201
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Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017; 7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss.
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Affiliation(s)
- Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Chia-Yun Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Ru Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
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202
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Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain. Sci Rep 2017; 7:44115. [PMID: 28327560 PMCID: PMC5361163 DOI: 10.1038/srep44115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 02/06/2017] [Indexed: 01/02/2023] Open
Abstract
Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.
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203
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Soufari H, Mackereth CD. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family. RNA (NEW YORK, N.Y.) 2017; 23:308-316. [PMID: 28003515 PMCID: PMC5311487 DOI: 10.1261/rna.059733.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/19/2016] [Indexed: 05/16/2023]
Abstract
Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets.
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Affiliation(s)
- Heddy Soufari
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
| | - Cameron D Mackereth
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
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204
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Huang Z, Qin K, Deng G, Wu G, Bai Y, Xu JF, Wang Z, Yu Z, Scherman OA, Zhang X. Supramolecular Chemistry of Cucurbiturils: Tuning Cooperativity with Multiple Noncovalent Interactions from Positive to Negative. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12352-12360. [PMID: 27348049 DOI: 10.1021/acs.langmuir.6b01709] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rational control of the cooperativity of multiple noncovalent interactions often plays an important role in the design and construction of supramolecular self-assemblies and materials, especially in precision supramolecular engineering. However, it still remains a challenge to control the cooperativity of multiple noncovalent interactions through tuning the hydrophobic effect. In this work, we demonstrate that the binding cooperativity of cucurbit[8]uril(CB[8])-mediated homoternary complexes is strongly influenced by the amphiphilicity of guest molecule side groups on account of an interplay between both classical (entropy-driven) and nonclassical (enthalpy-driven) hydrophobic effects. To this end, we rationally designed and prepared a series of guest molecules bearing a benzyl group as the CB[8] homoternary binding motif with various hydrophilic and hydrophobic side groups for cooperative control. By gradually tuning side groups of the guest molecules from hydrophilic to hydrophobic, we are able to control the binding from positive to negative cooperativity. An advanced molecular recognition process and self-assembling system can be developed by adjusting the positive and negative cooperativity. The ability to regulate and control the binding cooperativity will enrich the field of supramolecular chemistry, and employing cooperativity-controlled multiple noncovalent interactions in precision supramolecular engineering is highly anticipated.
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Affiliation(s)
| | | | | | - Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | | | | | | | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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205
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Kikuchi S, Borek DM, Otwinowski Z, Tomchick DR, Yu H. Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy. Proc Natl Acad Sci U S A 2016; 113:12444-12449. [PMID: 27791135 PMCID: PMC5098657 DOI: 10.1073/pnas.1611333113] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ring-shaped cohesin complex topologically entraps chromosomes and regulates chromosome segregation, transcription, and DNA repair. The cohesin core consists of the structural maintenance of chromosomes 1 and 3 (Smc1-Smc3) heterodimeric ATPase, the kleisin subunit sister chromatid cohesion 1 (Scc1) that links the two ATPase heads, and the Scc1-bound adaptor protein Scc3. The sister chromatid cohesion 2 and 4 (Scc2-Scc4) complex loads cohesin onto chromosomes. Mutations of cohesin and its regulators, including Scc2, cause human developmental diseases termed cohesinopathy. Here, we report the crystal structure of Chaetomium thermophilum (Ct) Scc2 and examine its interaction with cohesin. Similar to Scc3 and another Scc1-interacting cohesin regulator, precocious dissociation of sisters 5 (Pds5), Scc2 consists mostly of helical repeats that fold into a hook-shaped structure. Scc2 binds to Scc1 through an N-terminal region of Scc1 that overlaps with its Pds5-binding region. Many cohesinopathy mutations target conserved residues in Scc2 and diminish Ct Scc2 binding to Ct Scc1. Pds5 binding to Scc1 weakens the Scc2-Scc1 interaction. Our study defines a functionally important interaction between the kleisin subunit of cohesin and the hook of Scc2. Through competing with Scc2 for Scc1 binding, Pds5 might contribute to the release of Scc2 from loaded cohesin, freeing Scc2 for additional rounds of loading.
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Affiliation(s)
- Sotaro Kikuchi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Dominika M Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
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206
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Brewster JL, McKellar JLO, Finn TJ, Newman J, Peat TS, Gerth ML. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Sci Rep 2016; 6:35198. [PMID: 27734909 PMCID: PMC5062169 DOI: 10.1038/srep35198] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/26/2016] [Indexed: 01/26/2023] Open
Abstract
Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain (PscD-SD) from the plant pathogen Pseudomonas syringae pv. actinidiae (Psa). High-throughput fluorescence thermal shift assays, combined with isothermal thermal titration calorimetry, revealed that PscD-SD binds specifically to C2 (glycolate and acetate) and C3 (propionate and pyruvate) carboxylates. We solved the structure of PscD-SD in complex with propionate using X-ray crystallography. The structure reveals the key residues that comprise the ligand binding pocket and dictate the specificity of this sensor domain for C2 and C3 carboxylates. We also demonstrate that all four carboxylate ligands are chemoattractants for Psa, but only two of these (acetate and pyruvate) are utilisable carbon sources. This result suggests that in addition to guiding the bacteria towards nutrients, another possible role for carboxylate sensing is in locating potential sites of entry into the host plant.
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Affiliation(s)
- Jodi L Brewster
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - James L O McKellar
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Janet Newman
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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207
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Kantonen SA, Henriksen NM, Gilson MK. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta Gen Subj 2016; 1861:485-498. [PMID: 27599357 DOI: 10.1016/j.bbagen.2016.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/27/2016] [Accepted: 09/02/2016] [Indexed: 01/05/2023]
Abstract
BACKGROUND Isothermal titration calorimetry (ITC) is uniquely useful for characterizing binding thermodynamics, because it straightforwardly provides both the binding enthalpy and free energy. However, the precision of the results depends on the experimental setup and how thermodynamic results are obtained from the raw data. METHODS Experiments and Monte Carlo analysis are used to study how uncertainties in injection heat and concentration propagate to binding enthalpies in various scenarios. We identify regimes in which it is preferable to fix the stoichiometry parameter, N, and evaluate the reliability of uncertainties provided by the least squares method. RESULTS The noise in the injection heat is mainly proportional in character, with ~1% and ~3% uncertainty at 27C and 65C, respectively; concentration errors are ~1%. Simulations of experiments based on these uncertainties delineate how experimental design and curve fitting methods influence the uncertainty in the final results. CONCLUSIONS In most cases, experimental uncertainty is minimized by using more injections and by fixing N at its known value. With appropriate technique, the uncertainty in measured binding enthalpies can be kept below ~2% under many conditions, including low C values. GENERAL SIGNIFICANCE We quantify uncertainties in ITC data due to heat and concentration error, and identify practices to minimize these uncertainties. The resulting guidelines are important when ITC data are used quantitatively, such as to test computer simulations of binding. Reproducibility and further study are supported by free distribution of the new software developed here.
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Affiliation(s)
- Samuel A Kantonen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA.
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208
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Kumar GS, Gokhan E, De Munter S, Bollen M, Vagnarelli P, Peti W, Page R. The Ki-67 and RepoMan mitotic phosphatases assemble via an identical, yet novel mechanism. eLife 2016; 5. [PMID: 27572260 PMCID: PMC5005033 DOI: 10.7554/elife.16539] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/16/2016] [Indexed: 12/26/2022] Open
Abstract
Ki-67 and RepoMan have key roles during mitotic exit. Previously, we showed that Ki-67 organizes the mitotic chromosome periphery and recruits protein phosphatase 1 (PP1) to chromatin at anaphase onset, in a similar manner as RepoMan (Booth et al., 2014). Here we show how Ki-67 and RepoMan form mitotic exit phosphatases by recruiting PP1, how they distinguish between distinct PP1 isoforms and how the assembly of these two holoenzymes are dynamically regulated by Aurora B kinase during mitosis. Unexpectedly, our data also reveal that Ki-67 and RepoMan bind PP1 using an identical, yet novel mechanism, interacting with a PP1 pocket that is engaged only by these two PP1 regulators. These findings not only show how two distinct mitotic exit phosphatases are recruited to their substrates, but also provide immediate opportunities for the design of novel cancer therapeutics that selectively target the Ki-67:PP1 and RepoMan:PP1 holoenzymes.
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Affiliation(s)
- Ganesan Senthil Kumar
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, United States
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute for Environment, Health and Society, Brunel University London, Uxbridge, United Kingdom
| | - Sofie De Munter
- Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment, Health and Society, Brunel University London, Uxbridge, United Kingdom
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, United States
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, United States
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209
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Tellinghuisen J. Analysis of multitemperature isothermal titration calorimetry data at very low c: Global beats van't Hoff. Anal Biochem 2016; 513:43-46. [PMID: 27567993 DOI: 10.1016/j.ab.2016.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/06/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
Isothermal titration calorimetry data for very low c (≡K[M]0) must normally be analyzed with the stoichiometry parameter n fixed - at its known value or at any reasonable value if the system is not well characterized. In the latter case, ΔH° (and hence n) can be estimated from the T-dependence of the binding constant K, using the van't Hoff (vH) relation. An alternative is global or simultaneous fitting of data at multiple temperatures. In this Note, global analysis of low-c data at two temperatures is shown to estimate ΔH° and n with double the precision of the vH method.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States.
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210
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Alicea-Velázquez NL, Shinsky SA, Loh DM, Lee JH, Skalnik DG, Cosgrove MS. Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes. J Biol Chem 2016; 291:22357-22372. [PMID: 27563068 DOI: 10.1074/jbc.m116.752626] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
MLL1 belongs to the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, composed of MLL1-4 and SETd1A/B. MLL1 translocations are present in acute leukemias, and mutations in several family members are associated with cancer and developmental disorders. MLL1 associates with a subcomplex containing WDR5, RbBP5, ASH2L, and DPY-30 (WRAD), forming the MLL1 core complex required for H3K4 mono- and dimethylation and transcriptional activation. Core complex assembly requires interaction of WDR5 with the MLL1 Win (WDR5 interaction) motif, which is conserved across the SET1 family. Agents that mimic the SET1 family Win motif inhibit the MLL1 core complex and have become an attractive approach for targeting MLL1 in cancers. Like MLL1, other SET1 family members interact with WRAD, but the roles of the Win motif in complex assembly and enzymatic activity remain unexplored. Here, we show that the Win motif is necessary for interaction of WDR5 with all members of the human SET1 family. Mutation of the Win motif-WDR5 interface severely disrupts assembly and activity of MLL1 and SETd1A complexes but only modestly disrupts MLL2/4 and SETd1B complexes without significantly altering enzymatic activity in vitro Notably, in the absence of WDR5, MLL3 interacts with RAD and shows enhanced activity. To further probe the role of the Win motif-WDR5 interaction, we designed a peptidomimetic that binds WDR5 (Kd ∼3 nm) and selectively inhibits activity of MLL1 and SETd1A core complexes within the SET1 family. Our results reveal that SET1 family complexes with the weakest Win motif-WDR5 interaction are more susceptible to Win motif-based inhibitors.
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Affiliation(s)
- Nilda L Alicea-Velázquez
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Daniel M Loh
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Jeong-Heon Lee
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - David G Skalnik
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
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211
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Brautigam CA, Deka RK, Liu WZ, Norgard MV. The Tp0684 (MglB-2) Lipoprotein of Treponema pallidum: A Glucose-Binding Protein with Divergent Topology. PLoS One 2016; 11:e0161022. [PMID: 27536942 PMCID: PMC4990184 DOI: 10.1371/journal.pone.0161022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022] Open
Abstract
Treponema pallidum, the bacterium that causes syphilis, is an obligate human parasite. As such, it must acquire energy, in the form of carbon sources, from the host. There is ample evidence that the principal source of energy for this spirochete is D-glucose acquired from its environment, likely via an ABC transporter. Further, there is genetic evidence of a D-glucose chemotaxis system in T. pallidum. Both of these processes may be dependent on a single lipidated chemoreceptor: Tp0684, also called TpMglB-2 for its sequence homology to MglB of Escherichia coli. To broaden our understanding of this potentially vital protein, we determined a 2.05-Å X-ray crystal structure of a soluble form of the recombinant protein. Like its namesake, TpMglB-2 adopts a bilobed fold that is similar to that of the ligand-binding proteins (LBPs) of other ABC transporters. However, the protein has an unusual, circularly permuted topology. This feature prompted a series of biophysical studies that examined whether the protein's topological distinctiveness affected its putative chemoreceptor functions. Differential scanning fluorimetry and isothermal titration calorimetry were used to confirm that the protein bound D-glucose in a cleft between its two lobes. Additionally, analytical ultracentrifugation was employed to reveal that D-glucose binding is accompanied by a significant conformational change. TpMglB-2 thus appears to be fully functional in vitro, and given the probable central importance of the protein to T. pallidum's physiology, our results have implications for the viability and pathogenicity of this obligate human pathogen.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Ranjit K. Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Wei Z. Liu
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Michael V. Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
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212
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Hauenschild T, Reichenwallner J, Enkelmann V, Hinderberger D. Characterizing Active Pharmaceutical Ingredient Binding to Human Serum Albumin by Spin-Labeling and EPR Spectroscopy. Chemistry 2016; 22:12825-38. [DOI: 10.1002/chem.201601810] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Till Hauenschild
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Jörg Reichenwallner
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Volker Enkelmann
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Dariush Hinderberger
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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213
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Johnson DK, Stevenson MJ, Almadidy ZA, Jenkins SE, Wilcox DE, Grossoehme NE. Stabilization of Cu(I) for binding and calorimetric measurements in aqueous solution. Dalton Trans 2016; 44:16494-505. [PMID: 26327397 DOI: 10.1039/c5dt02689j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Conditions have been developed for the comproportionation reaction of Cu(2+) and copper metal to prepare aqueous solutions of Cu(+) that are stabilized from disproportionation by MeCN and other Cu(+)-stabilizing ligands. These solutions were then used in ITC measurements to quantify the thermodynamics of formation of a set of Cu(+) complexes (Cu(I)(MeCN)3(+), Cu(I)Me6Trien(+), Cu(I)(BCA)2(3-), Cu(I)(BCS)2(3-)), which have stabilities ranging over 15 orders of magnitude, for their use in binding and calorimetric measurements of Cu(+) interaction with proteins and other biological macromolecules. These complexes were then used to determine the stability and thermodynamics of formation of a 1 : 1 complex of Cu(+) with the biologically important tri-peptide glutathione, GSH. These results identify Me6Trien as an attractive Cu(+)-stabilizing ligand for calorimetric experiments, and suggest that caution should be used with MeCN to stabilize Cu(+) due to its potential for participating in unquantifiable ternary interactions.
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Affiliation(s)
- Destinee K Johnson
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 27933, USA.
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214
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Falconer RJ. Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015. J Mol Recognit 2016; 29:504-15. [PMID: 27221459 DOI: 10.1002/jmr.2550] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x-ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion-π and π-π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Robert J Falconer
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK.
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215
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Brautigam CA, Zhao H, Vargas C, Keller S, Schuck P. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions. Nat Protoc 2016; 11:882-94. [PMID: 27055097 PMCID: PMC7466939 DOI: 10.1038/nprot.2016.044] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
| | - Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Germany
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, U.S.A
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216
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Gardner NW, Monroe LK, Kihara D, Park C. Energetic Coupling between Ligand Binding and Dimerization in Escherichia coli Phosphoglycerate Mutase. Biochemistry 2016; 55:1711-23. [PMID: 26919584 DOI: 10.1021/acs.biochem.5b00980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Energetic coupling of two molecular events in a protein molecule is ubiquitous in biochemical reactions mediated by proteins, such as catalysis and signal transduction. Here, we investigate energetic coupling between ligand binding and folding of a dimer using a model system that shows three-state equilibrium unfolding of an exceptional quality. The homodimeric Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM) was found to be stabilized by ATP in a proteome-wide screen, although dPGM does not require or utilize ATP for enzymatic function. We investigated the effect of ATP on the thermodynamic stability of dPGM using equilibrium unfolding. We found that, in the absence of ATP, dPGM populates a partially unfolded, monomeric intermediate during equilibrium unfolding. However, addition of 1.0 mM ATP drastically reduces the population of the intermediate by selectively stabilizing the native dimer. Using a computational ligand docking method, we predicted ATP binds to the active site of the enzyme using the triphosphate group. By performing equilibrium unfolding and isothermal titration calorimetry with active-site variants of dPGM, we confirmed that active-site residues are involved in ATP binding. Our findings show that ATP promotes dimerization of the protein by binding to the active site, which is distal from the dimer interface. This cooperativity suggests an energetic coupling between the active site and the dimer interface. We also propose a structural link to explain how ligand binding to the active site is energetically coupled with dimerization.
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Affiliation(s)
- Nathan W Gardner
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Biological Sciences, ∥Department of Computer Science, and ⊥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Lyman K Monroe
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Biological Sciences, ∥Department of Computer Science, and ⊥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daisuke Kihara
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Biological Sciences, ∥Department of Computer Science, and ⊥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Chiwook Park
- Department of Medicinal Chemistry and Molecular Pharmacology, ‡Interdisciplinary Life Science Graduate Program, §Department of Biological Sciences, ∥Department of Computer Science, and ⊥Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States
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217
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Yin J, Babaoglu K, Brautigam CA, Clark L, Shao Z, Scheuermann TH, Harrell CM, Gotter AL, Roecker AJ, Winrow CJ, Renger JJ, Coleman PJ, Rosenbaum DM. Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors. Nat Struct Mol Biol 2016; 23:293-9. [PMID: 26950369 DOI: 10.1038/nsmb.3183] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/02/2016] [Indexed: 01/10/2023]
Abstract
The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) regulate sleep and other behavioral functions in mammals, and are therapeutic targets for sleep and wake disorders. The human receptors hOX1R and hOX2R, which are 64% identical in sequence, have overlapping but distinct physiological functions and potential therapeutic profiles. We determined structures of hOX1R bound to the OX1R-selective antagonist SB-674042 and the dual antagonist suvorexant at 2.8-Å and 2.75-Å resolution, respectively, and used molecular modeling to illuminate mechanisms of antagonist subtype selectivity between hOX1R and hOX2R. The hOX1R structures also reveal a conserved amphipathic α-helix, in the extracellular N-terminal region, that interacts with orexin-A and is essential for high-potency neuropeptide activation at both receptors. The orexin-receptor crystal structures are valuable tools for the design and development of selective orexin-receptor antagonists and agonists.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kerim Babaoglu
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lindsay Clark
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zhenhua Shao
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas H Scheuermann
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Charles M Harrell
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Anthony L Gotter
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Anthony J Roecker
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Christopher J Winrow
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - John J Renger
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Paul J Coleman
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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218
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Herrera I, Winnik MA. Differential Binding Models for Direct and Reverse Isothermal Titration Calorimetry. J Phys Chem B 2016; 120:2077-86. [PMID: 26889710 DOI: 10.1021/acs.jpcb.5b09202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Isothermal titration calorimetry (ITC) is a technique to measure the stoichiometry and thermodynamics from binding experiments. Identifying an appropriate mathematical model to evaluate titration curves of receptors with multiple sites is challenging, particularly when the stoichiometry or binding mechanism is not available. In a recent theoretical study, we presented a differential binding model (DBM) to study calorimetry titrations independently of the interaction among the binding sites (Herrera, I.; Winnik, M. A. J. Phys. Chem. B 2013, 117, 8659-8672). Here, we build upon our DBM and show its practical application to evaluate calorimetry titrations of receptors with multiple sites independently of the titration direction. Specifically, we present a set of ordinary differential equations (ODEs) with the general form d[S]/dV that can be integrated numerically to calculate the equilibrium concentrations of free and bound species S at every injection step and, subsequently, to evaluate the volume-normalized heat signal (δQ(V) = δq/dV) of direct and reverse calorimetry titrations. Additionally, we identify factors that influence the shape of the titration curve and can be used to optimize the initial concentrations of titrant and analyte. We demonstrate the flexibility of our updated DBM by applying these differentials and a global regression analysis to direct and reverse calorimetric titrations of gadolinium ions with multidentate ligands of increasing denticity, namely, diglycolic acid (DGA), citric acid (CIT), and nitrilotriacetic acid (NTA), and use statistical tests to validate the stoichiometries for the metal-ligand pairs studied.
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Affiliation(s)
- Isaac Herrera
- Chemistry Department, University of Toronto , 80 St. George Street, Toronto ON, Canada , M5S 3H6
| | - Mitchell A Winnik
- Chemistry Department, University of Toronto , 80 St. George Street, Toronto ON, Canada , M5S 3H6
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219
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Interaction of TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing. Proc Natl Acad Sci U S A 2016; 113:E1006-15. [PMID: 26869717 DOI: 10.1073/pnas.1519894113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptide loading of major histocompatibility complex class I (MHC-I) molecules is central to antigen presentation, self-tolerance, and CD8(+) T-cell activation. TAP binding protein, related (TAPBPR), a widely expressed tapasin homolog, is not part of the classical MHC-I peptide-loading complex (PLC). Using recombinant MHC-I molecules, we show that TAPBPR binds HLA-A*02:01 and several other MHC-I molecules that are either peptide-free or loaded with low-affinity peptides. Fluorescence polarization experiments establish that TAPBPR augments peptide binding by MHC-I. The TAPBPR/MHC-I interaction is reversed by specific peptides, related to their affinity. Mutational and small-angle X-ray scattering (SAXS) studies confirm the structural similarities of TAPBPR with tapasin. These results support a role of TAPBPR in stabilizing peptide-receptive conformation(s) of MHC-I, permitting peptide editing.
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220
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Affiliation(s)
- Jonathan B Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
| | - Lee D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
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221
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Scheuermann TH, Padrick SB, Gardner KH, Brautigam CA. On the acquisition and analysis of microscale thermophoresis data. Anal Biochem 2015; 496:79-93. [PMID: 26739938 DOI: 10.1016/j.ab.2015.12.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 01/30/2023]
Abstract
A comprehensive understanding of the molecular mechanisms underpinning cellular functions is dependent on a detailed characterization of the energetics of macromolecular binding, often quantified by the equilibrium dissociation constant, KD. While many biophysical methods may be used to obtain KD, the focus of this report is a relatively new method called microscale thermophoresis (MST). In an MST experiment, a capillary tube filled with a solution containing a dye-labeled solute is illuminated with an infrared laser, rapidly creating a temperature gradient. Molecules will migrate along this gradient, causing changes in the observed fluorescence. Because the net migration of the labeled molecules will depend on their liganded state, a binding curve as a function of ligand concentration can be constructed from MST data and analyzed to determine KD. Herein, simulations demonstrate the limits of KD that can be measured in current instrumentation. They also show that binding kinetics is a major concern in planning and executing MST experiments. Additionally, studies of two protein-protein interactions illustrate challenges encountered in acquiring and analyzing MST data. Combined, these approaches indicate a set of best practices for performing and analyzing MST experiments. Software for rigorous data analysis is also introduced.
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Affiliation(s)
- Thomas H Scheuermann
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
| | - Shae B Padrick
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA.
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222
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Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Nat Struct Mol Biol 2015; 23:45-52. [PMID: 26656854 DOI: 10.1038/nsmb.3142] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022]
Abstract
RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.
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223
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Bou-Abdallah F, Giffune TR. The thermodynamics of protein interactions with essential first row transition metals. Biochim Biophys Acta Gen Subj 2015; 1860:879-891. [PMID: 26569121 DOI: 10.1016/j.bbagen.2015.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/27/2015] [Accepted: 11/01/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND The binding of metal ions to proteins is a crucial process required for their catalytic activity, structural stability and/or functional regulation. Isothermal titration calorimetry provides a wealth of fundamental information which when combined with structural data allow for a much deeper understanding of the underlying molecular mechanism. SCOPE OF REVIEW A rigorous understanding of any molecular interaction requires in part an in-depth quantification of its thermodynamic properties. Here, we provide an overview of recent studies that have used ITC to quantify the interaction of essential first row transition metals with relevant proteins and highlight major findings from these thermodynamic studies. GENERAL SIGNIFICANCE The thermodynamic characterization of metal ion-protein interactions is one important step to understanding the role that metal ions play in living systems. Such characterization has important implications not only to elucidating proteins' structure-function relationships and biological properties but also in the biotechnology sector, medicine and drug design particularly since a number of metal ions are involved in several neurodegenerative diseases. MAJOR CONCLUSIONS Isothermal titration calorimetry measurements can provide complete thermodynamic profiles of any molecular interaction through the simultaneous determination of the reaction binding stoichiometry, binding affinity as well as the enthalpic and entropic contributions to the free energy change thus enabling a more in-depth understanding of the nature of these interactions.
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Affiliation(s)
- Fadi Bou-Abdallah
- State University of New York at Potsdam, Potsdam, NY 13676, United States.
| | - Thomas R Giffune
- State University of New York at Potsdam, Potsdam, NY 13676, United States
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224
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Ruiz FX, Cousido-Siah A, Porté S, Domínguez M, Crespo I, Rechlin C, Mitschler A, de Lera ÁR, Martín MJ, de la Fuente JÁ, Klebe G, Parés X, Farrés J, Podjarny A. Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10. ChemMedChem 2015; 10:1989-2003. [PMID: 26549844 DOI: 10.1002/cmdc.201500393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 12/15/2022]
Abstract
The human enzymes aldose reductase (AR) and AKR1B10 have been thoroughly explored in terms of their roles in diabetes, inflammatory disorders, and cancer. In this study we identified two new lead compounds, 2-(3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0048, 3) and 2-(2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0049, 4), which selectively target these enzymes. Although 3 and 4 share the 3-benzyluracil-1-acetic acid scaffold, they have different substituents in their aryl moieties. Inhibition studies along with thermodynamic and structural characterizations of both enzymes revealed that the chloronitrobenzyl moiety of compound 3 can open the AR specificity pocket but not that of the AKR1B10 cognate. In contrast, the larger atoms at the ortho and/or meta positions of compound 4 prevent the AR specificity pocket from opening due to steric hindrance and provide a tighter fit to the AKR1B10 inhibitor binding pocket, probably enhanced by the displacement of a disordered water molecule trapped in a hydrophobic subpocket, creating an enthalpic signature. Furthermore, this selectivity also occurs in the cell, which enables the development of a more efficient drug design strategy: compound 3 prevents sorbitol accumulation in human retinal ARPE-19 cells, whereas 4 stops proliferation in human lung cancer NCI-H460 cells.
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Affiliation(s)
- Francesc X Ruiz
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France. .,Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 08854-5627, Piscataway, NJ, (USA).
| | - Alexandra Cousido-Siah
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marta Domínguez
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Chris Rechlin
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - André Mitschler
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Ángel R de Lera
- Departmento de Química Orgánica and Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 363100, Vigo, Spain
| | - María Jesús Martín
- Biomar Microbial Technologies S.A., Parque Tecnológico de León, 24009, León, Spain
| | | | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alberto Podjarny
- Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, rue Laurent Fries, 67404, Illkirch CEDEX, France.
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225
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Protein-protein interactions: a supra-structural phenomenon demanding trans-disciplinary biophysical approaches. Curr Opin Struct Biol 2015; 35:76-86. [PMID: 26496626 DOI: 10.1016/j.sbi.2015.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/01/2015] [Accepted: 09/28/2015] [Indexed: 01/14/2023]
Abstract
Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can be obtained at increasing resolution, at relevant time-scales and under increasingly relevant experimental conditions, intricate data are interpreted reliably, and the questions posed and answered grow in complexity. With this review, highlights from the study of PPIs using a multitude of biophysical methods, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods.
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226
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Alberstein R, Grey R, Zimmet A, Simmons DK, Mayer ML. Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes. Proc Natl Acad Sci U S A 2015; 112:E6048-57. [PMID: 26460032 PMCID: PMC4640758 DOI: 10.1073/pnas.1513771112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis show that these form a distinct clade from the well-characterized AMPA, kainate, and NMDA iGluR subtypes found in vertebrates. Although annotated as glutamate and kainate receptors, crystal structures of the ML032222a and PbiGluR3 ligand-binding domains (LBDs) reveal endogenous glycine in the binding pocket, whereas ligand-binding assays show that glycine binds with nanomolar affinity; biochemical assays and structural analysis establish that glutamate is occluded from the binding cavity. Further analysis reveals ctenophore-specific features, such as an interdomain Arg-Glu salt bridge, present only in subunits that bind glycine, but also a conserved disulfide in loop 1 of the LBD that is found in all vertebrate NMDA but not AMPA or kainate receptors. We hypothesize that ctenophore iGluRs are related to an early ancestor of NMDA receptors, suggesting a common evolutionary path for ctenophores and bilaterian species, and suggest that future work should consider both glycine and glutamate as candidate neurotransmitters in ctenophore species.
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Affiliation(s)
- Robert Alberstein
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Richard Grey
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Austin Zimmet
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - David K Simmons
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080
| | - Mark L Mayer
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
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227
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Abstract
The real-time power response inherent in an isothermal titration calorimetry (ITC) experiment provides an opportunity to directly analyze association kinetics, which, together with the conventional measurement of thermodynamic quantities, can provide an incredibly rich description of molecular binding in a single experiment. Here, we detail our application of this method, in which interactions occurring with relaxation times ranging from slightly below the instrument response time constant (12.5 s in this case) to as large as 600 s can be fully detailed in terms of both the thermodynamics and kinetics. In a binding titration scenario, in the most general case an injection can reveal an association rate constant (kon). Under more restrictive conditions, the instrument time constant-corrected power decay following each injection is simply an exponential decay described by a composite rate constant (kobs), from which both kon and the dissociation rate constant (koff) can be extracted. The data also support the viability of this exponential approach, for kon only, for a slightly larger set of conditions. Using a bimolecular RNA folding model and a protein-ligand interaction, we demonstrate and have internally validated this approach to experiment design, data processing, and error analysis. An updated guide to thermodynamic and kinetic regimes accessible by ITC is provided.
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228
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Thermodynamics of protein–ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. J Comput Aided Mol Des 2015; 29:867-83. [DOI: 10.1007/s10822-015-9867-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/05/2015] [Indexed: 12/11/2022]
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229
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Yennawar NH, Fecko JA, Showalter SA, Bevilacqua PC. A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility. Methods Enzymol 2015; 567:435-60. [PMID: 26794364 PMCID: PMC6474912 DOI: 10.1016/bs.mie.2015.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many labs have conventional calorimeters where denaturation and binding experiments are setup and run one at a time. While these systems are highly informative to biopolymer folding and ligand interaction, they require considerable manual intervention for cleaning and setup. As such, the throughput for such setups is limited typically to a few runs a day. With a large number of experimental parameters to explore including different buffers, macromolecule concentrations, temperatures, ligands, mutants, controls, replicates, and instrument tests, the need for high-throughput automated calorimeters is on the rise. Lower sample volume requirements and reduced user intervention time compared to the manual instruments have improved turnover of calorimetry experiments in a high-throughput format where 25 or more runs can be conducted per day. The cost and efforts to maintain high-throughput equipment typically demands that these instruments be housed in a multiuser core facility. We describe here the steps taken to successfully start and run an automated biological calorimetry facility at Pennsylvania State University. Scientists from various departments at Penn State including Chemistry, Biochemistry and Molecular Biology, Bioengineering, Biology, Food Science, and Chemical Engineering are benefiting from this core facility. Samples studied include proteins, nucleic acids, sugars, lipids, synthetic polymers, small molecules, natural products, and virus capsids. This facility has led to higher throughput of data, which has been leveraged into grant support, attracting new faculty hire and has led to some exciting publications.
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Affiliation(s)
- Neela H Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julia A Fecko
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott A Showalter
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Philip C Bevilacqua
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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230
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Johnson RA, Manley OM, Spuches AM, Grossoehme NE. Dissecting ITC data of metal ions binding to ligands and proteins. Biochim Biophys Acta Gen Subj 2015; 1860:892-901. [PMID: 26327285 DOI: 10.1016/j.bbagen.2015.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND ITC is a powerful technique that can reliably assess the thermodynamic underpinnings of a wide range of binding events. When metal ions are involved, complications arise in evaluating the data due to unavoidable solution chemistry that includes metal speciation and a variety of linked equilibria. SCOPE OF REVIEW This paper identifies these concerns, provides recommendations to avoid common mistakes, and guides the reader through the mathematical treatment of ITC data to arrive at a set of thermodynamic state functions that describe identical chemical events and, ideally, are independent of solution conditions. Further, common metal chromophores used in biological metal sensing studies are proposed as a robust system to determine unknown solution competition. MAJOR CONCLUSIONS Metal ions present several complications in ITC experiments. This review presents strategies to avoid these pitfalls and proposes and experimentally validates mathematical approaches to deconvolute complex equilibria that exist in these systems. GENERAL SIGNIFICANCE This review discusses the wide range of complications that exists in metal-based ITC experiments. It provides a starting point for scientists new to this field and articulates concerns that will help experienced researchers troubleshoot experiments.
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Affiliation(s)
- Rachel A Johnson
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Olivia M Manley
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States
| | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States.
| | - Nicholas E Grossoehme
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States.
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231
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Reille-Seroussi M, Gaucher JF, Desole C, Gagey-Eilstein N, Brachet F, Broutin I, Vidal M, Broussy S. Vascular Endothelial Growth Factor Peptide Ligands Explored by Competition Assay and Isothermal Titration Calorimetry. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00722] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | | | | | | | - Michel Vidal
- UF Pharmacocinétique
et Pharmacochimie, hôpital Cochin, AP-HP, 27 rue du Faubourg Saint Jacques, Paris 75014, France
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232
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Brautigam CA. Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data. Methods Enzymol 2015; 562:109-33. [PMID: 26412649 DOI: 10.1016/bs.mie.2015.05.001] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The analysis of analytical ultracentrifugation (AUC) data has been greatly facilitated by the advances accumulated in recent years. These improvements include refinements in AUC-based binding isotherms, advances in the fitting of both sedimentation velocity (SV) and sedimentation equilibrium (SE) data, and innovations in calculations related to posttranslationally modified proteins and to proteins with a large amount of associated cosolute, e.g., detergents. To capitalize on these advances, the experimenter often must prepare and collate multiple data sets and parameters for subsequent analyses; these tasks can be cumbersome and unclear, especially for new users. Examples are the sorting of concentration-profile scans for SE data, the integration of sedimentation velocity distributions (c(s)) to arrive at weighted-average binding isotherms, and the calculations to determine the oligomeric state of glycoproteins and membrane proteins. The significant organizational and logistical hurdles presented by these approaches are streamlined by the software described herein, called GUSSI. GUSSI also creates publication-quality graphics for documenting and illustrating AUC and other biophysical experiments with minimal effort on the user's part. The program contains three main modules, allowing for plotting and calculations on c(s) distributions, SV signal versus radius data, and general data/fit/residual plots.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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233
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Zhuo Y, Cano KE, Wang L, Ilangovan U, Hinck AP, Sousa R, Lafer EM. Nuclear Magnetic Resonance Structural Mapping Reveals Promiscuous Interactions between Clathrin-Box Motif Sequences and the N-Terminal Domain of the Clathrin Heavy Chain. Biochemistry 2015; 54:2571-80. [PMID: 25844500 PMCID: PMC4429812 DOI: 10.1021/acs.biochem.5b00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The recruitment and organization
of clathrin at endocytic sites
first to form coated pits and then clathrin-coated vesicles depend
on interactions between the clathrin N-terminal domain (TD) and multiple
clathrin binding sequences on the cargo adaptor and accessory proteins
that are concentrated at such sites. Up to four distinct protein binding
sites have been proposed to be present on the clathrin TD, with each
site proposed to interact with a distinct clathrin binding motif.
However, an understanding of how such interactions contribute to clathrin
coat assembly must take into account observations that any three of
these four sites on clathrin TD can be mutationally ablated without
causing loss of clathrin-mediated endocytosis. To take an unbiased
approach to mapping binding sites for clathrin-box motifs on clathrin
TD, we used isothermal titration calorimetry (ITC) and nuclear magnetic
resonance spectroscopy. Our ITC experiments revealed that a canonical
clathrin-box motif peptide from the AP-2 adaptor binds to clathrin
TD with a stoichiometry of 3:1. Assignment of 90% of the total visible
amide resonances in the TROSY-HSQC spectrum of 13C-, 2H-, and 15N-labeled TD40 allowed us to map these
three binding sites by analyzing the chemical shift changes as clathrin-box
motif peptides were titrated into clathrin TD. We found that three
different clathrin-box motif peptides can each simultaneously bind
not only to the previously characterized clathrin-box site but also
to the W-box site and the β-arrestin splice loop site on a single
TD. The promiscuity of these binding sites can help explain why their
mutation does not lead to larger effects on clathrin function and
suggests a mechanism by which clathrin may be transferred between
different proteins during the course of an endocytic event.
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Affiliation(s)
- Yue Zhuo
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Kristin E Cano
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Liping Wang
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Udayar Ilangovan
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Andrew P Hinck
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Rui Sousa
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Eileen M Lafer
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
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234
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Boudker O, Oh S. Isothermal titration calorimetry of ion-coupled membrane transporters. Methods 2015; 76:171-182. [PMID: 25676707 PMCID: PMC4912014 DOI: 10.1016/j.ymeth.2015.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/17/2022] Open
Abstract
Binding of ligands, ranging from proteins to ions, to membrane proteins is associated with absorption or release of heat that can be detected by isothermal titration calorimetry (ITC). Such measurements not only provide binding affinities but also afford direct access to thermodynamic parameters of binding--enthalpy, entropy and heat capacity. These parameters can be interpreted in a structural context, allow discrimination between different binding mechanisms and guide drug design. In this review, we introduce advantages and limitations of ITC as a methodology to study molecular interactions of membrane proteins. We further describe case studies where ITC was used to analyze thermodynamic linkage between ions and substrates in ion-coupled transporters. Similar type of linkage analysis will likely be applicable to a wide range of transporters, channels, and receptors.
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Affiliation(s)
- Olga Boudker
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
| | - SeCheol Oh
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
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235
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Brautigam CA. Fitting two- and three-site binding models to isothermal titration calorimetric data. Methods 2014; 76:124-136. [PMID: 25484338 DOI: 10.1016/j.ymeth.2014.11.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/27/2022] Open
Abstract
As isothermal titration calorimetry (ITC) gains popularity for the characterization of enthalpies and equilibrium association constants of simple 1:1 biomolecular interactions, its use for more complex systems is growing. The method is increasingly used to study interactions in which a single binding partner (molecule "A") interacts with multiple copies of a second partner ("B"); thus examinations of ABB and ABBB interactions are not uncommon. The structure of ITC data (commonly formatted as isotherms) has a strong bearing on the ability of the researcher to extract the necessary parameters from them. Usually, only 10-30 injections are recorded in a single ITC experiment. Even if replicates are performed, the data must support the extraction of up to twelve parameters from an ABBB system. Further, the refinement of some of the parameters is largely driven by only a subset of the data. The ability of ITC data to guide the deterministic estimation of these parameters may therefore be questioned. This work assesses the ability of both empirical and simulated ITC data of ABB and ABBB systems to support the simultaneous estimation of the desired thermodynamic parameters. The results demonstrate that multiphasic isotherms tend to (but do not always) support the estimation of multiple parameters. On the other hand, uniphasic data obtained from multi-site binding systems are more problematic. In all cases, a thorough exploration of how precisely the estimated parameters are specified by the data is justified.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, United States.
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236
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Krainer G, Keller S. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry. Methods 2014; 76:116-123. [PMID: 25461813 DOI: 10.1016/j.ymeth.2014.10.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 11/27/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions.
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Affiliation(s)
- Georg Krainer
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany; B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
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