurately water and ion distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the Ornstein–Zernike equation needed to yield charge neutrality for charged solutes, which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all the counter- and co-ions are part of the “disordered” solvent. We present several calculations of proteins, RNAs, and small molecule crystals to show that x-ray scattering intensities and the solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with the experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 Å range. Prospects for incorporating integral equation models into crystallographic refinement are discussed.
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Affiliation(s)
- Jonathon G Gray
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - George M Giambaşu
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Northridge, California 91330, USA
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6
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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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7
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Ramos J, Laux V, Haertlein M, Forsyth VT, Mossou E, Larsen S, Langkilde AE. The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme. Acta Crystallogr D Struct Biol 2021; 77:1579-1590. [PMID: 34866613 PMCID: PMC8647175 DOI: 10.1107/s2059798321010950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
The biological function of a protein is intimately related to its structure and dynamics, which in turn are determined by the way in which it has been folded. In vitro refolding is commonly used for the recovery of recombinant proteins that are expressed in the form of inclusion bodies and is of central interest in terms of the folding pathways that occur in vivo. Here, biophysical data are reported for in vitro-refolded hydrogenated hen egg-white lysozyme, in combination with atomic resolution X-ray diffraction analyses, which allowed detailed comparisons with native hydrogenated and refolded perdeuterated lysozyme. Distinct folding modes are observed for the hydrogenated and perdeuterated refolded variants, which are determined by conformational changes to the backbone structure of the Lys97-Gly104 flexible loop. Surprisingly, the structure of the refolded perdeuterated protein is closer to that of native lysozyme than that of the refolded hydrogenated protein. These structural differences suggest that the observed decreases in thermal stability and enzymatic activity in the refolded perdeuterated and hydrogenated proteins are consequences of the macromolecular deuteration effect and of distinct folding dynamics, respectively. These results are discussed in the context of both in vitro and in vivo folding, as well as of lysozyme amyloidogenesis.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle ST5 5BG, United Kingdom
- Faculty of Medicine, Lund University, 221 00 Lund, Sweden
- LINXS Institute for Advanced Neutron and X-ray Science, Scheelvagen 19, 223 70 Lund, Sweden
| | - Estelle Mossou
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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8
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Greene DG, Modla S, Sandler SI, Wagner NJ, Lenhoff AM. Nanocrystalline protein domains via salting-out. Acta Crystallogr F Struct Biol Commun 2021; 77:412-419. [PMID: 34726180 PMCID: PMC8561819 DOI: 10.1107/s2053230x21009961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/24/2021] [Indexed: 11/10/2022] Open
Abstract
Protein salting-out is a well established phenomenon that in many cases leads to amorphous structures and protein gels, which are usually not considered to be useful for protein structure determination. Here, microstructural measurements of several different salted-out protein dense phases are reported, including of lysozyme, ribonuclease A and an IgG1, showing that salted-out protein gels unexpectedly contain highly ordered protein nanostructures that assemble hierarchically to create the gel. The nanocrystalline domains are approximately 10-100 nm in size, are shown to have structures commensurate with those of bulk crystals and grow on time scales in the order of an hour to a day. Beyond revealing the rich, hierarchical nanoscale to mesoscale structure of protein gels, the nanocrystals that these phases contain are candidates for structural biology on next-generation X-ray free-electron lasers, which may enable the study of biological macromolecules that are difficult or impossible to crystallize in bulk.
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Affiliation(s)
- Daniel G. Greene
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Shannon Modla
- Delaware Biotechnology Institute, Newark, DE 19713, USA
| | - Stanley I. Sandler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Norman J. Wagner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Abraham M. Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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9
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Tegze M, Bortel G. Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments. IUCRJ 2021; 8:980-991. [PMID: 34804550 PMCID: PMC8562656 DOI: 10.1107/s205225252100868x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
In single-particle imaging (SPI) experiments, diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. The crucial step of the data processing of SPI is finding the orientations of the recorded diffraction patterns in reciprocal space and reconstructing the 3D intensity distribution. Here, two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various XFEL pulse fluences, simulated diffraction patterns of biological molecules are used.
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Affiliation(s)
- Miklós Tegze
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly Thege Miklós út 29-33, Budapest, H-1121, Hungary
| | - Gábor Bortel
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly Thege Miklós út 29-33, Budapest, H-1121, Hungary
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10
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Pachetti M, D'Amico F, Pascolo L, Pucciarelli S, Gessini A, Parisse P, Vaccari L, Masciovecchio C. UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction. Biophys J 2021; 120:4575-4589. [PMID: 34474016 PMCID: PMC8553600 DOI: 10.1016/j.bpj.2021.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 06/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.
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Affiliation(s)
- Maria Pachetti
- Elettra - Sincrotrone Trieste, Trieste, Italy; Department of Physics, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.
| | | | - Lorella Pascolo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Pucciarelli
- University of Camerino, School of Biosciences and Veterinary Medicine, Camerino, Italy
| | | | - Pietro Parisse
- Elettra - Sincrotrone Trieste, Trieste, Italy; Istituto Officina dei Materiali - CNR (IOM-CNR), Trieste, Italy
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11
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Rius J, Torrelles X. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:339-347. [PMID: 34196295 PMCID: PMC8248888 DOI: 10.1107/s2053273321004915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
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Affiliation(s)
- Jordi Rius
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
| | - Xavier Torrelles
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
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12
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Strategies and open questions in solid-phase protein chemical synthesis. Curr Opin Chem Biol 2020; 58:1-9. [DOI: 10.1016/j.cbpa.2020.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/21/2022]
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13
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Diffuse X-ray scattering from correlated motions in a protein crystal. Nat Commun 2020; 11:1271. [PMID: 32152274 PMCID: PMC7062842 DOI: 10.1038/s41467-020-14933-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/07/2020] [Indexed: 11/29/2022] Open
Abstract
Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions. Protein motion in crystals causes diffuse X-ray scattering, which so far has been very challenging to measure and interpret. Here the authors present a finely sampled diffuse scattering map from triclinic lysozyme, which allows them to resolve inter- and intramolecular correlations and they further analyze the maps using all-atom molecular dynamics simulations and simple vibrational models, revealing the contribution of internal protein motion.
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14
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Perez CP, Elmore DE, Radhakrishnan ML. Computationally Modeling Electrostatic Binding Energetics in a Crowded, Dynamic Environment: Physical Insights from a Peptide–DNA System. J Phys Chem B 2019; 123:10718-10734. [DOI: 10.1021/acs.jpcb.9b09478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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16
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Cerutti DS, Case DA. Molecular Dynamics Simulations of Macromolecular Crystals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018; 9. [PMID: 31662799 DOI: 10.1002/wcms.1402] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
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17
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Juers DH, Farley CA, Saxby CP, Cotter RA, Cahn JKB, Holton-Burke RC, Harrison K, Wu Z. The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Acta Crystallogr D Struct Biol 2018; 74:922-938. [PMID: 30198901 PMCID: PMC6130464 DOI: 10.1107/s2059798318008793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/15/2018] [Indexed: 11/11/2022] Open
Abstract
Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.
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Affiliation(s)
- Douglas H. Juers
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Christopher A. Farley
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | | | - Rosemary A. Cotter
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Jackson K. B. Cahn
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | | | - Kaitlin Harrison
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Zhenguo Wu
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
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18
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Molitor C, Bijelic A, Rompel A. The potential of hexatungstotellurate(VI) to induce a significant entropic gain during protein crystallization. IUCRJ 2017; 4:734-740. [PMID: 29123675 PMCID: PMC5668858 DOI: 10.1107/s2052252517012349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/25/2017] [Indexed: 06/01/2023]
Abstract
The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid-liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein-TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process. Upon the formation of TEW-mediated protein-protein contacts, the release of water molecules from the hydration shells of both molecules, i.e. TEW and the protein, causes a reduced solvent-accessible surface area, leading to a significant gain in solvent entropy. Based on the crystal structures of aurone synthase (in the presence and absence of TEW), insights have also been provided into the formation of a metastable LLPS, which is caused by the formation of protein clusters, representing an ideal starting point in protein crystallization. The results strongly encourage the classification of TEW as a valuable crystallization additive.
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Affiliation(s)
- Christian Molitor
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Aleksandar Bijelic
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
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19
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Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery. Molecules 2017; 22:molecules22091447. [PMID: 28858250 PMCID: PMC6151718 DOI: 10.3390/molecules22091447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/27/2017] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is an infectious disease caused by Mycobacteriumtuberculosis, which triggers severe pulmonary diseases. Recently, multidrug/extensively drug-resistant tuberculosis strains have emerged and continue to threaten global health. Because of the development of drug-resistant tuberculosis, there is an urgent need for novel antibiotics to treat these drug-resistant bacteria. In light of the clinical importance of M. tuberculosis, 2067 structures of M. tuberculsosis proteins have been determined. Among them, 52 structures have been solved and studied using solution nuclear magnetic resonance (NMR). The functional details based on structural analysis of M. tuberculosis using NMR can provide essential biochemical data for the development of novel antibiotic drugs. In this review, we introduce diverse structural and biochemical studies on M. tuberculosis proteins determined using NMR spectroscopy.
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20
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Pang YP. FF12MC: A revised AMBER forcefield and new protein simulation protocol. Proteins 2016; 84:1490-516. [PMID: 27348292 PMCID: PMC5129589 DOI: 10.1002/prot.25094] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 12/25/2022]
Abstract
Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheral sp(3) atom, and (iii) reduced 1-4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left- and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490-1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN, 55905, USA.
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21
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Pang YP. Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins. Heliyon 2016; 2:e00161. [PMID: 27699282 PMCID: PMC5035356 DOI: 10.1016/j.heliyon.2016.e00161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 08/18/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022] Open
Abstract
Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2 for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA
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22
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Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput 2016; 12:3926-47. [PMID: 27399642 PMCID: PMC4980686 DOI: 10.1021/acs.jctc.6b00567] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We present the AMBER
ff15ipq force field for proteins, the second-generation
force field developed using the Implicitly Polarized Q (IPolQ) scheme
for deriving implicitly polarized atomic charges in the presence of
explicit solvent. The ff15ipq force field is a complete rederivation
including more than 300 unique atomic charges, 900 unique torsion
terms, 60 new angle parameters, and new atomic radii for polar hydrogens.
The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of
proteins and enables direct calculation of nuclear magnetic resonance
(NMR) relaxation parameters from molecular dynamics simulations. The
atomic radii improve the accuracy of modeling salt bridge interactions
relative to contemporary fixed-charge force fields, rectifying a limitation
of ff14ipq that resulted from its use of pair-specific Lennard-Jones
radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants
exceptionally well, gives reasonable agreement with NMR relaxation
rates, and maintains the expected conformational propensities of structured
proteins/peptides, as well as disordered peptides—all on the
microsecond (μs) time scale, which is a critical regime for
drug design applications. These encouraging results demonstrate the
power and robustness of our automated methods for deriving new force
fields. All parameters described here and the mdgx program used to
fit them are included in the AmberTools16 distribution.
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Affiliation(s)
- Karl T Debiec
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University , Pittsburgh, Pennsylvania, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - David S Cerutti
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Lewis R Baker
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , New Brunswick, New Jersey 08854, United States
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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23
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Tegze M, Bortel G. Coherent diffraction imaging: consistency of the assembled three-dimensional distribution. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016; 72:459-64. [PMID: 27357847 DOI: 10.1107/s2053273316008366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/23/2016] [Indexed: 11/10/2022]
Abstract
The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.
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Affiliation(s)
- Miklós Tegze
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, PO Box 49, Budapest, H-1525, Hungary
| | - Gábor Bortel
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, PO Box 49, Budapest, H-1525, Hungary
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24
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Tihonov MM, Kim VV, Noskov BA. Impact of a Reducing Agent on the Dynamic Surface Properties of Lysozyme Solutions. J Oleo Sci 2016; 65:413-8. [DOI: 10.5650/jos.ess15247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Janowski PA, Liu C, Deckman J, Case DA. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Protein Sci 2015; 25:87-102. [PMID: 26013419 DOI: 10.1002/pro.2713] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 11/12/2022]
Abstract
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics.
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Affiliation(s)
- Pawel A Janowski
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
| | - Chunmei Liu
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854.,The College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province, 450001, People's Republic of China
| | - Jason Deckman
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
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26
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Tihonov MM, Milyaeva OY, Noskov BA. Dynamic surface properties of lysozyme solutions. Impact of urea and guanidine hydrochloride. Colloids Surf B Biointerfaces 2015; 129:114-20. [PMID: 25835146 DOI: 10.1016/j.colsurfb.2015.03.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 11/29/2022]
Abstract
Urea and guanidine hydrochloride (GuHCl) have different influence on surface properties of lysozyme solutions. The increase of GuHCl concentration leads to noticeable changes of kinetic dependencies of the dynamic surface elasticity and ellipsometric angles while the main effect of urea reduces to a strong drop of the static surface tension. The difference between the effects of these two denaturants on the surface properties of other investigated globular proteins is significantly weaker and is mainly a consequence of a different extent of the globule unfolding in the surface layer at equal concentrations of the denaturants. The obtained results for lysozyme solutions are connected with the strongly different denaturation mechanisms under the influence of urea and GuHCl. In the former case the protein preserves its globular structure in the adsorption layer at high urea concentrations (up to 9M) but without tightly packed interior of the globule and with a dynamic tertiary structure (molten globule state). On the contrary, the increase of GuHCl concentration leads to partial destruction of the protein tertiary structure in the surface layer, although this effect is not as strong as in the case of previously studied bovine serum albumin and β-lactoglobulin.
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Affiliation(s)
- M M Tihonov
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - O Yu Milyaeva
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - B A Noskov
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia.
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27
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Neutze R. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130318. [PMID: 24914150 PMCID: PMC4052859 DOI: 10.1098/rstb.2013.0318] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 1012 X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.
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Affiliation(s)
- Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, 40530 Gothenburg, Sweden
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28
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Cerutti DS, Swope WC, Rice J, Case DA. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J Chem Theory Comput 2014; 10:4515-4534. [PMID: 25328495 PMCID: PMC4196740 DOI: 10.1021/ct500643c] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 01/25/2023]
Abstract
We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.
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Affiliation(s)
- David S. Cerutti
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - William C. Swope
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - Julia
E. Rice
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - David A. Case
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
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29
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Frankaer CG, Moroz OV, Turkenburg JP, Aspmo SI, Thymark M, Friis EP, Stahl K, Nielsen JE, Wilson KS, Harris P. Analysis of an industrial production suspension ofBacillus lentussubtilisin crystals by powder diffraction: a powerful quality-control tool. ACTA ACUST UNITED AC 2014; 70:1115-23. [DOI: 10.1107/s1399004714001497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/21/2014] [Indexed: 05/28/2023]
Abstract
A microcrystalline suspension ofBacillus lentussubtilisin (Savinase) produced during industrial large-scale production was analysed by X-ray powder diffraction (XRPD) and X-ray single-crystal diffraction (MX). XRPD established that the bulk microcrystal sample representative of the entire production suspension corresponded to space groupP212121, with unit-cell parametersa= 47.65,b= 62.43,c= 75.74 Å, equivalent to those for a known orthorhombic crystal form (PDB entry 1ndq). MX using synchrotron beamlines at the Diamond Light Source with beam dimensions of 20 × 20 µm was subsequently used to study the largest crystals present in the suspension, with diffraction data being collected from two single crystals (∼20 × 20 × 60 µm) to resolutions of 1.40 and 1.57 Å, respectively. Both structures also belonged to space groupP212121, but were quite distinct from the dominant form identified by XRPD, with unit-cell parametersa= 53.04,b = 57.55,c= 71.37 Å anda= 52.72,b= 57.13,c= 65.86 Å, respectively, and refined toR= 10.8% andRfree= 15.5% and toR= 14.1% andRfree= 18.0%, respectively. They are also different from any of the forms previously reported in the PDB. A controlled crystallization experiment with a highly purified Savinase sample allowed the growth of single crystals of the form identified by XRPD; their structure was solved and refined to a resolution of 1.17 Å with anRof 9.2% and anRfreeof 11.8%. Thus, there are at least three polymorphs present in the production suspension, albeit with the 1ndq-like microcrystals predominating. It is shown how the two techniques can provide invaluable and complementary information for such a production suspension and it is proposed that XRPD provides an excellent quality-control tool for such suspensions.
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Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J Chem Theory Comput 2014; 10:1341-1352. [PMID: 24803862 PMCID: PMC3985686 DOI: 10.1021/ct401042b] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Indexed: 12/24/2022]
Abstract
![]()
By
utilizing Graphics Processing Units, we show that constant pH
molecular dynamics simulations (CpHMD) run in Generalized Born (GB)
implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations.
To address this shortcoming, we present a method for performing constant
pH molecular dynamics simulations (CpHMD) in explicit solvent using
a
discrete protonation state model. The method involves standard molecular
dynamics (MD) being propagated in explicit solvent followed by protonation
state changes being attempted in GB implicit solvent at fixed intervals.
Replica exchange along the pH-dimension (pH-REMD) helps to obtain
acceptable titration behavior with the proposed method. We analyzed
the effects of various parameters and settings on the titration behavior
of CpHMD and pH-REMD in explicit solvent, including the size of the
simulation unit cell and the length of the relaxation dynamics following
protonation state changes. We tested the method with the amino acid
model compounds, a small pentapeptide with two titratable sites, and
hen egg white lysozyme (HEWL). The proposed method yields superior
predicted pKa values for HEWL over hundreds
of nanoseconds of simulation relative to corresponding predicted values
from simulations run in implicit solvent.
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Affiliation(s)
- Jason M Swails
- Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | - Adrian E Roitberg
- Quantum Theory Project, Chemistry Department, University of Florida , Gainesville, Florida 32611, United States
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Rusu VH, Horta VAC, Horta BAC, Lins RD, Baron R. MDWiZ: a platform for the automated translation of molecular dynamics simulations. J Mol Graph Model 2013; 48:80-6. [PMID: 24434017 DOI: 10.1016/j.jmgm.2013.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 11/17/2022]
Abstract
A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.
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Affiliation(s)
- Victor H Rusu
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
| | - Vitor A C Horta
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Computational Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Bruno A C Horta
- Department of Electrical Engineering, Pontíficia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil; Department of Biotechnology and Biological Sciences, Centro Universitário Estadual da Zona Oeste, Rio de Janeiro, Brazil
| | - Roberto D Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
| | - Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA.
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De Simone A, Montalvao RW, Dobson CM, Vendruscolo M. Characterization of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations. Biochemistry 2013; 52:6480-6. [PMID: 23941501 DOI: 10.1021/bi4007513] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hen lysozyme is an enzyme characterized by the presence of two domains whose relative motions are involved in the mechanism of binding and release of the substrates. By using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations, we characterize the breathing motions describing the interdomain fluctuations of this protein. We found that the ensemble of conformations that we determined spans the entire range of structures of hen lysozyme deposited in the Protein Data Bank, including both the free and bound states, suggesting that the thermal motions in the free state provide access to the structures populated upon binding. The approach that we present illustrates how the use of residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations makes it possible to explore conformational fluctuations of a relatively large amplitude in proteins.
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Affiliation(s)
- Alfonso De Simone
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
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34
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Description of local and global shape properties of protein helices. J Mol Model 2013; 19:2901-11. [PMID: 23529181 DOI: 10.1007/s00894-013-1819-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
Abstract
A new method, dubbed "HAXIS" is introduced to describe local and global shape properties of a protein helix via its axis. HAXIS is based on coarse-graining and spline-fitting of the helix backbone. At each Cα anchor point of the backbone, a Frenet frame is calculated, which directly provides the local vector presentation of the helix. After cubic spline-fitting of the axis line, its curvature and torsion are calculated. This makes a rapid comparison of different helix forms and the determination of helix similarity possible. Distortions of the helix caused by individual residues are projected onto the helix axis and presented either by the rise parameter per residue or by the local curvature of the axis. From a non-redundant set of 2,017 proteins, 15,068 helices were investigated in this way. Helix start and helix end as well as bending and kinking of the helix are accurately described. The global properties of the helix are assessed by a polynomial fit of the helix axis and the determination of its overall curving and twisting. Long helices are more regular shaped and linear whereas short helices are often strongly bent and twisted. The distribution of different helix forms as a function of helix length is analyzed.
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35
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Haupert LM, DeWalt EL, Simpson GJ. Modeling the SHG activities of diverse protein crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1513-21. [PMID: 23090400 DOI: 10.1107/s0907444912037638] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 08/31/2012] [Indexed: 11/10/2022]
Abstract
A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ~84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.
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Affiliation(s)
- Levi M Haupert
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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36
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Collins KD. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions. Biophys Chem 2012; 167:43-59. [DOI: 10.1016/j.bpc.2012.04.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 01/13/2023]
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37
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Modulation of physiological and pathological activities of lysozyme by biological membranes. Cell Mol Biol Lett 2012; 17:349-75. [PMID: 22544762 PMCID: PMC6275811 DOI: 10.2478/s11658-012-0015-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/18/2012] [Indexed: 11/21/2022] Open
Abstract
The molecular details of interactions between lipid membranes and lysozyme (Lz), a small polycationic protein with a wide range of biological activities, have long been the focus of numerous studies. The biological consequences of this process are considered to embrace at least two aspects: i) correlation between antimicrobial and membranotropic properties of this protein, and ii) lipid-mediated Lz amyloidogenesis. The mechanisms underlying the lipid-assisted protein fibrillogenesis and membrane disruption exerted by Lz in bacterial cells are believed to be similar. The present investigation was undertaken to gain further insight into Lz-lipid interactions and explore the routes by which Lz exerts its antimicrobial and amyloidogenic actions. Binding and Förster resonance energy transfer studies revealed that upon increasing the content of anionic lipids in lipid vesicles, Lz forms aggregates in a membrane environment. Total internal reflection fluorescence microscopy and pyrene excimerization reaction were employed to study the effect of Lz on the structural and dynamic properties of lipid bilayers. It was found that Lz induces lipid demixing and reduction of bilayer free volume, the magnitude of this effect being much more pronounced for oligomeric protein.
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38
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Zhang M, Wu Y. Pressure-induced structural and hydration changes of proteins in aqueous solutions. ANAL SCI 2012; 27:1139-42. [PMID: 22076342 DOI: 10.2116/analsci.27.1139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The effects of elevated hydrostatic pressure on four representative proteins, lysozyme, human serum albumin, ubiquitin and RNase A, were investigated by using Fourier transform infrared (FTIR) spectroscopy, by principal component analysis (PCA) and by moving-window two-dimensional (MW2D) correlation analysis. In addition, we revealed the pressure-induced changes of secondary structure elements using curve fitting. With pressure increase, the amide I band shifted to lower wavenumbers, with a transition at 200 MPa, which was indicative of hydration enhancement. Moreover, the pressure-induced behavior of pure water was studied, similar transition pressure was observed with protein in aqueous solution, suggesting that structure change of water around 200 MPa caused a hydration enhancement of protein. Under pressure higher than 200 MPa, the structural changes of the four proteins were obviously different except for the common features shifting to lower wavenumbers with pressure, basically due to the distinct structural differences among them.
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Affiliation(s)
- Min Zhang
- State Key Laboratory for Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China
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39
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PS – a program for the analysis of helix geometry. J Mol Graph Model 2012; 33:52-60. [DOI: 10.1016/j.jmgm.2011.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/24/2011] [Accepted: 11/24/2011] [Indexed: 11/22/2022]
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40
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Krause ME, Martin TT, Laurence JS. Mapping site-specific changes that affect stability of the N-terminal domain of calmodulin. Mol Pharm 2012; 9:734-43. [PMID: 22309490 DOI: 10.1021/mp2004109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biophysical tools have been invaluable in formulating therapeutic proteins. These tools characterize protein stability rapidly in a variety of solution conditions, but in general, the techniques lack the ability to discern site-specific information to probe how solution environment acts to stabilize or destabilize the protein. NMR spectroscopy can provide site-specific information about subtle structural changes of a protein under different conditions, enabling one to assess the mechanism of protein stabilization. In this study, NMR was employed to detect structural perturbations at individual residues as a result of altering pH and ionic strength. The N-terminal domain of calmodulin (N-CaM) was used as a model system, and the ¹H-¹⁵N heteronuclear single quantum coherence (HSQC) experiment was used to investigate effects of pH and ionic strength on individual residues. NMR analysis revealed that different solution conditions affect individual residues differently, even when the amino acid sequence and structure are highly similar. This study shows that addition of NMR to the formulation toolbox has the ability to extend understanding of the relationship between site-specific changes and overall protein stability.
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Affiliation(s)
- Mary E Krause
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
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41
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Sinitskiy AV, Saunders MG, Voth GA. Optimal number of coarse-grained sites in different components of large biomolecular complexes. J Phys Chem B 2012; 116:8363-74. [PMID: 22276676 DOI: 10.1021/jp2108895] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.
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Affiliation(s)
- Anton V Sinitskiy
- Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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42
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Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-011-1076-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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43
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Johnston CT, Premachandra GS, Szabo T, Lok J, Schoonheydt RA. Interaction of biological molecules with clay minerals: a combined spectroscopic and sorption study of lysozyme on saponite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:611-619. [PMID: 22047516 DOI: 10.1021/la203161n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The interaction of hen egg white lysozyme (HEWL) with Na- and Cs-exchanged saponite was investigated using sorption, structural, and spectroscopic methods as a model system to study clay-protein interactions. HEWL sorption to Na- and Cs-saponite was determined using the bicinchoninic acid (BCA) assay, thermogravimetric analysis, and C and N analysis. For Na-saponite, the TGA and elemental analysis-derived sorption maximum was 600 mg/g corresponding to a surface coverage of 0.85 ng/mm(2) with HEWL occupying 526 m(2)/g based on a cross-sectional area of 13.5 nm(2)/molecule. HEWL sorption on Na-saponite was accompanied by the release of 9.5 Na(+) ions for every molecule of HEWL sorbed consistent with an ion exchange mechanism between the positively charged HEWL (IEP 11) and the negatively charged saponite surface. The d-spacing of the HEWL-Na-saponite complex increased to a value of 4.4 nm consistent with the crystallographic dimensions of HEWL of 3 × 3 × 4.5 nm. In the case of Cs-saponite, there was no evidence of interlayer sorption; however, sorption of HEWL to the "external" surface of Cs-saponite showed a high affinity isotherm. FTIR and Raman analysis of the amide I region of the HEWL-saponite films prepared from water and D(2)O showed little perturbation to the secondary structure of the protein. The overall hydrophilic nature of the HEWL-Na-saponite complex was determined by water vapor sorption measurements. The clay retained its hydrophilic character with a water content of 18% at high humidity corresponding to 240 H(2)O molecules per molecule of HEWL.
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Affiliation(s)
- Cliff T Johnston
- Birck Nanotechnology Center, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States.
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44
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Gokarn YR, Fesinmeyer RM, Saluja A, Razinkov V, Chase SF, Laue TM, Brems DN. Effective charge measurements reveal selective and preferential accumulation of anions, but not cations, at the protein surface in dilute salt solutions. Protein Sci 2011; 20:580-7. [PMID: 21432935 DOI: 10.1002/pro.591] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specific-ion effects are ubiquitous in nature; however, their underlying mechanisms remain elusive. Although Hofmeister-ion effects on proteins are observed at higher (>0.3 M) salt concentrations, in dilute (<0.1 M) salt solutions nonspecific electrostatic screening is considered to be dominant. Here, using effective charge (Q*) measurements of hen-egg white lysozyme (HEWL) as a direct and differential measure of ion-association, we experimentally show that anions selectively and preferentially accumulate at the protein surface even at low (<100 mM) salt concentrations. At a given ion normality (50 mN), the HEWL Q* was dependent on anion, but not cation (Li(+), Na(+), K(+), Rb(+), Cs(+), GdnH(+), and Ca(2+)), identity. The Q* decreased in the order F(-) > Cl(-) > Br(-) > NO(3)(-) ∼ I(-) > SCN(-) > ClO(4)(-) ≫ SO(4)(2-), demonstrating progressively greater binding of the monovalent anions to HEWL and also show that the SO(4)(2-) anion, despite being strongly hydrated, interacts directly with the HEWL surface. Under our experimental conditions, we observe a remarkable asymmetry between anions and cations in their interactions with the HEWL surface.
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Affiliation(s)
- Yatin R Gokarn
- Process and Product Development, Amgen Inc. Seattle, Washington 98119, USA.
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45
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Structural characteristics of hydration sites in lysozyme. Biophys Chem 2011; 156:31-42. [DOI: 10.1016/j.bpc.2011.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/17/2011] [Accepted: 02/17/2011] [Indexed: 11/17/2022]
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46
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Haupt C, Bereza M, Kumar ST, Kieninger B, Morgado I, Hortschansky P, Fritz G, Röcken C, Horn U, Fändrich M. Pattern Recognition with a Fibril-Specific Antibody Fragment Reveals the Surface Variability of Natural Amyloid Fibrils. J Mol Biol 2011; 408:529-40. [DOI: 10.1016/j.jmb.2011.02.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/24/2011] [Accepted: 02/13/2011] [Indexed: 10/18/2022]
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47
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Higman VA, Boyd J, Smith LJ, Redfield C. Residual dipolar couplings: are multiple independent alignments always possible? JOURNAL OF BIOMOLECULAR NMR 2011; 49:53-60. [PMID: 21184138 PMCID: PMC3020303 DOI: 10.1007/s10858-010-9457-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/19/2010] [Indexed: 05/30/2023]
Abstract
RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the protein's interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment media (depending on the method used) and so far, such data have only been reported for three small 6-8 kDa proteins with identical folds: ubiquitin, GB1 and GB3. Our results suggest that HEWL is likely to be representative of many other medium to large sized proteins commonly studied by solution NMR. Comparisons with over 60 high-resolution crystal structures of HEWL reveal that the highest resolution structures are not necessarily always the best models for the protein structure in solution.
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Affiliation(s)
- Victoria A. Higman
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Jonathan Boyd
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Lorna J. Smith
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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48
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Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol 2010; 6. [PMID: 20865158 PMCID: PMC2928775 DOI: 10.1371/journal.pcbi.1000911] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/28/2010] [Indexed: 11/21/2022] Open
Abstract
It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable. There is a well-recognized gap between the dynamical motions of proteins required to execute function and the experimental techniques capable of capturing that motion at the atomic level. We show that much experimental detail of dynamical motion is already present in X-ray crystallographic data, which arises from being solved by different research groups using different methodologies under different crystallization conditions, which then capture an ensemble of structures whose variations can be quantified on a residue-by-residue level using local density correlations. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme by comparing the X-ray ensemble to MD ensembles as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD and they remain virtually identical to structural motions measured at 300K. It provides a novel analysis of large X-ray ensemble data that is useful for the broader structural biology community.
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Affiliation(s)
- Jonathan E. Kohn
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jory Z. Ruscio
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Paul D. Adams
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Teresa Head-Gordon
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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Pozharski E. Percentile-based spread: a more accurate way to compare crystallographic models. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:970-8. [PMID: 20823548 DOI: 10.1107/s0907444910027927] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 07/13/2010] [Indexed: 11/10/2022]
Abstract
The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.
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Guli M, Lambert E, Li M, Mann S. Template-Directed Synthesis of Nanoplasmonic Arrays by Intracrystalline Metalization of Cross-Linked Lysozyme Crystals. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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