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Katina N, Marchenkov V, Ryabova N, Ilyina N, Marchenko N, Balobanov V, Finkelstein A. Influence of Amino Acid Substitutions in ApoMb on Different Stages of Unfolding of Amyloids. Molecules 2023; 28:7736. [PMID: 38067466 PMCID: PMC10707739 DOI: 10.3390/molecules28237736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
To date, most research on amyloid aggregation has focused on describing the structure of amyloids and the kinetics of their formation, while the conformational stability of fibrils remains insufficiently explored. The aim of this work was to investigate the effect of amino acid substitutions on the stability of apomyoglobin (ApoMb) amyloids. A study of the amyloid unfolding of ApoMb and its six mutant variants by urea has been carried out. Changes in the structural features of aggregates during unfolding were recorded by far-UV CD and native electrophoresis. It was shown that during the initial stage of denaturation, amyloids' secondary structure partially unfolds. Then, the fibrils undergo dissociation and form intermediate aggregates weighing approximately 1 MDa, which at the last stage of unfolding decompose into 18 kDa monomeric unfolded molecules. The results of unfolding transitions suggest that the stability of the studied amyloids relative to the intermediate aggregates and of the latter relative to unfolded monomers is higher for ApoMb variants with substitutions that increase the hydrophobicity of the residues. The results presented provide a new insight into the mechanism of stabilization of protein aggregates and can serve as a base for further investigations of the amyloids' stability.
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Affiliation(s)
- Natalya Katina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 142290 Pushchino, Russia
| | - Victor Marchenkov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalya Ryabova
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Nelly Ilyina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalia Marchenko
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Vitalii Balobanov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Alexey Finkelstein
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
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2
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Majorina MA, Melnik TN, Glukhov AS, Melnik BS. Some useful ideas for multistate protein design: Effect of amino acid substitutions on the multistate proteins stability and the rate of protein structure formation. Front Mol Biosci 2022; 9:983009. [PMID: 36090043 PMCID: PMC9462454 DOI: 10.3389/fmolb.2022.983009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The design of new protein variants is usually confined to slightly “fixing” an already existing protein, adapting it to certain conditions or to a new substrate. This is relatively easy to do if the fragment of the protein to be affected, such as the active site of the protein, is known. But what if you need to “fix” the stability of a protein or the rate of its native or intermediate state formation? Having studied a large number of protein mutant forms, we have established the effect of various amino acid substitutions on the energy landscape of the protein. As a result, we have revealed a number of patterns to help researchers identify amino acid residues that determine the folding rate and the stability of globular proteins states and design a mutant form of a protein with desired properties.
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Affiliation(s)
- M. A. Majorina
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russia
| | - T. N. Melnik
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russia
| | - A. S. Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russia
| | - B. S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: B. S. Melnik,
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3
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Liutkute M, Maiti M, Samatova E, Enderlein J, Rodnina MV. Gradual compaction of the nascent peptide during cotranslational folding on the ribosome. eLife 2020; 9:60895. [PMID: 33112737 PMCID: PMC7593090 DOI: 10.7554/elife.60895] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
Nascent polypeptides begin to fold in the constrained space of the ribosomal peptide exit tunnel. Here we use force-profile analysis (FPA) and photo-induced energy-transfer fluorescence correlation spectroscopy (PET-FCS) to show how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally. Compaction starts vectorially as soon as the first α-helical segments are synthesized. As nascent chain grows, emerging helical segments dock onto each other and continue to rearrange at the vicinity of the ribosome. Inside or in the proximity of the ribosome, the nascent peptide undergoes structural fluctuations on the µs time scale. The fluctuations slow down as the domain moves away from the ribosome. Mutations that destabilize the packing of the domain's hydrophobic core have little effect on folding within the exit tunnel, but abolish the final domain stabilization. The results show the power of FPA and PET-FCS in solving the trajectory of cotranslational protein folding and in characterizing the dynamic properties of folding intermediates.
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Affiliation(s)
- Marija Liutkute
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Manisankar Maiti
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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4
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Majorina MA, Balobanov VA, Uversky VN, Melnik BS. Loops linking secondary structure elements affect the stability of the molten globule intermediate state of apomyoglobin. FEBS Lett 2020; 594:3293-3304. [PMID: 32770670 DOI: 10.1002/1873-3468.13905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 11/11/2022]
Abstract
Apomyoglobin is a widely used model for studying the molecular mechanisms of globular protein folding. This work aimed to analyze the effects of rigidity and length of loops linking protein secondary structure elements on the stability of the molten globule intermediate state. For this purpose, we studied folding/unfolding of mutant apomyoglobin forms with substitutions of loop-located proline residues to glycine and with loop extension by three or six glycine residues. The kinetic and equilibrium experiments performed gave an opportunity to calculate free energies of different apomyoglobin states. Our analysis revealed that the mutations introduced into the apomyoglobin loops have a noticeable effect on the stability of the intermediate state compared to the unfolded state.
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Affiliation(s)
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, Russia
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5
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Alamry KA, Srivastava S, Shahbaaz M, Khan P, Gupta P, Syed SB, Azum N, Asiri AM, Islam A, Ahmad F, Hassan MI. Unravelling the unfolding pathway of human Fas-activated serine/threonine kinase induced by urea. J Biomol Struct Dyn 2020; 39:5516-5525. [PMID: 32662329 DOI: 10.1080/07391102.2020.1790423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fas-activated serine/threonine kinase (FASTK) is a mitochondria-associated nuclear protein that inhibits Fas- and UV-induced apoptosis. This protein is generally activated during Fas-mediated apoptosis by phosphorylating a nuclear RNA-binding protein T-cell intracellular antigen-1 and thus considered as a modulator of apoptosis. In the present study, we have examined the equilibrium unfolding and conformational stability of the kinase domain of FASTK (FASTK353-444). The kinase domain of FASTK353-444 was cloned, expressed, and purified. The folding ↔ unfolding transitions of urea-induced denaturation was monitored with the help of circular dichroism, intrinsic fluorescence, and UV absorption spectroscopies. Analysis of transition curves obtained from different probes revealed a coincidence of denaturation curves, suggesting that folding/unfolding of FASTK follows a two-state process with the midpoint (Cm) value at 3.50 ± 0.1 M. Urea-induced denaturation curves were further analyzed to estimate change in the Gibbs free energy in the absence of urea (ΔGD0) associated with the equilibrium of denaturation. To get atomistic insights into the urea-induced denaturation of FASTK, we performed an all-atom molecular dynamics simulation for 100 ns. A close agreement was noticed between experimental and computational studies. This study will help to understand the unfolding mechanism and structural stability of the kinase domain of FASTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khalid A Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Saurabha Srivastava
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa.,Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sunayana Begum Syed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naved Azum
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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6
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Mills-Henry IA, Thol SL, Kosinski-Collins MS, Serebryany E, King JA. Kinetic Stability of Long-Lived Human Lens γ-Crystallins and Their Isolated Double Greek Key Domains. Biophys J 2019; 117:269-280. [PMID: 31266635 DOI: 10.1016/j.bpj.2019.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/25/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022] Open
Abstract
The γ-crystallins of the eye lens nucleus are among the longest-lived proteins in the human body. Synthesized in utero, they must remain folded and soluble throughout adulthood to maintain lens transparency and avoid cataracts. γD- and γS-crystallin are two major monomeric crystallins of the human lens. γD-crystallin is concentrated in the oldest lens fiber cells, the lens nucleus, whereas γS-crystallin is concentrated in the younger cells of the lens cortex. The kinetic stability parameters of these two-domain proteins and their isolated domains were determined and compared. Kinetic unfolding experiments monitored by fluorescence spectroscopy in varying concentrations of guanidinium chloride were used to extrapolate unfolding rate constants and half-lives of the crystallins in the absence of the denaturant. Consistent with their long lifespans in the lens, extrapolated half-lives for the initial unfolding step were on the timescale of years. Both proteins' isolated N-terminal domains were less kinetically stable than their respective C-terminal domains at denaturant concentrations predicted to disrupt the domain interface, but at low denaturant concentrations, the relative kinetic stabilities were reversed. Cataract-associated aggregation has been shown to proceed from partially unfolded intermediates in these proteins; their extreme kinetic stability likely evolved to protect the lens from the initiation of aggregation reactions. Our findings indicate that the domain interface is the source of significant kinetic stability. The gene duplication and fusion event that produced the modern two-domain architecture of vertebrate lens crystallins may be the origin of their high kinetic as well as thermodynamic stability.
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Affiliation(s)
- Ishara A Mills-Henry
- Department of Chemistry and Food Science, Framingham State University, Framingham, Massachusetts
| | | | | | - Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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7
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Majorina MA, Glukhova KA, Marchenkov VV, Melnik BS. Effect of Substitutions in Surface Amino Acid on Energy Profile of Apomyoglobin. Mol Biol 2018. [DOI: 10.1134/s0026893318010119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Bychkova VE, Semisotnov GV, Balobanov VA, Finkelstein AV. The Molten Globule Concept: 45 Years Later. BIOCHEMISTRY (MOSCOW) 2018; 83:S33-S47. [DOI: 10.1134/s0006297918140043] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Nemtseva EV, Lashchuk OO, Gerasimova MA, Melnik TN, Nagibina GS, Melnik BS. Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II. Methods Appl Fluoresc 2017; 6:015006. [PMID: 29119952 DOI: 10.1088/2050-6120/aa994a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.
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Affiliation(s)
- Elena V Nemtseva
- Siberian Federal University, 660041 Krasnoyarsk, Russia. Institute of Biophysics SB RAS, Federal Research Center 'Krasnoyarsk Science Center SB RAS', 660036, Krasnoyarsk, Russia
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10
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Katina NS, Balobanov VA, Ilyina NB, Vasiliev VD, Marchenkov VV, Glukhov AS, Nikulin AD, Bychkova VE. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Biophys J 2017; 113:991-1001. [PMID: 28877500 DOI: 10.1016/j.bpj.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Investigation of the molecular mechanisms underlying amyloid-related human diseases attracts close attention. These diseases, the number of which currently is above 40, are characterized by formation of peptide or protein aggregates containing a cross-β structure. Most of the amyloidogenesis mechanisms described so far are based on experimental studies of aggregation of short peptides, intrinsically disordered proteins, or proteins under denaturing conditions, and studies of amyloid aggregate formations by structured globular proteins under conditions close to physiological ones are still in the initial stage. We investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents. Stability and aggregation of mutated sw ApoMb were studied using circular dichroism, Fourier transform infrared spectroscopy, x-ray diffraction, native electrophoresis, and electron microscopy techniques. Here, we demonstrate that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates. Specifically, structurally stable mutants show low aggregation propensity and moderately destabilized sw ApoMb variants form amyloids, whereas their strongly destabilized mutants form both amyloids and nonamyloid aggregates.
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Affiliation(s)
- Natalya S Katina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nelly B Ilyina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor D Vasiliev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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11
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Balobanov VA, Katina NS, Finkelstein AV, Bychkova VE. Intermediate states of apomyoglobin: Are they parts of the same area of conformations diagram? BIOCHEMISTRY (MOSCOW) 2017; 82:625-631. [DOI: 10.1134/s0006297917050108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Vorob’ev II, Proskurina OV, Khodak YA, Gosudarev AI, Semikhin AS, Byrikhina DV, Krasil’shchikova MS, Mel’nik BS, Serebryakova MV, Polzikov MA. Physicochemical Properties, Toxicity, and Specific Activity of a Follitropin Alpha Biosimilar. Pharm Chem J 2017. [DOI: 10.1007/s11094-017-1525-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E. Int J Biol Macromol 2016; 91:1051-61. [DOI: 10.1016/j.ijbiomac.2016.06.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/16/2022]
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14
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Thapliyal C, Jain N, Chaudhuri (Chattopadhyay) P. Investigation of folding unfolding process of a new variant of dihydrofolate reductase protein from Zebrafish. Int J Biol Macromol 2016; 91:736-43. [DOI: 10.1016/j.ijbiomac.2016.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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15
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He E, Ren W, Wang J, Li W, Wang W. Effects of heme binding on myoglobin folding: Coarse grained molecular simulations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633615500595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability.
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Affiliation(s)
- Erbin He
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Weitong Ren
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
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16
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Melnik TN, Majorina MA, Larina DS, Kashparov IA, Samatova EN, Glukhov AS, Melnik BS. Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state. PLoS One 2014; 9:e98645. [PMID: 24892675 PMCID: PMC4043776 DOI: 10.1371/journal.pone.0098645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/06/2014] [Indexed: 01/07/2023] Open
Abstract
At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Maria A. Majorina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Daria S. Larina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ivan A. Kashparov
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ekaterina N. Samatova
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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17
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Karamitros CS, Konrad M. Human 60-kDa lysophospholipase contains an N-terminal L-asparaginase domain that is allosterically regulated by L-asparagine. J Biol Chem 2014; 289:12962-75. [PMID: 24657844 PMCID: PMC4036312 DOI: 10.1074/jbc.m113.545038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/02/2014] [Indexed: 11/06/2022] Open
Abstract
The structural and functional characterization of human enzymes that are of potential medical and therapeutic interest is of prime significance for translational research. One of the most notable examples of a therapeutic enzyme is L-asparaginase, which has been established as an antileukemic protein drug for more than four decades. Up until now, only bacterial enzymes have been used in therapy despite a plethora of undesired side effects mainly attributed to the bacterial origins of these enzymes. Therefore, the replacement of the currently approved bacterial drugs by human homologs aiming at the elimination of adverse effects is of great importance. Recently, we structurally and biochemically characterized the enzyme human L-asparaginase 3 (hASNase3), which possesses L-asparaginase activity and belongs to the N-terminal nucleophile superfamily of enzymes. Inspired by the necessity for the development of a protein drug of human origin, in the present study, we focused on the characterization of another human L-asparaginase, termed hASNase1. This bacterial-type cytoplasmic L-asparaginase resides in the N-terminal subdomain of an overall 573-residue protein previously reported to function as a lysophospholipase. Our kinetic, mutagenesis, structural modeling, and fluorescence labeling data highlight allosteric features of hASNase1 that are similar to those of its Escherichia coli homolog, EcASNase1. Differential scanning fluorometry and urea denaturation experiments demonstrate the impact of particular mutations on the structural and functional integrity of the L-asparaginase domain and provide a direct comparison of sites critical for the conformational stability of the human and E. coli enzymes.
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Affiliation(s)
- Christos S. Karamitros
- From the Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany
| | - Manfred Konrad
- From the Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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18
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Dahiya V, Chaudhuri TK. Functional Intermediate in the Refolding Pathway of a Large and Multidomain Protein Malate Synthase G. Biochemistry 2013; 52:4517-30. [DOI: 10.1021/bi400328a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vinay Dahiya
- Kusuma School of Biological
Sciences, Indian Institute of Technology Delhi, Hauz Khas, New
Delhi − 110016, India
| | - Tapan K. Chaudhuri
- Kusuma School of Biological
Sciences, Indian Institute of Technology Delhi, Hauz Khas, New
Delhi − 110016, India
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Morris ER, Searle MS. Overview of protein folding mechanisms: experimental and theoretical approaches to probing energy landscapes. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2012; Chapter 28:28.2.1-28.2.22. [PMID: 22470128 DOI: 10.1002/0471140864.ps2802s68] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present an overview of the current experimental and theoretical approaches to studying protein folding mechanisms, set against current models of the folding energy landscape. We describe how stability and folding kinetics can be determined experimentally and how this data can be interpreted in terms of the characteristic features of various models from the simplest two-state pathway to a multi-state mechanism. We summarize the pros and cons of a range of spectroscopic methods for measuring folding rates and present a theoretical framework, coupled with protein engineering approaches, for elucidating folding mechanisms and structural features of folding transition states. A series of case studies are used to show how experimental kinetic data can be interpreted in the context of non-native interactions, populated intermediates, parallel folding pathways, and sequential transition states. We also show how computational methods now allow transient species of high energy, such as folding transition states, to be modeled on the basis of experimental Φ-value analysis derived from the effects of point mutations on folding kinetics.
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Affiliation(s)
- Elizabeth R Morris
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, United Kingdom
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Samatova EN, Melnik BS, Balobanov VA, Katina NS, Dolgikh DA, Semisotnov GV, Finkelstein AV, Bychkova VE. Folding intermediate and folding nucleus for I-->N and U-->I-->N transitions in apomyoglobin: contributions by conserved and nonconserved residues. Biophys J 2010; 98:1694-702. [PMID: 20409491 DOI: 10.1016/j.bpj.2009.12.4326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 12/22/2009] [Accepted: 12/30/2009] [Indexed: 11/19/2022] Open
Abstract
Kinetic investigation on the wild-type apomyoglobin and its 12 mutants with substitutions of hydrophobic residues by Ala was performed using stopped-flow fluorescence. Characteristics of the kinetic intermediate I and the folding nucleus were derived solely from kinetic data, namely, the slow-phase folding rate constants and the burst-phase amplitudes of Trp fluorescence intensity. This allowed us to pioneer the phi-analysis for apomyoglobin. As shown, these mutations drastically destabilized the native state N and produced minor (for conserved residues of G, H helices) or even negligible (for nonconserved residues of B, C, D, E helices) destabilizing effect on the state I. On the other hand, conserved residues of A, G, H helices made a smaller contribution to stability of the folding nucleus at the rate-limiting I-->N transition than nonconserved residues of B, D, E helices. Thus, conserved side chains of the A-, G-, H-residues become involved in the folding nucleus before crossing the main barrier, whereas nonconserved side chains of the B-, D-, E-residues join the nucleus in the course of the I-->N transition.
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Affiliation(s)
- Ekaterina N Samatova
- Institute of Protein Research, Russian Academy of Sciences, Moscow, Russian Federation
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21
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Equilibrium and kinetics of the unfolding and refolding of Escherichia coli Malate Synthase G monitored by circular dichroism and fluorescence spectroscopy. Biochimie 2010; 92:491-8. [DOI: 10.1016/j.biochi.2010.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 01/11/2010] [Indexed: 11/20/2022]
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22
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Samatova EN, Katina NS, Balobanov VA, Melnik BS, Dolgikh DA, Bychkova VE, Finkelstein AV. How strong are side chain interactions in the folding intermediate? Protein Sci 2009; 18:2152-9. [PMID: 19693934 DOI: 10.1002/pro.229] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Influence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH-induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15-50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.
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Affiliation(s)
- Ekaterina N Samatova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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23
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Zheng F, Qiu Y, Chen Y, Chen P, Zhu Y, Xie W, Zhu H, Zhu J. Cloning, purification and bioactivity assay of human CD28 single-chain antibody in Escherichia coli. Cytotechnology 2009; 60:85-94. [PMID: 19771526 DOI: 10.1007/s10616-009-9218-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022] Open
Abstract
Engineered single chain antibodies have become a powerful source of immunotherapy against a wide range of diseases. Here, we present the generation of human CD28 single-chain antibody gene (CD28-ScFv), which contained variable fragments of heavy chain and light chain (VH and VL) of the anti-CD28 antibody, and a linking peptide (Gly4Ser)3 inserted in the middle of VH and VL. The fused gene CD28-ScFv was successfully expressed in BL21 (DE3) cells and confirmed by western blotting assay. The molecular weight of CD28-ScFv was 43 kDa and the major fraction was expressed as an insoluble body. By dissolving the insoluble bodies, renaturing in vitro and purifying with a Ni-NTA affinity column, highly purified expression products of CD28-ScFv were obtained. This product could recognize and bind to CD28+ positive T cells. The proliferation capacity of peripheral blood T cells was increased by purified CD28-ScFv. In this study, we improved orthodox renaturing techniques by combining the dilution renaturation with phase gradient dialysis. With this new method, highly purified CD28-ScFv products were developed and biological activity of the products was similar to that of the mouse monoclonal anti-human CD28 antibody.
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Affiliation(s)
- Fengfeng Zheng
- College of Life Sciences, Suzhou University, Suzhou, People's Republic of China
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24
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Baryshnikova (Samatova) EN, Melnik BS, Balobanov VA, Katina NS, Finkelshtein AV, Semisotnov GV, Bychkova VE. On the role of some conserved and nonconserved amino acid residues in the transitional state and intermediate of apomyoglobin folding. Mol Biol 2009. [DOI: 10.1134/s0026893309010178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Nikitina J, Shutova T, Melnik B, Chernyshov S, Marchenkov V, Semisotnov G, Klimov V, Samuelsson G. Importance of a single disulfide bond for the PsbO protein of photosystem II: protein structure stability and soluble overexpression in Escherichia coli. PHOTOSYNTHESIS RESEARCH 2008; 98:391-403. [PMID: 18709441 DOI: 10.1007/s11120-008-9327-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 07/01/2008] [Indexed: 05/09/2023]
Abstract
PsbO protein is an important constituent of the water-oxidizing complex, located on the lumenal side of photosystem II. We report here the efficient expression of the spinach PsbO in E. coli where the solubility depends entirely on the formation of the disulfide bond. The PsbO protein purified from a pET32 system that includes thioredoxin fusion is properly folded and functionally active. Urea unfolding experiments imply that the reduction of the single disulfide bridge decreases stability of the protein. Analysis of inter-residue contact density through the PsbO molecule shows that Cys51 is located in a cluster with high contact density. Reduction of the Cys28-Cys51 bond is proposed to perturb the packing interactions in this cluster and destabilize the protein as a whole. Taken together, our results give evidence that PsbO exists in solution as a compact highly ordered structure, provided that the disulfide bridge is not reduced.
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Affiliation(s)
- Julia Nikitina
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umea, Sweden
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Melnik BS, Marchenkov VV, Evdokimov SR, Samatova EN, Kotova NV. Multy-state protein: Determination of carbonic anhydrase free-energy landscape. Biochem Biophys Res Commun 2008; 369:701-6. [PMID: 18313396 DOI: 10.1016/j.bbrc.2008.02.096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 02/20/2008] [Indexed: 11/28/2022]
Abstract
Studies of the folding pathway of large proteins whose kinetics is complicated due to the formation of several intermediate states are most frequently impeded or totally impossible because of rapid folding phase occurring during instrument dead time. In this paper the obtaining of energy characteristics of one of such proteins-carbonic anhydrase B-is reported. Tryptophan fluorescence and absorption methods have been used to measure the folding and unfolding kinetics of carbonic anhydrase B at different urea concentrations. In spite of the fact that the formation of the initial intermediate state of this protein takes place during the instrument dead time, the population of this state has been estimated in a wide range of urea concentrations. The use of the population of the rapidly formed intermediate state and the effective rates of slow phases of the protein folding/unfolding permitted us to calculate free energies of all the protein states and the height of energy barriers between them. It has been shown that folding of carbonic anhydrase B can be described by a consecutive reaction scheme. The possibility to obtain energy characteristics of carbonic anhydrase would allow studying structural characteristics of both intermediate and transition states via site-directed mutations.
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Affiliation(s)
- B S Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Baryshnikova EN, Balobanov VA, Katina NS, Melnik BS, Dolgikh DA, Semisotnov GV, Bychkova VE. Equilibrium unfolding of mutant apomyoglobins carrying substitutions of conserved nonfunctional residues with alanine. Mol Biol 2007. [DOI: 10.1134/s0026893307040139] [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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28
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Abstract
Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic behavior of a protein molecule could be simulated only in the neighborhood of the experimental conformation (or protein unfolding could be simulated at high temperature), the advent of distributed computing, new techniques such as replica-exchange MD, new approaches (based on, e.g., the stochastic difference equation), and physics-based reduced models of proteins now make it possible to study protein-folding pathways from completely unfolded structures. In this review, we present algorithms for MD and their extensions and applications to protein-folding studies, using all-atom models with explicit and implicit solvent as well as reduced models of polypeptide chains.
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Affiliation(s)
- Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
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