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Jing Y, Cheng Y, Li F, Li Y, Liu F, Zhang J. Linkage of nanosecond protein motion with enzymatic methyl transfer by nicotinamide N-methyltransferase. Turk J Biol 2021; 45:333-341. [PMID: 34377057 PMCID: PMC8313939 DOI: 10.3906/biy-2101-54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/19/2021] [Indexed: 11/17/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT), a key cytoplasmic protein in the human body, is accountable to catalyze the nicotinamide (NCA) N1-methylation through S-adenosyl-L-methionine (SAM) as a methyl donor, which has been linked to many diseases. Although extensive studies have concerned about the biological aspect, the detailed mechanism study of the enzyme function, especially in the part of protein dynamics is lacking. Here, wild-type nicotinamide N-methyltransferase together with the mutation at position 20 with Y20F, Y20G, and free tryptophan were carried out to explore the connection between protein dynamics and catalysis using time-resolved fluorescence lifetimes. The results show that wild-type nicotinamide N-methyltransferase prefers to adapt a less flexible protein conformation to achieve enzyme catalysis.
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Affiliation(s)
- Yahui Jing
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China
| | - Yiting Cheng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China
| | - Fangya Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China
| | - Yuping Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China.,Binzhou Institute for Food and Drug Control, Binzhou, Shandong China
| | - Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin China
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2
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Timofeev VI, Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Kleymenov SY, Bocharov EV, Rakitina TV. Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold. J Biomol Struct Dyn 2017; 36:4392-4404. [PMID: 29283021 DOI: 10.1080/07391102.2017.1417162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins of the bacterial nucleoid, which shares high sequence and structural similarity with IHF but differs from the latter in DNA-specificity. Here, we perform an analysis of structural-dynamic properties of HU protein from Spiroplasma melliferum and compare its behavior in solution to that of another mycoplasmal HU from Mycoplasma gallisepticum. The high-resolution heteronuclear NMR spectroscopy was coupled with molecular-dynamics study and comparative analysis of thermal denaturation of both mycoplasmal HU proteins. We suggest that stacking interactions in two aromatic clusters in the HUSpm dimeric interface determine not only high thermal stability of the protein, but also its structural plasticity experimentally observed as slow conformational exchange. One of these two centers of stacking interactions is highly conserved among the known HU and IHF proteins. Second aromatic core described recently in IHFs and IHF-like proteins is considered as a discriminating feature of IHFs. We performed an electromobility shift assay to confirm high affinities of HUSpm to both normal and distorted dsDNA, which are the characteristics of HU protein. MD simulations of HUSpm with alanine mutations of the residues forming the non-conserved aromatic cluster demonstrate its role in dimer stabilization, as both partial and complete distortion of the cluster enhances local flexibility of HUSpm.
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Affiliation(s)
- Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,b Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- c Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Sergey Yu Kleymenov
- d Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation.,e Russian Academy of Sciences, Koltzov Institute of Developmental Biology , ul. Vavilova, 26, Moscow 119334 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,f Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
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3
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Altukhov DA, Talyzina AA, Agapova YK, Vlaskina AV, Korzhenevskiy DA, Bocharov EV, Rakitina TV, Timofeev VI, Popov VO. Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum. J Biomol Struct Dyn 2016; 36:45-53. [PMID: 27884082 DOI: 10.1080/07391102.2016.1264893] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins. In this work, we studied the structural dynamic properties of the HUMgal dimer by NMR spectroscopy and MD simulations. The obtained all-atom model displays compliance with the NMR data and confirms the heterogeneous backbone flexibility of HUMgal. We found that HUMgal, being folded into a dimeric conformation typical for HU proteins, has a labile α-helical body with protruded β-stranded arms forming DNA-binding domain that are highly flexible in the absence of DNA. The amino acid substitutions in conserved regions of the protein are likely to affect the conformational lability of the HUMgal dimer that can be responsible for complex functional behavior of HUMgal in vivo, e.g. facilitating its spatial adaptation to non-canonical DNA-targets.
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Affiliation(s)
- Dmitry A Altukhov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna A Talyzina
- b Moscow Institute of Physics and Technology , Institutskiy per., 9, Dolgoprudny, Moscow Region 141700 , Russian Federation
| | - Yulia K Agapova
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Anna V Vlaskina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Dmitry A Korzhenevskiy
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation
| | - Eduard V Bocharov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Tatiana V Rakitina
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,c Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS , str. Miklukho-Maklaya 16/10, Moscow 117997 , Russian Federation
| | - Vladimir I Timofeev
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,d Federal Scientific Research Center 'Crystallography and Photonics' RAS , Leninskii pr., 59, Moscow 119333 , Russian Federation
| | - Vladimir O Popov
- a National Research Centre 'Kurchatov Institute', Kurchatov Complex of NBICS-Technologies , Akad. Kurchatova sqr., 1, Moscow 123182 , Russian Federation.,e Bach Institute of Biochemistry , Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt. 33, bld. 2, Moscow 119071 , Russian Federation
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4
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Shapiro YE, Polimeno A, Freed JH, Meirovitch E. Methyl dynamics of a Ca2+-calmodulin-peptide complex from NMR/SRLS. J Phys Chem B 2011; 115:354-65. [PMID: 21166433 PMCID: PMC3062514 DOI: 10.1021/jp107130m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS accounts for dynamical coupling between the tumbling of the protein and the local motion of the probe and for general tensorial properties. It is the generalization of the traditional model-free (MF) method, which does not account for mode-coupling and treats only simple tensorial properties. SRLS is applied herein to ²H relaxation of ¹³CDH₂ groups in the complex of Ca(2+)-calmodulin with the peptide smMLCKp. Literature data comprising ²H T₁ and T₂ acquired at 14.1 and 17.6 T, and 288, 295, 308, and 320 K, are used. We find that mode-coupling is a small effect for methyl dynamics. On the other hand, general tensorial properties are important. In particular, it is important to allow for the asymmetry of the local spatial restrictions, which can be represented in SRLS by a rhombic local ordering tensor with components S(0)(2) and S(2)(2). The principal axes frame of this tensor is obviously different from the axial frames of the magnetic tensors. Here, we find that -0.2 ≤ S(0)(2) ≤ 0.5 and -0.4 ≤ S(2)(2) ≤ 0. MF features a single "generalized" order parameter, S, confined to the 0-0.316 range; the local geometry is inherently simple. The parameter S is inaccurate, having absorbed unaccounted for effects, notably S(2)(2) ≠ 0. We find that the methionine methyls (the other methyl types) reorient with rates of 8.6 × 10⁹ to 21.4 × 10⁹ (0.67 × 10⁹ to 6.5 × 10⁹) 1/s. The corresponding activation energies are 10 (10-27) kJ/mol. By contrast, MF yields inaccurate effective local motional correlation times, τ(e), with nonphysical temperature dependence. Thus, the problematic S- and τ(e)-based MF picture of methyl dynamics has been replaced with an insightful physical picture based on a local ordering tensor related to structural features, and a local diffusion tensor that yields accurate activation energies.
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Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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5
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Meirovitch E, Zerbetto M, Polimeno A, Freed JH. Backbone dynamics of deoxy and carbonmonoxy hemoglobin by NMR/SRLS. J Phys Chem B 2011; 115:143-57. [PMID: 21162544 PMCID: PMC3071157 DOI: 10.1021/jp107553j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The slowly relaxing local structure (SRLS) approach, developed for NMR spin relaxation analysis in proteins, is applied herein to amide ¹⁵N relaxation in deoxy and carbonmonoxy hemoglobin. Experimental data including ¹⁵N T₁, T₂ and ¹⁵N-{¹H} NOE, acquired at 11.7 and 14.1 T, and 29 and 34 °C, are analyzed. The restricted local motion of the N-H bond is described in terms of the principal value (S(0)(2)) and orientation (β(D)) of an axial local ordering tensor, S, and the principal values (R(||)(L) and R(⊥)(L)) and orientation (β(O)) of an axial local diffusion tensor, R(L). The parameters c₀² (the potential coefficient in terms of which S(0)(2) is defined), R(||)(L), β(D), and β(O) are determined by data fitting; R(⊥)(L) is set equal to the global motional rate, R(C), found previously to be (5.2-5.8) × 10⁶ 1/s in the temperature range investigated. The principal axis of S is (nearly) parallel to the C(i-1)(α)-C(i)(α) axis; when the two axes are parallel, β(D) = -101.3° (in the frame used). The principal axis of R(L) is (nearly) parallel to the N-H bond; when the two axes are parallel, β(O) = -101.3°. For "rigid" N-H bonds located in secondary structure elements the best-fit parameters are S(0)(2) = 0.88-0.95 (corresponding to local potentials of 8.6-19.9 k(B)T), R(||)(L) = 10⁹-10¹⁰ 1/s, β(D) = -101.3° ± 2.0°, and β(O) = -101.3° ± 4°. For flexible N-H bonds located in loops the best-fit values are S(0)(2) = 0.75-0.80 (corresponding to local potentials of 4.5-5.5 k(B)T), R(||)(L) = (1.0-6.3) × 10⁸ 1/s, β(D) = -101.3° ± 4.0°, and β(O) = -101.3° ± 10°. These results are important in view of their physical clarity, inherent potential for further interpretation, consistency, and new qualitative insights provided (vide infra).
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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6
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Ferrage F, Reichel A, Battacharya S, Cowburn D, Ghose R. On the measurement of ¹⁵N-{¹H} nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 207:294-303. [PMID: 20951618 PMCID: PMC3638772 DOI: 10.1016/j.jmr.2010.09.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 09/17/2010] [Accepted: 09/19/2010] [Indexed: 05/12/2023]
Abstract
Measurement of steady-state (15)N-{(1)H} nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008) 302-313; J. Am. Chem. Soc. 131 (2009) 6048-6049) reevaluated spin-dynamics during steady-state (or "saturated") and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state (15)N-{(1)H} NOE's without artifacts and with the highest possible accuracy.
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Affiliation(s)
- Fabien Ferrage
- Département de Chimie, Ecole Normale Supérieure and CNRS UMR 7203, Laboratoire des Biomolécules, 24, rue Lhomond, 75231 Paris Cedex 05, France.
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7
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Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 346] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
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8
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Nicholas MP, Eryilmaz E, Ferrage F, Cowburn D, Ghose R. Nuclear spin relaxation in isotropic and anisotropic media. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:111-158. [PMID: 20633361 PMCID: PMC4015737 DOI: 10.1016/j.pnmrs.2010.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/13/2010] [Indexed: 05/28/2023]
Affiliation(s)
- Matthew P. Nicholas
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
| | - Ertan Eryilmaz
- Department of Chemistry, City College of the City University
of New York, New York 10031, U.S.A
- Graduate Center of the City University of New York, New York
10016, U.S.A
| | - Fabien Ferrage
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
- Département de Chimie, Ecole Normale
Supérieure, and CNRS, UMR 7203; 24 rue Lhomond, 75231 Paris cedex 05,
France
| | - David Cowburn
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
| | - Ranajeet Ghose
- Department of Chemistry, City College of the City University
of New York, New York 10031, U.S.A
- Graduate Center of the City University of New York, New York
10016, U.S.A
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9
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:360-405. [PMID: 20625480 PMCID: PMC2899824 DOI: 10.1016/j.pnmrs.2010.03.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
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Teilum K, Olsen JG, Kragelund BB. Functional aspects of protein flexibility. Cell Mol Life Sci 2009; 66:2231-47. [PMID: 19308324 PMCID: PMC11115794 DOI: 10.1007/s00018-009-0014-6] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 12/29/2022]
Abstract
Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions. The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed as an integral part of their structure.
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Johan G. Olsen
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
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11
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Trott O, Siggers K, Rost B, Palmer AG. Protein conformational flexibility prediction using machine learning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:37-47. [PMID: 18313957 PMCID: PMC2413295 DOI: 10.1016/j.jmr.2008.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 12/15/2007] [Accepted: 01/26/2008] [Indexed: 05/26/2023]
Abstract
Using a data set of 16 proteins, a neural network has been trained to predict backbone 15N generalized order parameters from the three-dimensional structures of proteins. The final network parameterization contains six input features. The average prediction accuracy, as measured by the Pearson's correlation coefficient between experimental and predicted values of the square of the generalized order parameter is >0.70. Predicted order parameters for non-terminal amino acid residues depends most strongly on the local packing density and the probability that the residue is located in regular secondary structure.
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Affiliation(s)
| | | | | | - Arthur G. Palmer
- * Corresponding author. Fax: (212) 305-6949. E-mail address: (A. G. Palmer)
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