A mechanistic insight into protein-ligand interaction, folding, misfolding, aggregation and inhibition of protein aggregates: An overview.
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Maroof Ali | Gulam Rabbani | R. H. Khan | Maroof Ali | G. Rabbani | Tajalli Ilm Chandel | Masihuz Zaman | M. Khan | Mohd Ishtikhar | Rizwan Hasan Khan | Masihuz Zaman | Mohsin Vahid Khan | Mohd Ishtikhar | M. Zaman
[1] G. Glenner,et al. X-RAY DIFFRACTION STUDIES ON AMYLOID FILAMENTS , 1968, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.
[2] Masayuki Mishima,et al. Chromosomal aberrations, clastogens vs aneugens. , 2017, Frontiers in bioscience.
[3] M. Otagiri,et al. Effect of Oxidative Stress on the Structure and Function of Human Serum Albumin , 2001, Pharmaceutical Research.
[4] António J. M. Ribeiro,et al. Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. , 2013, Current medicinal chemistry.
[5] M Karplus,et al. The Levinthal paradox: yesterday and today. , 1997, Folding & design.
[6] A. Lajtha,et al. Handbook of neurochemistry and molecular neurobiology : neural protein metabolism and function , 2007 .
[7] Susmita Das,et al. Fluorescence probing of albumin-surfactant interaction. , 2005, Journal of colloid and interface science.
[8] M. Groves,et al. A method for the general identification of protein crystals in crystallization experiments using a noncovalent fluorescent dye. , 2007, Acta crystallographica. Section D, Biological crystallography.
[9] H. Schluesener,et al. Natural polyphenols binding to amyloid: a broad class of compounds to treat different human amyloid diseases. , 2015, Molecular nutrition & food research.
[10] E. F. ARMSTRONG,et al. Annual Review of Biochemistry , 1944, Nature.
[11] R. Abagyan,et al. Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. , 2010, Journal of the American Chemical Society.
[12] A. Fink,et al. Conformational states of beta-lactamase: molten-globule states at acidic and alkaline pH with high salt. , 1989, Biochemistry.
[13] P. Alam,et al. Interaction of anticancer drug clofarabine with human serum albumin and human &agr;‐1 acid glycoprotein. Spectroscopic and molecular docking approach , 2017, Journal of pharmaceutical and biomedical analysis.
[14] S. Gill,et al. An equation of state describing hydrophobic interactions. , 1976, Proceedings of the National Academy of Sciences of the United States of America.
[15] A. Fersht. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[16] B. Frank,et al. Conformation of proinsulin. A comparison of insulin and proinsulin self-association at neutral pH. , 1972, Biochemistry.
[17] P. Tsvetkov,et al. Binding of ATP to Heat Shock Protein 90 , 2002, The Journal of Biological Chemistry.
[18] I D Campbell,et al. Studies of protein-ligand interactions by NMR. , 2003, Biochemical Society transactions.
[19] J. Bradbury. Chaperones: keeping a close eye on protein folding , 2003, The Lancet.
[20] B H Frank,et al. Altering the association properties of insulin by amino acid replacement. , 1992, Protein engineering.
[21] J. Frydman,et al. Protein misfolding in neurodegenerative diseases: implications and strategies , 2017, Translational Neurodegeneration.
[22] P. Ross,et al. Thermodynamics of protein association reactions: forces contributing to stability. , 1981, Biochemistry.
[23] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[24] Pawel Sikorski,et al. Molecular basis for amyloid fibril formation and stability. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[25] J. Schellman,et al. Temperature, stability, and the hydrophobic interaction. , 1997, Biophysical journal.
[26] G. Giacomello,et al. Proteins structure. , 1957, Scientia medica italica. English ed.
[27] G. Rabbani,et al. Calorimetric and spectroscopic binding studies of amoxicillin with human serum albumin , 2017, Journal of Thermal Analysis and Calorimetry.
[28] C B Anfinsen,et al. The formation and stabilization of protein structure. , 1972, The Biochemical journal.
[29] M R Eftink,et al. Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A. , 1983, Biochemistry.
[30] P. Alam,et al. Insight into the interaction of antitubercular and anticancer compound clofazimine with human serum albumin: spectroscopy and molecular modelling , 2017, Journal of biomolecular structure & dynamics.
[31] R. Jaenicke,et al. Advances in protein chemistry, vol. 29 , 1976 .
[32] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[33] G. Barone,et al. Differential scanning calorimetry as a tool to study protein-ligand interactions , 1995 .
[34] R. Norel,et al. Electrostatic aspects of protein-protein interactions. , 2000, Current opinion in structural biology.
[35] Maurizio Pellecchia,et al. NMR-based structural characterization of large protein-ligand interactions , 2002, Journal of biomolecular NMR.
[36] Michele Vendruscolo,et al. Protein folding and misfolding: a paradigm of self–assembly and regulation in complex biological systems , 2003, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.
[37] Thomas Peters,et al. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. , 2003, Angewandte Chemie.
[38] I. Bahar,et al. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[39] P. Ross,et al. Heat of interaction of DNA with polylysine, spermine, and Mg++. , 1974, Biopolymers.
[40] Jayaraman Chandrasekhar,et al. Strategies and tactics for optimizing the Hit-to-Lead process and beyond--a computational chemistry perspective. , 2008, Drug discovery today.
[41] S. Paul,et al. Protein‐misfolding diseases and chaperone‐based therapeutic approaches , 2006, The FEBS journal.
[42] A. Bronowska,et al. Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design , 2011 .
[43] Stephen K. Burley,et al. Electrostatic interactions in aromatic oligopeptides contribute to protein stability , 1989 .
[44] G. Montich,et al. Protein stability induced by ligand binding correlates with changes in protein flexibility , 2003, Protein science : a publication of the Protein Society.
[45] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[46] Yuan-Ling Xia,et al. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods , 2016, International journal of molecular sciences.
[47] Aamir Ahmad,et al. Rosin Surfactant QRMAE Can Be Utilized as an Amorphous Aggregate Inducer: A Case Study of Mammalian Serum Albumin , 2015, PloS one.
[48] Giampaolo Merlini,et al. Amyloid: Toward terminology clarification Report from the Nomenclature Committee of the International Society of Amyloidosis , 2005, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.
[49] Yun-Xin Fu,et al. Protein Folding, Binding and Energy Landscape: A Synthesis , 2012 .
[50] Shimon Weiss,et al. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy , 2000, Nature Structural Biology.
[51] Elena Papaleo,et al. Protein aggregation: mechanisms and functional consequences. , 2012, The international journal of biochemistry & cell biology.
[52] J. Wouters,et al. Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design. , 2005, Current medicinal chemistry.
[53] R. Nussinov,et al. Folding funnels and binding mechanisms. , 1999, Protein engineering.
[54] W. Klunk,et al. Quantifying amyloid by congo red spectral shift assay. , 1999, Methods in enzymology.
[55] N. Grigorieff,et al. Structural polymorphism of Alzheimer Aβ and other amyloid fibrils , 2009, Prion.
[56] Wayne A Hendrickson,et al. What is 'current opinion' in structural biology? , 2011, Current opinion in structural biology.
[57] M. Hosokawa,et al. Fluorometric determination of amyloid fibrils in vitro using the fluorescent dye, thioflavin T1. , 1989, Analytical biochemistry.
[58] A J Carlson,et al. Frederick R. Rickles, MD, FACP, Appointed Executive Director of the Federation of American Societies for Experimental Biology , 2004, Journal of Investigative Medicine.
[59] P. Ladewig. Double-Refringence of the Amyloid-Congo-Red-Complex in Histological Sections , 1945, Nature.
[60] Tjelvar S. G. Olsson,et al. The thermodynamics of protein-ligand interaction and solvation: insights for ligand design. , 2008, Journal of molecular biology.
[61] W. Nau,et al. Design of a fluorescent dye for indicator displacement from cucurbiturils: a macrocycle-responsive fluorescent switch operating through a pKa shift. , 2008, Organic letters.
[62] D S Goodsell,et al. Automated docking of flexible ligands: Applications of autodock , 1996, Journal of molecular recognition : JMR.
[63] D. Wetlaufer. Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.
[64] I. Kurinov,et al. X‐ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs , 1999, Protein science : a publication of the Protein Society.
[65] David S. Goodsell,et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..
[66] S. Radford,et al. Conformational Conversion during Amyloid Formation at Atomic Resolution , 2011, Molecular cell.
[67] M. Mayer,et al. Spatially and kinetically resolved changes in the conformational dynamics of the Hsp90 chaperone machine , 2009, The EMBO journal.
[68] Huub Schellekens,et al. Antibody response to aggregated human interferon alpha2b in wild-type and transgenic immune tolerant mice depends on type and level of aggregation. , 2006, Journal of Pharmacy and Science.
[69] N. Puri,et al. Spectrofluorimetric assessment of the surface hydrophobicity of proteins. , 1992, The Biochemical journal.
[70] J. Onuchic,et al. Protein folding funnels: a kinetic approach to the sequence-structure relationship. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[71] A. Heuer. Energy Landscapes. Applications to Clusters, Biomolecules and Glasses. By David J. Wales. , 2005 .
[72] J. Szulmajster. Protein folding , 1988, Bioscience reports.
[73] M. Karplus,et al. Protein-folding dynamics , 1976, Nature.
[74] Mathias Jucker,et al. Self-propagation of pathogenic protein aggregates in neurodegenerative diseases , 2013, Nature.
[75] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[76] G. Folkers,et al. Thermodynamics of Protein–Ligand Interactions: History, Presence, and Future Aspects , 2004, Journal of receptor and signal transduction research.
[77] K. Dill. Theory for the folding and stability of globular proteins. , 1985, Biochemistry.
[78] R. H. Khan,et al. Anti-aggregation property of thymoquinone induced by copper-nanoparticles: A biophysical approach. , 2016, International journal of biological macromolecules.
[79] Theodore W Randolph,et al. IgG particle formation during filling pump operation: a case study of heterogeneous nucleation on stainless steel nanoparticles. , 2009, Journal of pharmaceutical sciences.
[80] P. Acharya,et al. Stability Studies on a Lipase from Bacillus subtilis in Guanidinium Chloride , 2003, Journal of protein chemistry.
[81] V. Uversky,et al. Conformational constraints for amyloid fibrillation: the importance of being unfolded. , 2004, Biochimica et biophysica acta.
[82] D. Koshland. Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.
[83] D. Shiao,et al. Heats of binding protons to globular proteins , 1976, Biopolymers.
[84] P. Alam,et al. Protein misfolding and aggregation: Mechanism, factors and detection , 2016 .
[85] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[86] James R. Williamson,et al. Annual review of biophysics , 2008 .
[87] B. Yao,et al. Kinetics and thermodynamics study of lead adsorption on to activated carbons from coconut and seed hull of the palm tree , 2007 .
[88] R. L. Baldwin,et al. How does protein folding get started? , 1989, Trends in biochemical sciences.
[89] F. Hartl,et al. The role of molecular chaperones in human misfolding diseases , 2009, FEBS letters.
[90] P. Alam,et al. Attenuation of amyloid fibrillation in presence of Warfarin: A biophysical investigation. , 2017, International journal of biological macromolecules.
[91] C. Levinthal. Are there pathways for protein folding , 1968 .
[92] Theodore W Randolph,et al. High concentration formulations of recombinant human interleukin-1 receptor antagonist: II. Aggregation kinetics. , 2008, Journal of pharmaceutical sciences.
[93] C. Schütte,et al. Supplementary Information for “ Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations ” , 2009 .
[94] H. Levine,et al. Thioflavine T interaction with synthetic Alzheimer's disease β‐amyloid peptides: Detection of amyloid aggregation in solution , 1993, Protein science : a publication of the Protein Society.
[95] A. Fersht. Nucleation mechanisms in protein folding. , 1997, Current opinion in structural biology.
[96] L. Serpell,et al. The protofilament substructure of amyloid fibrils. , 2000, Journal of molecular biology.
[98] P. Alam,et al. Fibrillogenesis of human serum albumin in the presence of levodopa - spectroscopic, calorimetric and microscopic studies. , 2017, International journal of biological macromolecules.
[99] Miss A.O. Penney. (b) , 1974, The New Yale Book of Quotations.
[100] M. Manning,et al. Heterogeneous nucleation-controlled particulate formation of recombinant human platelet-activating factor acetylhydrolase in pharmaceutical formulation. , 2005, Journal of pharmaceutical sciences.
[101] K. Dill. Dominant forces in protein folding. , 1990, Biochemistry.
[102] Alexei V Finkelstein. Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding , 2007, Chemistry Central journal.
[103] L. Stryer,et al. The interaction of a naphthalene dye with apomyoglobin and apohemoglobin. A fluorescent probe of non-polar binding sites. , 1965, Journal of molecular biology.
[104] W. Kauzmann. Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.
[105] I. Wadsö,et al. A test and calibration process for microcalorimeters used as thermal power meters. , 1982, Journal of biochemical and biophysical methods.
[106] J D Dunitz,et al. Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions. , 1995, Chemistry & biology.
[107] J. Sipe,et al. Review: history of the amyloid fibril. , 2000, Journal of structural biology.
[108] J. Chaires,et al. Calorimetry and thermodynamics in drug design. , 2008, Annual review of biophysics.
[109] John B. Shoven,et al. I , Edinburgh Medical and Surgical Journal.
[110] Gastone Gilli,et al. Enthalpy-entropy compensation in drug-receptor binding , 1994 .
[111] K. Yokoyama,et al. Spectroscopic and calorimetric studies of congo red dye-amyloid peptide complexes , 2010 .
[112] Wim Jiskoot,et al. Extrinsic Fluorescent Dyes as Tools for Protein Characterization , 2008, Pharmaceutical Research.
[113] Lewis E. Kay,et al. New Tools Provide New Insights in NMR Studies of Protein Dynamics , 2006, Science.
[114] R. Leblanc,et al. Aggregation of insulin at the interface. , 2014, The journal of physical chemistry. B.
[115] A. Donald,et al. The binding of thioflavin-T to amyloid fibrils: localisation and implications. , 2005, Journal of structural biology.
[116] S. Harrison,et al. Is there a single pathway for the folding of a polypeptide chain? , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[117] Sheena E. Radford,et al. Folding versus aggregation: Polypeptide conformations on competing pathways , 2008, Archives of biochemistry and biophysics.
[118] S. V. Anisimov,et al. Congo red and protein aggregation in neurodegenerative diseases , 2007, Brain Research Reviews.
[119] J A Asenjo,et al. A theory of protein-resin interaction in hydrophobic interaction chromatography. , 2005, Journal of chromatography. A.
[120] J. Sambrook,et al. Protein folding in the cell , 1992, Nature.
[121] Shoji Takada,et al. Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins , 2009, Proceedings of the National Academy of Sciences.
[122] J. King,et al. Aggregation of granulocyte‐colony stimulating factor in vitro involves a conformationally altered monomeric state , 2005, Protein science : a publication of the Protein Society.
[123] R. Ellis,et al. Medicine: Danger — misfolding proteins , 2002, Nature.
[124] K. Kuwajima,et al. The molten globule state as a clue for understanding the folding and cooperativity of globular‐protein structure , 1989, Proteins.
[125] P. Alam,et al. Binding of anti-cardiovascular drug to serum albumin: an insight in the light of spectroscopic and computational approaches , 2018, Journal of biomolecular structure & dynamics.
[126] A. Velázquez‐Campoy,et al. Isothermal titration calorimetry , 1990 .
[127] N. Hooper. Could inhibition of the proteasome cause mad cow disease? , 2003, Trends in biotechnology.
[128] R. H. Khan,et al. Characterization of a partially folded intermediate of stem bromelain at low pH. , 2002, European journal of biochemistry.
[129] J. Carpenter,et al. A transient expansion of the native state precedes aggregation of recombinant human interferon-gamma. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[130] Tsuyoshi Murata,et al. {m , 1934, ACML.
[131] Gerhard Klebe,et al. What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs? , 1996 .
[132] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[133] M. Lindgren,et al. Detection and characterization of aggregates, prefibrillar amyloidogenic oligomers, and protofibrils using fluorescence spectroscopy. , 2005, Biophysical journal.
[134] Xiaoqin Zou,et al. Advances and Challenges in Protein-Ligand Docking , 2010, International journal of molecular sciences.
[135] Qing-xiang Guo,et al. Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation. , 2001, Chemical reviews.
[136] A. Fersht,et al. Is there a unifying mechanism for protein folding? , 2003, Trends in biochemical sciences.
[137] R. Nussinov,et al. Folding funnels, binding funnels, and protein function , 1999, Protein science : a publication of the Protein Society.
[138] P. S. Kim,et al. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. , 1982, Annual review of biochemistry.
[139] R. H. Khan,et al. Amyloidogenic behavior of different intermediate state of stem bromelain: A biophysical insight. , 2016, International journal of biological macromolecules.
[140] C. Dobson,et al. Protein misfolding, functional amyloid, and human disease. , 2006, Annual review of biochemistry.
[141] R J Fletterick,et al. Structural clues to prion replication. , 1994, Science.
[142] P. Guptasarma,et al. Use of a hydrophobic dye to indirectly probe the structural organization and conformational plasticity of molecules in amorphous aggregates of carbonic anhydrase. , 2002, Biochemical and biophysical research communications.
[143] T. Pollard,et al. Annual review of biophysics and biomolecular structure , 1992 .
[144] T. Arakawa,et al. Mechanisms of protein aggregation. , 2009, Current pharmaceutical biotechnology.
[145] L. Olsen,et al. Study on the binding of Thioflavin T to β-sheet-rich and non- β-sheet cavities , 2007 .
[146] M. Gilson,et al. Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.
[147] J. Changeux,et al. ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.
[148] Marius Schmidt,et al. Protein-ligand interaction probed by time-resolved crystallography. , 2005, Methods in molecular biology.
[149] V. Uversky,et al. Is Congo Red an Amyloid-specific Dye?* , 2001, The Journal of Biological Chemistry.
[150] A. Gliozzi,et al. Amyloid fibrils formation and amorphous aggregation in concanavalin A. , 2007, Biophysical chemistry.
[151] J F Brandts,et al. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. , 1989, Analytical biochemistry.
[152] H. Ahsan,et al. Conformational behavior of alpha-2-macroglobulin: Aggregation and inhibition induced by TFE. , 2017, International journal of biological macromolecules.
[153] J. Emsley. Very strong hydrogen bonding , 1980 .
[154] L. Mendonça-Hagler,et al. Trends in biotechnology and biosafety in Brazil. , 2008, Environmental biosafety research.
[155] P. Privalov,et al. Energetics of protein structure. , 1995, Advances in protein chemistry.
[156] Gulam Rabbani,et al. Non-fluorinated cosolvents: A potent amorphous aggregate inducer of metalloproteinase-conalbumin (ovotransferrin). , 2015, International journal of biological macromolecules.
[157] H. Saibil. Conformational changes studied by cryo-electron microscopy , 2000, Nature Structural Biology.
[158] Hirotsugu Ogi,et al. Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation , 2012, Proceedings of the National Academy of Sciences.
[159] L. Craig,et al. Structural requirements for binding and fluorescence enhancement of the fluorescent probe TNS with peptides. , 1973, Nature: New biology.
[160] A. Miele,et al. Free energy of burying hydrophobic residues in the interface between protein subunits. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[161] U. Bornscheuer,et al. Protein Engineering , 2018, Methods in Molecular Biology.
[162] Ejaz Ahmad,et al. Nanoparticles in relation to peptide and protein aggregation , 2014, International journal of nanomedicine.
[163] J. Frydman. Folding of newly translated proteins in vivo: the role of molecular chaperones. , 2001, Annual review of biochemistry.
[164] J. Pettegrew,et al. Quantitative evaluation of congo red binding to amyloid-like proteins with a beta-pleated sheet conformation. , 1989, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.