1
|
Shukla S, Bhattacharya A, Sehrawat P, Agarwal P, Shobhawat R, Malik N, Duraisamy K, Rangan NS, Hosur RV, Kumar A. Disorder in CENP-A Cse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore. Structure 2024; 32:690-705.e6. [PMID: 38565139 DOI: 10.1016/j.str.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The centromere is epigenetically marked by a histone H3 variant-CENP-A. The budding yeast CENP-A called Cse4, consists of an unusually long N-terminus that is known to be involved in kinetochore assembly. Its disordered chaperone, Scm3 is responsible for the centromeric deposition of Cse4 as well as in the maintenance of a segregation-competent kinetochore. In this study, we show that the Cse4 N-terminus is intrinsically disordered and interacts with Scm3 at multiple sites, and the complex does not gain any substantial structure. Additionally, the complex forms a synergistic association with an essential inner kinetochore component (Ctf19-Mcm21-Okp1-Ame1), and a model has been suggested to this effect. Thus, our study provides mechanistic insights into the Cse4 N-terminus-chaperone interaction and also illustrates how intrinsically disordered proteins mediate assembly of complex multiprotein networks, in general.
Collapse
Affiliation(s)
- Shivangi Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | | | - Parveen Sehrawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Prakhar Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Kalaiyarasi Duraisamy
- Centre for Advanced Protein Studies, Syngene International Limited, Bangalore, India
| | | | - Ramakrishna V Hosur
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India.
| |
Collapse
|
2
|
Das NR, Chaudhury KN, Pal D. Improved NMR-data-compliant protein structure modeling captures context-dependent variations and expands the scope of functional inference. Proteins 2023; 91:412-435. [PMID: 36287124 DOI: 10.1002/prot.26439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/12/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can reveal conformational states of a protein in physiological conditions. However, sparsely available NMR data for a protein with large degrees of freedom can introduce structural artifacts in the built models. Currently used state-of-the-art methods deriving protein structure and conformation from NMR deploy molecular dynamics (MD) coupled with simulated annealing for building models. We provide an alternate graph-based modeling approach, where we first build substructures from NMR-derived distance-geometry constraints combined in one shot to form the core structure. The remaining molecule with inadequate data is modeled using a hybrid approach respecting the observed distance-geometry constraints. One-shot structure building is rarely undertaken for large and sparse data systems, but our data-driven bottom-up approach makes this uniquely feasible by suitable partitioning of the problem. A detailed comparison of select models with state-of-art methods reveals differences in the secondary structure regions wherein the correctness of our models is confirmed by NMR data. Benchmarking of 106 protein-folds covering 38-282 length structures shows minimal experimental-constraint violations while conforming to other structure quality parameters such as the proper folding, steric clash, and torsion angle violation based on Ramachandran plot criteria. Comparative MD studies using select protein models from a state-of-art method and ours under identical experimental parameters reveal distinct conformational dynamics that could be attributed to protein structure-function. Our work is thus useful in building enhanced NMR-evidence-based models that encapsulate the contextual secondary and tertiary structure variations present during the experimentation and expand the scope of functional inference.
Collapse
Affiliation(s)
- Niladri R Das
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore, India.,Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Kunal N Chaudhury
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| |
Collapse
|
3
|
The A39G FF domain folds on a volcano-shaped free energy surface via separate pathways. Proc Natl Acad Sci U S A 2021; 118:2115113118. [PMID: 34764225 DOI: 10.1073/pnas.2115113118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
Conformational dynamics play critical roles in protein folding, misfolding, function, misfunction, and aggregation. While detecting and studying the different conformational states populated by protein molecules on their free energy surfaces (FESs) remain a challenge, NMR spectroscopy has emerged as an invaluable experimental tool to explore the FES of a protein, as conformational dynamics can be probed at atomic resolution over a wide range of timescales. Here, we use chemical exchange saturation transfer (CEST) to detect "invisible" minor states on the energy landscape of the A39G mutant FF domain that exhibited "two-state" folding kinetics in traditional experiments. Although CEST has mostly been limited to studies of processes with rates between ∼5 to 300 s-1 involving sparse states with populations as low as ∼1%, we show that the line broadening that is often associated with minor state dips in CEST profiles can be exploited to inform on additional conformers, with lifetimes an order of magnitude shorter and populations close to 10-fold smaller than what typically is characterized. Our analysis of CEST profiles that exploits the minor state linewidths of the 71-residue A39G FF domain establishes a folding mechanism that can be described in terms of a four-state exchange process between interconverting states spanning over two orders of magnitude in timescale from ∼100 to ∼15,000 μs. A similar folding scheme is established for the wild-type domain as well. The study shows that the folding of this small domain proceeds through a pair of sparse, partially structured intermediates via two discrete pathways on a volcano-shaped FES.
Collapse
|
4
|
Skeens E, East KW, Lisi GP. 1H, 13C, 15 N backbone resonance assignment of the recognition lobe subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:25-28. [PMID: 32935194 PMCID: PMC8635283 DOI: 10.1007/s12104-020-09977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Rec3 is a subdomain of the recognition (Rec) lobe within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein Cas9 that is involved in nucleic acid binding and is critical to HNH endonuclease activation. Here, we report the backbone resonance assignments of an engineered construct of the Rec3 subdomain from Streptococcus pyogenes Cas9. We also analyze backbone chemical shift data to predict secondary structure and an overall fold that is consistent with that of Rec3 from the full-length S. pyogenes Cas9 protein.
Collapse
Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Kyle W East
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - George P Lisi
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA.
| |
Collapse
|
5
|
Miller MC, Nesmelova IV, Daragan VA, Ippel H, Michalak M, Dregni A, Kaltner H, Kopitz J, Gabius HJ, Mayo KH. Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function. Biochem J 2020; 477:3147-3165. [PMID: 32766716 PMCID: PMC7473712 DOI: 10.1042/bcj20200499] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023]
Abstract
Human galectin-7 (Gal-7; also termed p53-induced gene 1 product) is a multifunctional effector by productive pairing with distinct glycoconjugates and protein counter-receptors in the cytoplasm and nucleus, as well as on the cell surface. Its structural analysis by NMR spectroscopy detected doubling of a set of particular resonances, an indicator of Gal-7 existing in two conformational states in slow exchange on the chemical shift time scale. Structural positioning of this set of amino acids around the P4 residue and loss of this phenomenon in the bioactive P4L mutant indicated cis-trans isomerization at this site. Respective resonance assignments confirmed our proposal of two Gal-7 conformers. Mapping hydrogen bonds and considering van der Waals interactions in molecular dynamics simulations revealed a structural difference for the N-terminal peptide, with the trans-state being more exposed to solvent and more mobile than the cis-state. Affinity for lactose or glycan-inhibitable neuroblastoma cell surface contact formation was not affected, because both conformers associated with an overall increase in order parameters (S2). At low µM concentrations, homodimer dissociation is more favored for the cis-state of the protein than its trans-state. These findings give direction to mapping binding sites for protein counter-receptors of Gal-7, such as Bcl-2, JNK1, p53 or Smad3, and to run functional assays at low concentration to test the hypothesis that this isomerization process provides a (patho)physiologically important molecular switch for Gal-7.
Collapse
Affiliation(s)
- Michelle C. Miller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
| | - Irina V. Nesmelova
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
| | - Vladimir A. Daragan
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
| | - Hans Ippel
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
- Department of Biochemistry, CARIM, University of Maastricht, Maastricht, The Netherlands
| | - Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Aurelio Dregni
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximillians-University Munich, Munich, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximillians-University Munich, Munich, Germany
| | - Kevin H. Mayo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 U.S.A
| |
Collapse
|
6
|
Tiwari VP, Vallurupalli P. A CEST NMR experiment to obtain glycine 1H α chemical shifts in 'invisible' minor states of proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:443-455. [PMID: 32696193 DOI: 10.1007/s10858-020-00336-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Chemical exchange saturation transfer (CEST) experiments are routinely used to study protein conformational exchange between a 'visible' major state and 'invisible' minor states because they can detect minor states with lifetimes varying from ~ 3 to ~ 100 ms populated to just ~ 0.5%. Consequently several 1H, 15N and 13C CEST experiments have been developed to study exchange and obtain minor state chemical shifts at almost all backbone and sidechain sites in proteins. Conspicuously missing from this extensive set of CEST experiments is a 1H CEST experiment to study exchange at glycine (Gly) 1Hα sites as the existing 1H CEST experiments that have been designed to study dynamics in amide 1H-15N spin systems and methyl 13CH3 groups with three equivalent protons while suppressing 1H-1H NOE induced dips are not suitable for studying exchange in methylene 13CH2 groups with inequivalent protons. Here a Gly 1Hα CEST experiment to obtain the minor state Gly 1Hα chemical shifts is presented. The utility of this experiment is demonstrated on the L99A cavity mutant of T4 Lysozyme (T4L L99A) that undergoes conformational exchange between two compact conformers. The CEST derived minor state Gly 1Hα chemical shifts of T4L L99A are in agreement with those obtained previously using CPMG techniques. The experimental strategy presented here can also be used to obtain methylene proton minor state chemical shifts from protein sidechain and nucleic acid backbone sites.
Collapse
Affiliation(s)
- Ved Prakash Tiwari
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India.
| |
Collapse
|
7
|
Chen D, Wang Z, Guo D, Orekhov V, Qu X. Review and Prospect: Deep Learning in Nuclear Magnetic Resonance Spectroscopy. Chemistry 2020; 26:10391-10401. [PMID: 32251549 DOI: 10.1002/chem.202000246] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Since the concept of deep learning (DL) was formally proposed in 2006, it has had a major impact on academic research and industry. Nowadays, DL provides an unprecedented way to analyze and process data with demonstrated great results in computer vision, medical imaging, natural language processing, and so forth. Herein, applications of DL in NMR spectroscopy are summarized, and a perspective for DL as an entirely new approach that is likely to transform NMR spectroscopy into a much more efficient and powerful technique in chemistry and life sciences is outlined.
Collapse
Affiliation(s)
- Dicheng Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
| | - Zi Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
| | - Di Guo
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, 361024, P.R. China
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, P.O. Box 979, Xiamen, 361005, P.R. China
| |
Collapse
|
8
|
Intracellular Delivery of DNA and Protein by a Novel Cell-Permeable Peptide Derived from DOT1L. Biomolecules 2020; 10:biom10020217. [PMID: 32024261 PMCID: PMC7072583 DOI: 10.3390/biom10020217] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/27/2022] Open
Abstract
Cellular uptake and intracellular release efficiency of biomacromolecules is low because of hurdles in the cell membrane that result in limited access to intra-cellular targets with few functional effects. Cell-penetrating peptides (CPPs) act as cargo delivery vehicles to promote therapeutic molecule translocation. Here, we describe the novel CPP-Dot1l that not only penetrates by itself, but also mediates cargo translocation in cultured cells, as confirmed by fluorescence microscopy and fluorescence spectrophotometry. We conducted cytotoxicity assays and safety evaluations, and determined peptide-membrane interactions to understand the possible pathway for cargo translocation. Additional nucleic acid and covalently conjugated green fluorescence protein (GFP) studies mediated by CPP-Dot1l were conducted to show functional delivery potential. Results indicate that CPP-Dot1l is a novel and effective CPP due to its good penetrating properties in different cell lines and its ability to enter cells in a concentration-dependent manner. Its penetration efficiency can be prompted by DMSO pretreatment. In addition, not only can it mediate plasmid delivery, but CPP-Dot1l can also deliver GFP protein into cytosol. In conclusion, the findings of this study showed CPP-Dot1l is an attractive pharmaceutical and biochemical tool for future drug, regenerative medicine, cell therapy, gene therapy, and gene editing-based therapy development.
Collapse
|
9
|
East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J Am Chem Soc 2020; 142:1348-1358. [PMID: 31885264 PMCID: PMC7497131 DOI: 10.1021/jacs.9b10521] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.
Collapse
Affiliation(s)
- Kyle W. East
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Jocelyn C. Newton
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Yogesh Narkhede
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| |
Collapse
|
10
|
Takeuchi K, Baskaran K, Arthanari H. Structure determination using solution NMR: Is it worth the effort? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:195-201. [PMID: 31345771 DOI: 10.1016/j.jmr.2019.07.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
It has been almost 40 years since solution NMR joined X-ray crystallography as a technique for determining high-resolution structures of proteins. Since then NMR derived structure has contributed in fundamental ways to our understanding of the function of biomolecules. With the already existing mature field of X-ray crystallography and the emergence of cryo-EM as techniques to tackle high-resolution structures of large protein complexes, the role of NMR in structure determination has been questioned. However, NMR has the unique ability to recapitulate the dynamic motion of proteins in their structures, while size limitations of the biomolecular systems that can be routinely studied still present challenges. The field has continually developed methodology and instrumentation since its introduction, pushing its frontiers and redefining its limits. Here we present a brief overview of NMR-based structure determination over the past 40 years. We outline the current state of the field and look ahead to the challenges that still need to be addressed to realize the future potential of NMR as a structural technique.
Collapse
Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Kumaran Baskaran
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI 53706, United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| |
Collapse
|
11
|
Abstract
Biological molecules are often highly dynamic, and this flexibility can be critical for function. The large range of sampled timescales and the fact that many of the conformers that are continually explored are only transiently formed and sparsely populated challenge current biophysical approaches. Solution nuclear magnetic resonance (NMR) spectroscopy has emerged as a powerful method for characterizing biomolecular dynamics in detail, even in cases where excursions involve short-lived states. Here, we briefly review a number of NMR experiments for studies of biomolecular dynamics on the microsecond-to-second timescale and focus on applications to protein and nucleic acid systems that clearly illustrate the functional relevance of motion in both health and disease.
Collapse
Affiliation(s)
- Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| |
Collapse
|
12
|
Bräuer M, Zich MT, Önder K, Müller N. The influence of commonly used tags on structural propensities and internal dynamics of peptides. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
13
|
Interleukin-37 monomer is the active form for reducing innate immunity. Proc Natl Acad Sci U S A 2019; 116:5514-5522. [PMID: 30819901 DOI: 10.1073/pnas.1819672116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Interleukin-37 (IL-37), a member of the IL-1 family of cytokines, is a fundamental suppressor of innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, and biological studies to elucidate the unique characteristics of IL-37. Our studies reveal that single amino acid mutations at the IL-37 dimer interface that result in the stable formation of IL-37 monomers also remain monomeric at high micromolar concentrations and that these monomeric IL-37 forms comprise higher antiinflammatory activities than native IL-37 on multiple cell types. We find that, because native IL-37 forms dimers with nanomolar affinity, higher IL-37 only weakly suppresses downstream markers of inflammation whereas lower concentrations are more effective. We further show that IL-37 is a heparin binding protein that modulates this self-association and that the IL-37 dimers must block the activity of the IL-37 monomer. Specifically, native IL-37 at 2.5 nM reduces lipopolysaccharide (LPS)-induced vascular cell adhesion molecule (VCAM) protein levels by ∼50%, whereas the monomeric D73K mutant reduced VCAM by 90% at the same concentration. Compared with other members of the IL-1 family, both the N and the C termini of IL-37 are extended, and we show they are disordered in the context of the free protein. Furthermore, the presence of, at least, one of these extended termini is required for IL-37 suppressive activity. Based on these structural and biological studies, we present a model of IL-37 interactions that accounts for its mechanism in suppressing innate inflammation.
Collapse
|
14
|
Wang CK, Craik DJ. Toward Structure Determination of Disulfide-Rich Peptides Using Chemical Shift-Based Methods. J Phys Chem B 2019; 123:1903-1912. [PMID: 30730741 DOI: 10.1021/acs.jpcb.8b10649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide-rich peptides are a class of molecules for which NMR spectroscopy has been the primary tool for structural characterization. Here, we explore whether the process can be achieved by using structural information encoded in chemical shifts. We examine (i) a representative set of five cyclic disulfide-rich peptides that have high-resolution NMR and X-ray structures and (ii) a larger set of 100 disulfide-rich peptides from the PDB. Accuracy of the calculated structures was dependent on the methods used for searching through conformational space and for identifying native conformations. Although Hα chemical shifts could be predicted reasonably well using SHIFTX, agreement between predicted and experimental chemical shifts was sufficient for identifying native conformations for only some peptides in the representative set. Combining chemical shift data with the secondary structure information and potential energy calculations improved the ability to identify native conformations. Additional use of sparse distance restraints or homology information to restrict the search space also improved the resolution of the calculated structures. This study demonstrates that abbreviated methods have potential for elucidation of peptide structures to high resolution and further optimization of these methods, e.g., improvement in chemical shift prediction accuracy, will likely help transition these methods into the mainstream of disulfide-rich peptide structural biology.
Collapse
Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| |
Collapse
|
15
|
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM. Proc Natl Acad Sci U S A 2019; 116:2935-2944. [PMID: 30718402 PMCID: PMC6386705 DOI: 10.1073/pnas.1808696116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HuR is a pivotal player in binding mRNAs containing AU-rich elements and regulating their stability and decay. HuR embeds three RNA recognition motifs (RRMs). The function of RRM3 is not completely understood, and the structure of the entire Hu protein family is so far unknown. Here, we provide structural and mechanistic insights into how HuR RRM3 discriminates between U-rich and AU-rich targets. RRM3 uses additional mechanisms, like multiple-register binding and homodimerization, to fine-tune its affinity for RNA. These results highlight the multifunctional role of HuR RRM3 but also the subtle adaptability of RRMs, the most abundant RNA-binding domain in eukaryotes. Since elevated HuR levels are associated with disease, our structure may help develop new therapeutic strategies. Human antigen R (HuR) is a key regulator of cellular mRNAs containing adenylate/uridylate–rich elements (AU-rich elements; AREs). These are a major class of cis elements within 3′ untranslated regions, targeting these mRNAs for rapid degradation. HuR contains three RNA recognition motifs (RRMs): a tandem RRM1 and 2, followed by a flexible linker and a C-terminal RRM3. While RRM1 and 2 are structurally characterized, little is known about RRM3. Here we present a 1.9-Å-resolution crystal structure of RRM3 bound to different ARE motifs. This structure together with biophysical methods and cell-culture assays revealed the mechanism of RRM3 ARE recognition and dimerization. While multiple RNA motifs can be bound, recognition of the canonical AUUUA pentameric motif is possible by binding to two registers. Additionally, RRM3 forms homodimers to increase its RNA binding affinity. Finally, although HuR stabilizes ARE-containing RNAs, we found that RRM3 counteracts this effect, as shown in a cell-based ARE reporter assay and by qPCR with native HuR mRNA targets containing multiple AUUUA motifs, possibly by competing with RRM12.
Collapse
|
16
|
Alazmi M, Abbas A, Guo X, Fan M, Li L, Gao X. A Slice-based 13C-detected NMR Spin System Forming and Resonance Assignment Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1999-2008. [PMID: 29994483 DOI: 10.1109/tcbb.2018.2849728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is attracting more attention in the field of computational structural biology. Till recently, 1H-detected experiments are the dominant NMR technique used due to the high sensitivity of 1H nuclei. However, the current availability of high magnetic fields and cryogenically cooled probe heads allow researchers to overcome the low sensitivity of 13C nuclei. Consequently, 13C-detected experiments have become a popular technique in different NMR applications especially resonance assignment and structure determination of large proteins. In this paper, we propose the first spin system forming method for 13C-detected NMR spectra. Our method is able to accurately form spin systems based on as few as two 13C-detected spectra, CBCACON, and CBCANCO. Our method picks slices from the more trusted spectrum and uses them as feedback to direct the slice picking in the less trusted one. This feedback leads to picking the accurate slices that consequently helps to form better spin systems. We tested our method on a real dataset of 'Ubiquitin' and a benchmark simulated dataset consisting of 12 proteins. We fed our spin systems as inputs to a genetic algorithm to generate the chemical shift assignment, and obtained 92 percent correct chemical shift assignment for Ubiquitin. For the simulated dataset, we obtained an average recall of 86 percent and an average precision of 88 percent. Finally, our chemical shift assignment of Ubiquitin was given as an input to CS-ROSETTA server that generated structures close to the experimentally determined structure.
Collapse
|
17
|
Zhang M, Zhao X, Geng J, Liu H, Zeng F, Qin Y, Li J, Liu C, Wang H. Efficient penetration of Scp01-b and its DNA transfer abilities into cells. J Cell Physiol 2018; 234:6539-6547. [PMID: 30230543 DOI: 10.1002/jcp.27392] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022]
Abstract
The in vivo application potential of viral-based gene delivery approaches is hindered by a risk of insertional oncogenesis. Of the many delivery methods, cell-penetrating peptides (CPP)-based delivery has good biocompatibility and biodegradability. However, low efficiency is still the disadvantage of CPPs-based nucleic acid transfection, and delivery efficiency may vary from different CPPs. Here, we describe Scp01-b, as a new CPP, which can enter cultured cell lines and primary cultured cells examined by fluorescence microscopy and quantitative assay, the internalization process is a concentration, temperature, and incubation time-dependent manner. Scp01-b does not insert into the membrane directly and its uptake is mediated through endocytosis pathway. Moreover, Scp01-b could mediate the uptake of plasmid DNA into the Caski and HSC-T6 cells, and we noted that Scp01-b-mediated transfection efficiency was nearly the same with traditional liposome (TurboFectin)-mediated transfection. These findings suggest that Scp01-b can act as a useful tool for non-viral-based delivery in further application such as reprogramming and gene editing.
Collapse
Affiliation(s)
- Ming Zhang
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- Department of Orthopedics Surgery, Puren Hospital, Wuhan University of Science and Technology, Wuhan, China
| | - Xueli Zhao
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Jingping Geng
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
| | - Huiting Liu
- Department of Nuclear Medicine, Chongqing Three Gorges Central Hospital, Wanzhou, China
| | - Fanhui Zeng
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Yanyan Qin
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Jason Li
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Changbai Liu
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Hu Wang
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
18
|
Papaleo E, Camilloni C, Teilum K, Vendruscolo M, Lindorff-Larsen K. Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs. PeerJ 2018; 6:e5125. [PMID: 30013831 PMCID: PMC6035720 DOI: 10.7717/peerj.5125] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/08/2018] [Indexed: 01/24/2023] Open
Abstract
Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed, e.g., by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-timescale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other.
Collapse
Affiliation(s)
- Elena Papaleo
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Current affiliation: Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Current affiliation: Department of Biosciences, University of Milano, Milano, Italy
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
19
|
Gopalan AB, Vallurupalli P. Measuring the signs of the methyl 1H chemical shift differences between major and 'invisible' minor protein conformational states using methyl 1H multi-quantum spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 70:187-202. [PMID: 29564579 DOI: 10.1007/s10858-018-0171-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and 'invisible' minor states. The exchange rate(s) ([Formula: see text]), population(s) of the minor state(s) and the absolute value of the chemical shift difference [Formula: see text] (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of [Formula: see text] that is required to reconstruct the spectrum of the 'invisible' minor state(s) cannot be obtained from CPMG data alone. Building upon the recently developed triple quantum (TQ) methyl [Formula: see text] CPMG experiment (Yuwen in Angew Chem 55:11490-11494, 2016) we have developed pulse sequences that use carbon detection to generate and evolve single quantum (SQ), double quantum (DQ) and TQ coherences from methyl protons in the indirect dimension to measure the chemical exchange-induced shifts of the SQ, DQ and TQ coherences from which the sign of [Formula: see text] is readily obtained for two state exchange. Further a combined analysis of the CPMG data and the difference in exchange induced shifts between the SQ and DQ resonances and between the SQ and TQ resonances improves the estimates of exchange parameters like the population of the minor state. We demonstrate the use of these experiments on two proteins undergoing exchange: (1) the ~ 18 kDa cavity mutant of T4 Lysozyme ([Formula: see text]) and (2) the [Formula: see text] kDa Peripheral Sub-unit Binding Domain (PSBD) from the acetyl transferase of Bacillus stearothermophilus ([Formula: see text]).
Collapse
Affiliation(s)
- Anusha B Gopalan
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal Ranga Reddy District, Hyderabad, Telangana, 500107, India
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal Ranga Reddy District, Hyderabad, Telangana, 500107, India.
| |
Collapse
|
20
|
Sauvé S, Gingras G, Aubin Y. NMR study of mutations of glycine-52 of the catalytic domain of diphtheria toxin. J Pharm Biomed Anal 2018; 150:72-79. [DOI: 10.1016/j.jpba.2017.11.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 11/15/2022]
|
21
|
Rao Kakita VM, Bopardikar M, Kumar Shukla V, Rachineni K, Ranjan P, Singh JS, Hosur R. An efficient combination of BEST and NUS methods in multidimensional NMR spectroscopy for high throughput analysis of proteins. RSC Adv 2018; 8:17616-17621. [PMID: 35542095 PMCID: PMC9080477 DOI: 10.1039/c8ra00527c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/01/2018] [Indexed: 11/23/2022] Open
Abstract
Application of Non Uniform Sampling (NUS) along with Band-selective Excitation Short-Transient (BEST) NMR experiments has been demonstrated for obtaining the important residue-specific atomic level backbone chemical shift values in short durations of time. This application has been demonstrated with both well-folded (ubiquitin) and unfolded (α-synuclein) proteins alike. With this strategy, the experiments required for determining backbone chemical shifts can be performed very rapidly, i.e., in ∼2 hours of spectrometer time, and this data can be used to calculate the backbone folds of proteins using well established algorithms. This will be of great value for structural proteomic investigations on one hand, where the speed of structure determination is a limiting factor and for application in the study of slow kinetic processes involving proteins, such as fibrillization, on the other hand. Application of NUS along with BEST NMR experiments has been demonstrated for obtaining the important residue-specific atomic level backbone chemical shift values in short durations of time.![]()
Collapse
Affiliation(s)
| | - Mandar Bopardikar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research (TIFR)
- Mumbai 400 005
- India
| | - Vaibhav Kumar Shukla
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
| | - Kavitha Rachineni
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
| | - Priyatosh Ranjan
- Department of Biosciences & Bioengineering
- Indian Institute of Technology-Bombay (IIT-B)
- Mumbai 400076
- India
| | - Jai Shankar Singh
- Department of Biosciences & Bioengineering
- Indian Institute of Technology-Bombay (IIT-B)
- Mumbai 400076
- India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400 098
- India
- Department of Chemical Sciences
| |
Collapse
|
22
|
Hafsa NE, Berjanskii MV, Arndt D, Wishart DS. Rapid and reliable protein structure determination via chemical shift threading. JOURNAL OF BIOMOLECULAR NMR 2018; 70:33-51. [PMID: 29196969 DOI: 10.1007/s10858-017-0154-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .
Collapse
Affiliation(s)
- Noor E Hafsa
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Mark V Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David Arndt
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| |
Collapse
|
23
|
Zhou N, Wu J, Qin YY, Zhao XL, Ding Y, Sun LS, He T, Huang XW, Liu CB, Wang H. Novel peptide MT23 for potent penetrating and selective targeting in mouse melanoma cancer cells. Eur J Pharm Biopharm 2017; 120:80-88. [DOI: 10.1016/j.ejpb.2017.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/15/2017] [Accepted: 08/25/2017] [Indexed: 10/19/2022]
|
24
|
Unraveling the meaning of chemical shifts in protein NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1564-1576. [PMID: 28716441 DOI: 10.1016/j.bbapap.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022]
Abstract
Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
Collapse
|
25
|
Shukla VK, Singh JS, Vispute N, Ahmad B, Kumar A, Hosur RV. Unfolding of CPR3 Gets Initiated at the Active Site and Proceeds via Two Intermediates. Biophys J 2017; 112:605-619. [PMID: 28256221 DOI: 10.1016/j.bpj.2016.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/01/2016] [Accepted: 12/13/2016] [Indexed: 12/29/2022] Open
Abstract
Cyclophilin catalyzes the ubiquitous process "peptidyl-prolyl cis-trans isomerization," which plays a key role in protein folding, regulation, and function. Here, we present a detailed characterization of the unfolding of yeast mitochondrial cyclophilin (CPR3) induced by urea. It is seen that CPR3 unfolding is reversible and proceeds via two intermediates, I1 and I2. The I1 state has native-like secondary structure and shows strong anilino-8-naphthalenesulphonate binding due to increased exposure of the solvent-accessible cluster of non-polar groups. Thus, it has some features of a molten globule. The I2 state is more unfolded, but it retains some residual secondary structure, and shows weak anilino-8-naphthalenesulphonate binding. Chemical shift perturbation analysis by 1H-15N heteronuclear single quantum coherence spectra reveals disruption of the tertiary contacts among the regions close to the active site in the first step of unfolding, i.e., the N-I1 transition. Both of the intermediates, I1 and I2, showed a propensity to self-associate under stirring conditions, but their kinetic profiles are different; the native protein did not show any such tendency under the same conditions. All these observations could have significant implications for the function of the protein.
Collapse
Affiliation(s)
- Vaibhav Kumar Shukla
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Jai Shankar Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Neha Vispute
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Basir Ahmad
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India.
| | - Ramakrishna V Hosur
- UM-DAE-Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
| |
Collapse
|
26
|
Kassem MM, Wang Y, Boomsma W, Lindorff-Larsen K. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. Biophys J 2017; 110:2342-2348. [PMID: 27276252 DOI: 10.1016/j.bpj.2016.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/28/2022] Open
Abstract
Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.
Collapse
Affiliation(s)
- Maher M Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
27
|
Ziarek JJ, Baptista D, Wagner G. Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. J Mol Med (Berl) 2017. [PMID: 28643003 DOI: 10.1007/s00109-017-1560-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors. The goal of this mini-review is to empower the clinical researcher with a general knowledge of the strengths and weaknesses of nuclear magnetic resonance (NMR) spectroscopy in molecular medicine. Although NMR can determine protein structures at atomic resolution, its unrivaled strength lies in sensing subtle changes in a nuclei's chemical environment as a result of intrinsic conformational dynamics, solution conditions, and binding interactions. These can be recorded at atomic resolution, without explicit structure determination, and then incorporated with static structures or molecular dynamics simulations to produce a complete biological picture.
Collapse
Affiliation(s)
- Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Diego Baptista
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
| |
Collapse
|
28
|
Zhuravleva A, Korzhnev DM. Protein folding by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:52-77. [PMID: 28552172 DOI: 10.1016/j.pnmrs.2016.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 06/07/2023]
Abstract
Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these nonnative states may also serve as precursors for protein misfolding and aggregation associated with a range of devastating diseases, including neuro-degeneration, diabetes and cancer. Therefore, in vivo protein folding is often reshaped co- and post-translationally through interactions with the ribosome, molecular chaperones and/or other cellular components. Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes in vitro and in vivo. NMR relaxation dispersion and saturation transfer methods provide the means for a detailed characterization of protein folding kinetics and thermodynamics under native-like conditions, as well as modeling high-resolution structures of weakly populated short-lived conformational states on the protein folding energy landscape. Continuing development of isotope labeling strategies and NMR methods to probe high molecular weight protein assemblies, along with advances of in-cell NMR, have recently allowed protein folding to be studied in the context of ribosome-nascent chain complexes and molecular chaperones, and even inside living cells. Here we review solution NMR approaches to investigate the protein folding energy landscape, and discuss selected applications of NMR methodology to studying protein folding in vitro and in vivo. Together, these examples highlight a vast potential of solution NMR in providing atomistic insights into molecular mechanisms of protein folding and homeostasis in health and disease.
Collapse
Affiliation(s)
- Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology and Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA.
| |
Collapse
|
29
|
New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA. Sci Rep 2017; 7:40665. [PMID: 28094776 PMCID: PMC5240567 DOI: 10.1038/srep40665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 01/13/2023] Open
Abstract
PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity.
Collapse
|
30
|
Hartlmüller C, Göbl C, Madl T. Prediction of Protein Structure Using Surface Accessibility Data. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
| | - Christoph Göbl
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
| | - Tobias Madl
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
- Institute of Molecular Biology & Biochemistry Center of Molecular Medicine Medical University of Graz 8010 Graz Austria
| |
Collapse
|
31
|
Hartlmüller C, Göbl C, Madl T. Prediction of Protein Structure Using Surface Accessibility Data. Angew Chem Int Ed Engl 2016; 55:11970-4. [PMID: 27560616 PMCID: PMC5026166 DOI: 10.1002/anie.201604788] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/12/2016] [Indexed: 11/06/2022]
Abstract
An approach to the de novo structure prediction of proteins is described that relies on surface accessibility data from NMR paramagnetic relaxation enhancements by a soluble paramagnetic compound (sPRE). This method exploits the distance-to-surface information encoded in the sPRE data in the chemical shift-based CS-Rosetta de novo structure prediction framework to generate reliable structural models. For several proteins, it is demonstrated that surface accessibility data is an excellent measure of the correct protein fold in the early stages of the computational folding algorithm and significantly improves accuracy and convergence of the standard Rosetta structure prediction approach.
Collapse
Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany. .,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany. .,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria.
| |
Collapse
|
32
|
Kim HJ, Lee KY, Kim Y, Kwon AR, Lee BJ. Secondary structure analysis of MRA1997 from Mycobacterium tuberculosis and characterization of DNA binding property. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2016. [DOI: 10.6564/jkmrs.2016.20.2.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
33
|
Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. JOURNAL OF BIOMOLECULAR NMR 2016; 65:51-7. [PMID: 27169728 PMCID: PMC4921114 DOI: 10.1007/s10858-016-0036-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.
Collapse
Affiliation(s)
- Woonghee Lee
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Chad M Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jaime L Stark
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
34
|
Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
Collapse
Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| |
Collapse
|
35
|
Shraberg J, Rick SW, Rannulu N, Cole RB. A study of procyanidin binding to Histatin 5 using Electrospray Ionization Tandem Mass Spectrometry (ESI-MS/MS) and molecular simulations. Phys Chem Chem Phys 2016; 17:12247-58. [PMID: 25893227 DOI: 10.1039/c4cp05586a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tannins act as antioxidants, anticarcinogens, cardio-protectants, anti-inflammatory and anti-microbial agents and bind to salivary peptides by hydrophilic and hydrophobic mechanisms. Electrospray Ionization Mass Spectrometry (ESI-MS) has been used to assess both hydrophilic and hydrophobic components of noncovalent binding in protein complexes. In the present study, direct infusion Electrospray-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ES-FTICR MS) is used to assess relative binding affinities of procyanidin tannin stereoisomers for salivary peptides arising from aqueous solutions. The condensed tannins procyanidin B1, B2, B3, and B4 demonstrate significantly different binding affinities for the salivary peptide Histatin 5. Rigid docking combined with molecular dynamics optimization is used to investigate procyanidin-Histatin 5 binding mechanisms and as a basis to rationalize trends found in the corresponding ES-FTICR MS experiments. The relative binding affinities of the four procyanidin rotamers are different in the gas and liquid phases. The simulation results indicate that many of the same contact points are made in both phases, but there is a increase in strong electrostatic interactions and an decrease in π-π contacts upon transfer from the liquid to the gas phase. The simulations reveal that the tannin interactions can make close contacts with a variety of amino acid residues on the peptide.
Collapse
Affiliation(s)
- Joshua Shraberg
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
| | | | | | | |
Collapse
|
36
|
Rosenzweig R, Kay LE. Solution NMR Spectroscopy Provides an Avenue for the Study of Functionally Dynamic Molecular Machines: The Example of Protein Disaggregation. J Am Chem Soc 2015; 138:1466-77. [PMID: 26651836 DOI: 10.1021/jacs.5b11346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solution-based NMR spectroscopy has been an important tool for studying the structure and dynamics of relatively small proteins and protein complexes with aggregate molecular masses under approximately 50 kDa. The development of new experiments and labeling schemes, coupled with continued improvements in hardware, has significantly reduced this size limitation, enabling atomic-resolution studies of molecular machines in the 1 MDa range. In this Perspective, some of the important advances are highlighted in the context of studies of molecular chaperones involved in protein disaggregation. New insights into the structural biology of disaggregation obtained from NMR studies are described, focusing on the unique capabilities of the methodology for obtaining atomic-resolution descriptions of dynamic systems.
Collapse
Affiliation(s)
- Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8.,Program in Molecular Structure and Function, Hospital for Sick Children , 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| |
Collapse
|
37
|
Berjanskii M, Arndt D, Liang Y, Wishart DS. A robust algorithm for optimizing protein structures with NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2015; 63:255-264. [PMID: 26345175 DOI: 10.1007/s10858-015-9982-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.
Collapse
Affiliation(s)
- Mark Berjanskii
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - David Arndt
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Yongjie Liang
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, T6G 2M9, Canada.
| |
Collapse
|
38
|
Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
Collapse
Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| |
Collapse
|
39
|
Xu Y, Ong ACM, Williamson MP, Hounslow AM. Backbone assignment and secondary structure of the PLAT domain of human polycystin-1. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:369-373. [PMID: 25943267 DOI: 10.1007/s12104-015-9612-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Polycystin-1 is a large transmembrane protein mutated in the common genetic disorder autosomal dominant polycystic kidney disease. One of the predicted intracellular domains of polycystin-1 is PLAT (Polycystin-1, Lipoxygenase and Alpha Toxin), which consists of 116 amino acids and is anchored to the membrane by linkers at both ends. It is predicted to have a large number of hydrophobic residues on the surface. Assignment of the NMR spectrum was hampered by considerable line broadening, and hence a programme of site-directed mutagenesis and searching for suitable solution conditions was undertaken. The optimum construct required fusion of the GB1 domain at the N-terminus and a His tag at the C-terminus, and proved to have several additional amino acids at both ends beyond the canonical domain boundaries, as well as mutation of W3128 to alanine. Optimum solubility required 500 mM sodium chloride, and usable spectra could only be obtained by perdeuteration. Backbone assignment was made using standard triple resonance spectra and is 88 % complete. The chemical shifts obtained suggest that a loop consisting of residues 3223-3228 is mobile in solution, and that the protein is similar in structure to a prediction produced by Swiss-Model based on the structure of a homologous protein.
Collapse
Affiliation(s)
- Yaoxian Xu
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Kidney Genetics Group, Academic Unit of Nephrology, Department of Infection and Immunity, University of Sheffield Medical School, Sheffield, S10 2RX, UK
| | - Albert C M Ong
- Kidney Genetics Group, Academic Unit of Nephrology, Department of Infection and Immunity, University of Sheffield Medical School, Sheffield, S10 2RX, UK.
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| |
Collapse
|
40
|
Scheiba RM, de Opakua AI, Díaz-Quintana A, Cruz-Gallardo I, Martínez-Cruz LA, Martínez-Chantar ML, Blanco FJ, Díaz-Moreno I. The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets. RNA Biol 2015; 11:1250-61. [PMID: 25584704 DOI: 10.1080/15476286.2014.996069] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human antigen R (HuR) is a 32 kDa protein with 3 RNA Recognition Motifs (RRMs), which bind to Adenylate and uridylate Rich Elements (AREs) of mRNAs. Whereas the N-terminal and central domains (RRM1 and RRM2) are essential for AREs recognition, little is known on the C-terminal RRM3 beyond its implication in HuR oligomerization and apoptotic signaling. We have developed a detergent-based strategy to produce soluble RRM3 for structural studies. We have found that it adopts the typical RRM fold, does not interact with the RRM1 and RRM2 modules, and forms dimers in solution. Our NMR measurements, combined with Molecular Dynamics simulations and Analytical Ultracentrifugation experiments, show that the protein dimerizes through a helical region that contains the conserved W261 residue. We found that HuR RRM3 binds to 5'-mer U-rich RNA stretches through the solvent exposed side of its β-sheet, located opposite to the dimerization site. Upon mimicking phosphorylation by the S318D replacement, RRM3 mutant shows less ability to recognize RNA due to an electrostatic repulsion effect with the phosphate groups. Our study brings new insights of HuR RRM3 as a domain involved in protein oligomerization and RNA interaction, both functions regulated by 2 surfaces on opposite sides of the RRM domain.
Collapse
Key Words
- AREs, Adenylate and uridylate Rich Elements
- AU, Analytical Ultracentrifugation
- CARM1, Coactivator associated Arginine Methyltransferase 1
- CD, Circular Dichroism
- Cdk1, Cyclin-dependent kinase 1
- Chk2, Checkpoint kinase 2
- ELAV1, Embryonic Lethal Abnormal Vision system human homolog 1
- EMSA, Electrophoretic Mobility Shift Assay
- FIR, FBP-Interacting Repressor
- FL, Full-Length, HNS, HuR Nucleocytoplasmic Shuttling Sequence
- HSQC, Heteronuclear Single-Quantum Correlation
- HuR, Human antigen R
- Human antigen R (HuR)
- MD, Molecular Dynamics
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhauser Effect
- Nuclear Magnetic Resonance (NMR)
- PCA, Principal Component Analysis
- PKCα, Protein Kinase C α
- PKCδ, Protein Kinase C δ
- PMSF, PhenylMethylSulfonyl Fluoride
- PTB, Polypyrimidine Tract Binding protein
- RBPs, RNA Binding Proteins
- RNA binding
- RNA binding protein (RBP)
- RNA recognition motif (RRM)
- RRMs, RNA Recognition Motifs
- SPR, Surface Plasmon Resonance
- Serine Phosphorylation
- WT, Wild-Type
- dimerization
- hnRNP1, heterogeneous nuclear RiboNucleoprotein C protein
Collapse
Affiliation(s)
- Rafael M Scheiba
- a Instituto de Bioquímica Vegetal y Fotosíntesis; cicCartuja ; Sevilla , Spain
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Jang R, Wang Y, Xue Z, Zhang Y. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment. JOURNAL OF BIOMOLECULAR NMR 2015; 62:511-525. [PMID: 25737244 PMCID: PMC4560687 DOI: 10.1007/s10858-015-9914-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/21/2015] [Indexed: 05/30/2023]
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.
Collapse
Affiliation(s)
- Richard Jang
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA
| | - Yan Wang
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA
| | - Zhidong Xue
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
42
|
Shen Y, Bax A. Homology modeling of larger proteins guided by chemical shifts. Nat Methods 2015; 12:747-50. [PMID: 26053889 PMCID: PMC4521993 DOI: 10.1038/nmeth.3437] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/25/2015] [Indexed: 12/22/2022]
Abstract
We describe an approach to the structure determination of large proteins that relies on experimental NMR chemical shifts, plus sparse nuclear Overhauser effect (NOE) data if available. Our alignment method, POMONA (protein alignments obtained by matching of NMR assignments), directly exploits pre-existing bioinformatics algorithms to match experimental chemical shifts to values predicted for the crystallographic database. Protein templates generated by POMONA are subsequently used as input for chemical shift-based Rosetta comparative modeling (CS-RosettaCM) to generate reliable full-atom models.
Collapse
Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
43
|
van der Schot G, Bonvin AMJJ. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 62:497-502. [PMID: 25982706 PMCID: PMC4569659 DOI: 10.1007/s10858-015-9942-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/28/2015] [Indexed: 05/05/2023]
Abstract
We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.
Collapse
Affiliation(s)
- Gijs van der Schot
- Faculty of Science - Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 75 124, Uppsala, Sweden
| | - Alexandre M J J Bonvin
- Faculty of Science - Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
44
|
Wu P, Petersen MÅ, Petersen R, Rasmussen MO, Bonnet K, Nielsen TE, Clausen MH. Synthesis of (Arylamido)pyrrolidinone Libraries through Ritter-Type Cascade Reactions of Dihydroxylactams. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
45
|
Pustovalova Y, Kukic P, Vendruscolo M, Korzhnev DM. Probing the Residual Structure of the Low Populated Denatured State of ADA2h under Folding Conditions by Relaxation Dispersion Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2015; 54:4611-22. [DOI: 10.1021/acs.biochem.5b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| |
Collapse
|
46
|
Carr JM, Whittleston CS, Wade DC, Wales DJ. Energy landscapes of a hairpin peptide including NMR chemical shift restraints. Phys Chem Chem Phys 2015; 17:20250-8. [PMID: 26186565 DOI: 10.1039/c5cp01259g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methods recently introduced to improve the efficiency of protein structure prediction simulations by adding a restraint potential to a molecular mechanics force field introduce additional input parameters that can affect the performance. Here we investigate the changes in the energy landscape as the relative weight of the two contributions, force field and restraint potential, is systematically altered, for restraint functions constructed from calculated nuclear magnetic resonance chemical shifts. Benchmarking calculations were performed on a 12-residue peptide, tryptophan zipper 1, which features both secondary structure (a β-hairpin) and specific packing of tryptophan sidechains. Basin-hopping global optimization was performed to assess the efficiency with which lowest-energy structures are located, and the discrete path sampling approach was employed to survey the energy landscapes between unfolded and folded structures. We find that inclusion of the chemical shift restraints improves the efficiency of structure prediction because the energy landscape becomes more funnelled and the proportion of local minima classified as native increases. However, the funnelling nature of the landscape is reduced as the relative contribution of the chemical shift restraint potential is increased past an optimal value.
Collapse
Affiliation(s)
- Joanne M Carr
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | | | | | |
Collapse
|
47
|
Li D, Brüschweiler R. PPM_One: a static protein structure based chemical shift predictor. JOURNAL OF BIOMOLECULAR NMR 2015; 62:403-9. [PMID: 26091586 DOI: 10.1007/s10858-015-9958-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 06/12/2015] [Indexed: 05/07/2023]
Abstract
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.
Collapse
Affiliation(s)
- Dawei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA
| | | |
Collapse
|
48
|
Hafsa NE, Arndt D, Wishart DS. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res 2015; 43:W370-7. [PMID: 25979265 PMCID: PMC4489240 DOI: 10.1093/nar/gkv494] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/02/2015] [Indexed: 11/14/2022] Open
Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
Collapse
Affiliation(s)
- Noor E Hafsa
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - David Arndt
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
| |
Collapse
|
49
|
Zhu T, Zhang JZH, He X. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Phys Chem Chem Phys 2015; 16:18163-9. [PMID: 25052367 DOI: 10.1039/c4cp02553a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.
Collapse
Affiliation(s)
- Tong Zhu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
| | | | | |
Collapse
|
50
|
Reddy JG, Kumar D, Hosur RV. Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:79-87. [PMID: 25178811 DOI: 10.1002/mrc.4135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 06/03/2023]
Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins.
Collapse
Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1-Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | | | | |
Collapse
|