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Three-Way DNA Junction as an End Label for DNA in Atomic Force Microscopy Studies. Int J Mol Sci 2022; 23:ijms231911404. [PMID: 36232705 PMCID: PMC9569629 DOI: 10.3390/ijms231911404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes.
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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3
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Kaur A, Khan IA, Banipal PK, Banipal TS. Deciphering the complexation process of a fluoroquinolone antibiotic, levofloxacin, with bovine serum albumin in the presence of additives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:259-270. [PMID: 29045929 DOI: 10.1016/j.saa.2017.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 10/04/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
The current work aims to explore the thermodynamic and conformational aspects for the binding of fluoroquinolone antibacterial drug, levofloxacin (LFC), with bovine serum albumin (BSA) using calorimetric, spectroscopic (UV-visible, fluorescence, circular dichroism, and 1H NMR), dynamic light scattering (DLS) and computational methods (molecular docking). The binding of LFC with BSA at two sequential sites with higher affinity (~103M-1) at the first site has been explored by calorimetry whereas the binding at a single site with affinity of the order of ~104M-1 has been observed from fluorescence spectroscopy. The calorimetric study in the presence of additives along with docking analysis reveals the significant role of electrostatic, hydrogen bonding, and hydrophobic interactions in the association process. The slight conformational changes in protein as well as the changes in the water network structure around the binding cavity of protein have been observed from spectroscopic and DLS measurements. The LFC induced quenching of BSA fluorescence was observed to be initiated mainly through the static quenching process and this suggests the formation of ground state LFC-BSA association complex. The stronger interactions of LFC in the cavity of Sudlow site I (subdomain IIA) of protein have been explored from site marker calorimetric and molecular docking study.
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Affiliation(s)
- Amandeep Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Imran Ahmd Khan
- School of Pharmaceutical Science and Technology,Tianjin University, Tianjin 300072, PR China
| | | | - Tarlok Singh Banipal
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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Banipal TS, Kaur A, Banipal PK. Physicochemical aspects of the energetics of binding of sulphanilic acid with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 170:214-225. [PMID: 27450119 DOI: 10.1016/j.saa.2016.07.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/10/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023]
Abstract
The thermodynamic study of the binding of sulphanilic acid with model transport protein bovine serum albumin is a promising approach in the area of synthesizing new sulfa drugs with improved therapeutic effect. Thus, such binding studies play an important role in the rational drug design process. The binding between sulphanilic acid and bovine serum albumin has been studied using calorimetry, light scattering in combination with spectroscopic and microscopic techniques. The calorimetric data reveals the presence of two sequential nature of binding sites where the first binding site has stronger affinity (~10(4)M(-1)) and second binding site has weaker affinity (~10(3)M(-1)). However, the spectroscopic (absorption and fluorescence) results suggest the presence of single low affinity binding site (~10(3)M(-1)) on protein. The contribution of polar and non-polar interactions to the binding process has been explored in the presence of various additives. It is found that sulphanilic acid binds with high affinity at Sudlow site II and with low affinity at Sudlow site I of protein. Light scattering and circular dichroism measurements have been used to study the effect on the molecular topology and conformation of protein, respectively. Thus these studies provide important insights into the binding of sulphanilic acid with bovine serum albumin both quantitatively and qualitatively.
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Affiliation(s)
- Tarlok S Banipal
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
| | - Amandeep Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Parampaul K Banipal
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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5
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Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations. PLoS One 2016; 11:e0166487. [PMID: 27870861 PMCID: PMC5117683 DOI: 10.1371/journal.pone.0166487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
We report here interesting synergistic effects of proline and sorbitol, two well-known chemical chaperones, in the inhibition of fibrillation of two proteins, insulin and lysozyme. A combination of many biophysical techniques has been used to understand the structural morphology and modes of interaction of the chaperones with the proteins during fibrillation. Both the chaperones establish stronger polar interactions in the elongation and saturation stages of fibrillation compared to that in the native stage. However, when presented as a mixture, we also see contribution of hydrophobic interactions. Thus, a co-operative adjustment of polar and hydrophobic interactions between the chaperones and the protein surface seems to drive the synergistic effects in the fibrillation process. In insulin, this synergy is quantitatively similar in all the stages of the fibrillation process. These observations would have significant implications for understanding protein folding concepts, in general, and for designing combination therapies against protein fibrillation, in particular.
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Wang A, Perera YR, Davidson MB, Fitzkee NC. Electrostatic Interactions and Protein Competition Reveal a Dynamic Surface in Gold Nanoparticle-Protein Adsorption. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:24231-24239. [PMID: 27822335 PMCID: PMC5096844 DOI: 10.1021/acs.jpcc.6b08469] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gold nanoparticle- (AuNP-) protein conjugates are potentially useful in a broad array of diagnostic and therapeutic applications, but the physical basis of the simultaneous adsorption of multiple proteins onto AuNP surfaces remains poorly understood. Here, we investigate the contribution of electrostatic interactions to protein-AuNP binding by studying the pH-dependent binding behavior of two proteins, GB3 and ubiquitin. For both proteins, binding to 15-nm citrate-coated AuNPs closely tracks with the predicted net charge using standard pKa values, and a dramatic reduction in binding is observed when lysine residues are chemically methylated. This suggests that clusters of basic residues are involved in binding, and using this hypothesis, we model the pKa shifts induced by AuNP binding. Then, we employ a novel NMR-based approach to monitor the binding competition between GB3 and ubiquitin in situ at different pH values. In light of our model, the NMR measurements reveal that the net charge, binding association constant, and size of each protein play distinct roles at different stages of protein adsorption. When citrate-coated AuNPs and proteins first interact, net charge appears to dominate. However, as citrate molecules are displaced by protein, the surface chemistry changes, and the energetics of binding becomes far more complex. In this case, we observed that GB3 is able to displace ubiquitin at intermediate time scales, even though it has a lower net charge. The thermodynamic model for binding developed here could be the first step toward predicting the binding behavior in biological fluids, such as blood plasma.
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7
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Banipal TS, Kaur A, Khan IA, Banipal PK. Exploring the thermodynamics and conformational aspects of nicotinic acid binding with bovine serum albumin: a detailed calorimetric, spectroscopic and molecular docking study. RSC Adv 2016. [DOI: 10.1039/c5ra28028a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
An attempt to obtain a physicochemical and conformational outlook on the binding interaction of vitamin B3 (NA) with a model transport protein BSA using calorimetry, light scattering, molecular docking, and spectroscopic techniques.
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Affiliation(s)
| | - Amandeep Kaur
- Department of Chemistry
- Guru Nanak Dev University
- Amritsar – 143005
- India
| | - Imran Ahmd Khan
- Department of Chemistry
- Guru Nanak Dev University
- Amritsar – 143005
- India
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8
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Pica A, Graziano G. On the Effect of Sodium Chloride and Sodium Sulfate on Cold Denaturation. PLoS One 2015; 10:e0133550. [PMID: 26197394 PMCID: PMC4511003 DOI: 10.1371/journal.pone.0133550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 11/28/2022] Open
Abstract
Both sodium chloride and sodium sulfate are able to stabilize yeast frataxin, causing an overall increase of its thermodynamic stability curve, with a decrease in the cold denaturation temperature and an increase in the hot denaturation one. The influence of low concentrations of these two salts on yeast frataxin stability can be assessed by the application of a theoretical model based on scaled particle theory. First developed to figure out the mechanism underlying cold denaturation in water, this model is able to predict the stabilization of globular proteins provided by these two salts. The densities of the salt solutions and their temperature dependence play a fundamental role.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia – 80126 Napoli, Italy
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port’Arsa 11–82100 Benevento, Italy
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9
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013; 52:9544-9. [DOI: 10.1002/anie.201302161] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Indexed: 01/07/2023]
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10
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Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302161] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Pica A, Russo Krauss I, Castellano I, La Cara F, Graziano G, Sica F, Merlino A. Effect of NaCl on the conformational stability of the thermophilic γ-glutamyltranspeptidase from Geobacillus thermodenitrificans: Implication for globular protein halotolerance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:149-57. [DOI: 10.1016/j.bbapap.2012.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/10/2012] [Accepted: 09/27/2012] [Indexed: 12/28/2022]
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12
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Moreau MJJ, Schaeffer PM. Dissecting the salt dependence of the Tus–Ter protein–DNA complexes by high-throughput differential scanning fluorimetry of a GFP-tagged Tus. MOLECULAR BIOSYSTEMS 2013; 9:3146-54. [DOI: 10.1039/c3mb70426b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Choudhary S, Kishore N. Unraveling the Energetics and Mode of the Recognition of Antibiotics Tetracycline and Rolitetracycline by Bovine Serum Albumin. Chem Biol Drug Des 2012; 80:693-705. [DOI: 10.1111/cbdd.12009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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de Jong S, Epelbaum N, Liyanage R, Krylov SN. A semipermanent coating for preventing protein adsorption at physiological pH in kinetic capillary electrophoresis. Electrophoresis 2012; 33:2584-90. [DOI: 10.1002/elps.201200153] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Ostanina ES, Varlamov VP, Yakovlev GI. Inhibition of lipase activity by low-molecular-weight chitosan. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808010055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Erba EB, Zenobi R. Mass spectrometric studies of dissociation constants of noncovalent complexes. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1pc90006d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Varhač R, Tomášková N, Fabián M, Sedlák E. Kinetics of cyanide binding as a probe of local stability/flexibility of cytochrome c. Biophys Chem 2009; 144:21-6. [DOI: 10.1016/j.bpc.2009.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 05/30/2009] [Accepted: 06/01/2009] [Indexed: 10/20/2022]
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18
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Niiranen L, Altermark B, Brandsdal BO, Leiros HS, Helland R, Smalås AO, Willassen NP. Effects of salt on the kinetics and thermodynamic stability of endonuclease I from
Vibrio salmonicida
and
Vibrio cholerae. FEBS J 2008; 275:1593-1605. [DOI: 10.1111/j.1742-4658.2008.06317.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Laila Niiranen
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Norway
| | - Bjørn Altermark
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Bjørn O. Brandsdal
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Hanna‐Kirsti S. Leiros
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Ronny Helland
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Arne O. Smalås
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Nils P. Willassen
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Norway
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19
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Ostanina ES, Varlamov VP, Yakovlev GI. Inhibition of lipase activity by low-molecular-weight chitosan. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Yakovlev GI, Mitkevich VA, Struminskaya NK, Varlamov VP, Makarov AA. Low molecular weight chitosan is an efficient inhibitor of ribonucleases. Biochem Biophys Res Commun 2007; 357:584-8. [PMID: 17442276 DOI: 10.1016/j.bbrc.2007.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 03/05/2007] [Indexed: 11/19/2022]
Abstract
RNase inhibitors are commonly used to block the RNase activity in manipulations with RNA-containing preparations. Recently RNase inhibitors, either synthetic or natural, have been intensively sought because they appeared to be promising for therapy of cancer and allergy. However, there is only a limited number of efficient RNase inhibitors. We have shown that a low molecular weight chitosan (M(r) approximately 6 kDa) inhibits activity of pancreatic RNase A and some bacterial RNases with inhibition constants in the range of 30-220 nM at pH 7.0 and ionic strength 0.14 M. The preferential contribution to the chitosan complex formation with RNases is due to establishment of 5-6 ion pairs. The results of this work show that polycations may efficiently inhibit ribonuclease activities.
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Affiliation(s)
- Gennady I Yakovlev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia.
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Ababou A, Ladbury JE. Survey of the year 2005: literature on applications of isothermal titration calorimetry. J Mol Recognit 2007; 20:4-14. [PMID: 17006876 DOI: 10.1002/jmr.803] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of an interaction. Its usage does not suffer from constraints of molecular size, shape or chemical constitution. Neither is there any need for chemical modification or attachment to solid support. This ease of use has made it an invaluable instrumental resource and led to its appearance in many laboratories. Despite this, the value of the thermodynamic parameterization has, only quite recently, become widely appreciated. Although our understanding of the correlation between thermodynamic data and structural details continues to be somewhat naïve, a large number of publications have begun to improve the situation. In this overview of the literature for 2005, we have attempted to highlight works of interest and novelty. Furthermore, we draw attention to those works which we feel have provided a route to better analysis and increased our ability to understand the meaning of thermodynamic change on binding.
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Affiliation(s)
- Adessamad Ababou
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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Henrotte V, Muller RN, Bartholet A, Elst LV. The presence of halide salts influences the non-covalent interaction of MRI contrast agents and human serum albumin. CONTRAST MEDIA & MOLECULAR IMAGING 2007; 2:258-61. [DOI: 10.1002/cmmi.153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Hoffmann M, Eitner K, von Grotthuss M, Rychlewski L, Banachowicz E, Grabarkiewicz T, Szkoda T, Kolinski A. Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. J Comput Aided Mol Des 2006; 20:305-19. [PMID: 16972168 PMCID: PMC7088412 DOI: 10.1007/s10822-006-9057-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 07/17/2006] [Indexed: 10/29/2022]
Abstract
The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.
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Affiliation(s)
- Marcin Hoffmann
- BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland.
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24
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Formaneck MS, Ma L, Cui Q. Effects of temperature and salt concentration on the structural stability of human lymphotactin: insights from molecular simulations. J Am Chem Soc 2006; 128:9506-17. [PMID: 16848488 PMCID: PMC2600855 DOI: 10.1021/ja061620o] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Extensive molecular dynamics (MD) simulations ( approximately 70 ns total) with explicit solvent molecules and salt ions are carried out to probe the effects of temperature and salt concentration on the structural stability of the human Lymphotactin (hLtn). The distribution of ions near the protein surface and the stability of various structural motifs are observed to exhibit interesting dependence on the local sequence and structure. Whereas chloride association to the protein is overall enhanced as the temperature increases, the sodium distribution in the C-terminal helical region and, to a smaller degree, the chloride distribution in the same region are found higher at the lower temperature. The similar trend is also observed in nonlinear Poisson-Boltzmann calculations with a temperature-dependent water dielectric constant, once conformational averaging over a series of MD snapshots is done. The unexpected temperature dependence in the ion distribution is explained on the basis of the cancellation of association entropy for ion-side chain pairs of opposite-charge and like-charge characters, which have positive and negative contributions, respectively. The C-terminal helix is observed to partially melt whereas a short beta strand forms at the higher temperature with little salt dependence. The N-terminal region, by contrast, develops partial helical structure at a higher salt concentration. These observed behaviors are consistent with solvent and salt screening playing an important role in stabilizing the canonical chemokine fold of hLtn.
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Affiliation(s)
- Mark S Formaneck
- Department of Chemistry and Theoretical Chemistry Institute, Graduate Program in Biophysics, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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25
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Kozlov AG, Lohman TM. Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA. Biochemistry 2006; 45:5190-205. [PMID: 16618108 PMCID: PMC2516749 DOI: 10.1021/bi052543x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously shown that the linkage of temperature-dependent protonation and DNA base unstacking equilibria contribute significantly to both the negative enthalpy change (DeltaH(obs)) and the negative heat capacity change (DeltaC(p,obs)) for Escherichia coli SSB homotetramer binding to single-stranded (ss) DNA. Using isothermal titration calorimetry we have now examined DeltaH(obs) over a much wider temperature range (5-60 degrees C) and as a function of monovalent salt concentration and type for SSB binding to (dT)(70) under solution conditions that favor the fully wrapped (SSB)(65) complex (monovalent salt concentration >or=0.20 M). Over this wider temperature range we observe a strongly temperature-dependent DeltaC(p,obs). The DeltaH(obs) decreases as temperature increases from 5 to 35 degrees C (DeltaC(p,obs) <0) but then increases at higher temperatures up to 60 degrees C (DeltaC(p,obs) >0). Both salt concentration and anion type have large effects on DeltaH(obs) and DeltaC(p,obs). These observations can be explained by a model in which SSB protein can undergo a temperature- and salt-dependent conformational transition (below 35 degrees C), the midpoint of which shifts to higher temperature (above 35 degrees C) for SSB bound to ssDNA. Anions bind weakly to free SSB, with the preference Br(-) > Cl(-) > F(-), and these anions are then released upon binding ssDNA, affecting both DeltaH(obs) and DeltaC(p,obs). We conclude that the experimentally measured values of DeltaC(p,obs) for SSB binding to ssDNA cannot be explained solely on the basis of changes in accessible surface area (ASA) upon complex formation but rather result from a series of temperature-dependent equilibria (ion binding, protonation, and protein conformational changes) that are coupled to the SSB-ssDNA binding equilibrium. This is also likely true for many other protein-nucleic acid interactions.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA
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Friedman R, Nachliel E, Gutman M. Molecular dynamics of a protein surface: ion-residues interactions. Biophys J 2005; 89:768-81. [PMID: 15894639 PMCID: PMC1366628 DOI: 10.1529/biophysj.105.058917] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 04/28/2005] [Indexed: 11/18/2022] Open
Abstract
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty for Life Sciences, Tel Aviv University, Israel
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