1
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Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
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Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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2
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Galicová T, Hasoň S, Ostatná V. Interaction of lectin Sambucus nigra with sialylated trisaccharides in the presence of osmolytes. Chronopotentiometric sensing. Bioelectrochemistry 2023; 152:108457. [PMID: 37196453 DOI: 10.1016/j.bioelechem.2023.108457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Trisaccharides bind to their interaction partners-lectins relatively weakly, which makes detection of their complexes challenging. In this work, we show that an osmolyte presence improves the distinguishing complexes of lectin Sambucus nigra with trisialyllactoses with various binding affinities. The addition of osmolyte, non-binding sugar mannose significantly improved the precision of binding experiments performed using chronopotentiometric stripping at the electrode surface and fluorescence analysis in solution. Osmolytes minimized nonspecific interactions between binding sugar and lectin. Obtained findings can be utilized in any in vitro methods studying interactions of carbohydrates, respectively their conjugates with proteins. The study of carbohydrate interactions appears important since they play essential roles in a variety of biological processes including carcinogenesis.
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Affiliation(s)
- Tatiana Galicová
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Stanislav Hasoň
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic.
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3
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Cell Cycle Progression Influences Biofilm Formation in Saccharomyces cerevisiae 1308. Microbiol Spectr 2022; 10:e0276521. [PMID: 35670600 PMCID: PMC9241733 DOI: 10.1128/spectrum.02765-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm-immobilized continuous fermentation is a novel fermentation strategy that has been utilized in ethanol fermentation. Continuous fermentation contributes to the self-proliferation of Saccharomyces cerevisiae biofilms. Previously, we successfully described the cell cycle differences between biofilm-immobilized fermentation and calcium alginate-immobilized fermentation. In the present study, we investigated the relationship between biofilm formation and the cell cycle. We knocked down CLN3, SIC1, and ACE2 and found that Δcln3 and Δsic1 exhibited a predominance of G2/M phase cells, increased biofilm formation, and significantly increased extracellular polysaccharide formation and expression of genes in the FLO gene family during immobilisation fermentation. Δace2 exhibited a contrasting performance. These findings suggest that the increase in the proportion of cells in the G2/M phase of the cell cycle facilitates biofilm formation and that the cell cycle influences biofilm formation by regulating cell adhesion and polysaccharide formation. This opens new avenues for basic research and may also help to provide new ideas for biofilm prevention and optimization. IMPORTANCE Immobilised fermentation can be achieved using biofilm resistance, resulting in improved fermentation efficiency and yield. The link between the cell cycle and biofilms deserves further study since reports are lacking in this area. This study showed that the ability of Saccharomyces cerevisiae to produce biofilm differed when cell cycle progression was altered. Further studies suggested that cell cycle regulatory genes influenced biofilm formation by regulating cell adhesion and polysaccharide formation. Findings related to cell cycle regulation of biofilm formation set the stage for biofilm in Saccharomyces cerevisiae and provide a theoretical basis for the development of a new method to improve biofilm-based industrial fermentation.
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4
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Nagao M, Kichize M, Hoshino Y, Miura Y. Influence of Monomer Structures for Polymeric Multivalent Ligands: Consideration of the Molecular Mobility of Glycopolymers. Biomacromolecules 2021; 22:3119-3127. [PMID: 34152744 DOI: 10.1021/acs.biomac.1c00553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mobility is important for interactions of biofunctional polymers with target molecules. Monomer structures for synthetic biofunctional polymers are usually selected based on their compatibility with polymerization systems, whereas the influence of monomer structures on the interaction with target molecules is hardly considered. In this report, we evaluate the correlation between the monomer structures of glycopolymers and their interactions with concanavalin A (ConA) with respect to the molecular mobility. Two types of glycopolymers bearing mannose are synthesized with acrylamide or acrylate monomers. Despite the similar structures, except for amide or ester bonds in the side chains, the acrylate-type glycopolymers exhibit stronger interaction with ConA both in the isothermal titration calorimetry measurement and in a hemagglutination inhibition assay. Characterization of the acrylate-type glycopolymers suggests that the higher binding constant arises from the higher molecular mobility of mannose units, which results from the rotational freedom of ester bonds in their side chains.
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Affiliation(s)
- Masanori Nagao
- Department of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Masaya Kichize
- Department of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshiko Miura
- Department of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
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5
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Zhang D, Wang F, Yu Y, Ding S, Chen T, Sun W, Liang C, Yu B, Ying H, Liu D, Chen Y. Effect of quorum-sensing molecule 2-phenylethanol and ARO genes on Saccharomyces cerevisiae biofilm. Appl Microbiol Biotechnol 2021; 105:3635-3648. [PMID: 33852023 DOI: 10.1007/s00253-021-11280-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Biofilms are a form of microbial community that can be beneficial for industrial fermentation because of their remarkable environmental resistance. However, the mechanism of biofilm formation in Saccharomyces cerevisiae remains to be fully explored, and this may enable improved industrial applications for this organism. Although quorum-sensing (QS) molecules are known to be involved in bacteria biofilm formation, few studies have been undertaken with these in fungi. 2-phenylethanol (2-PE) is considered a QS molecule in S. cerevisiae. Here, we found that exogenous 2-PE could stimulate biofilm formation at low cell concentrations. ARO8p and ARO9p are responsible for the synthesis of 2-PE and were crucial to the formation of biofilm. Deletion of the ARO8 and ARO9 genes reduced the content of 2-PE in the early stage of fermentation, reduced ethanol yield and decreased biofilm formation. The expression of FLOp, which is involved in cell adhesion, and the content of extracellular polysaccharides of mutant strains ΔARO8 and ΔARO9 were also significantly reduced. These findings indicate that the production of 2-PE had a positive effect on biofilm formation in S. cerevisiae, thereby providing further key details for studying the formation of biofilm mechanism in the future. KEY POINTS: • Quorum-sensing molecule 2-PE positively affects biofilm formation in S. cerevisiae. • 2-PE synthetic genes ARO8 and ARO9 deletion reduced extracellular polysaccharide. • ARO8 and ARO9 deletion reduced the gene expression of the FLO family.
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Affiliation(s)
- Deli Zhang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Fangjuan Wang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Ying Yu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Sai Ding
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Tianpeng Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wenjun Sun
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Caice Liang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Bin Yu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450000, China
| | - Dong Liu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China. .,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China. .,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450000, China.
| | - Yong Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China. .,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.
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6
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Stadmiller SS, Pielak GJ. Protein-complex stability in cells and in vitro under crowded conditions. Curr Opin Struct Biol 2020; 66:183-192. [PMID: 33285342 DOI: 10.1016/j.sbi.2020.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 11/29/2022]
Abstract
Biology is beginning to appreciate the effects of the crowded and complex intracellular environment on the equilibrium thermodynamics and kinetics of protein folding. The next logical step involves the interactions between proteins. We review quantitative, wet-experiment based efforts aimed at understanding how and why high concentrations of small molecules, synthetic polymers, biologically relevant cosolutes and the interior of living cells affect the energetics of protein-protein interactions. We then address popular theories used to explain the effects and suggest expeditious paths for a more methodical integration of experiment and simulation.
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Affiliation(s)
- Samantha S Stadmiller
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA.
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7
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Mukherjee M, Mondal J. Osmolyte-Induced Macromolecular Aggregation Is Length-Scale Dependent. J Phys Chem B 2019; 123:8697-8703. [DOI: 10.1021/acs.jpcb.9b07746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mrinmoy Mukherjee
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, 36/P Gopanpally, Serilingampally Mandal, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, 36/P Gopanpally, Serilingampally Mandal, Hyderabad 500107, India
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8
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Understanding the Role of Preferential Exclusion of Sugars and Polyols from Native State IgG1 Monoclonal Antibodies and its Effect on Aggregation and Reversible Self-Association. Pharm Res 2019; 36:109. [DOI: 10.1007/s11095-019-2642-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/07/2019] [Indexed: 11/27/2022]
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9
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Hasan T, Kumari K, Devi SC, Handa J, Rehman T, Ansari NA, Singh LR. Osmolytes in vaccine production, flocculation and storage: a critical review. Hum Vaccin Immunother 2018; 15:514-525. [PMID: 30273503 DOI: 10.1080/21645515.2018.1526585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small molecule osmolytes, responsible for protecting stresses have long been known to rescue proteins and enzymes from loss of function. In addition to protecting macromolecules integrity, many osmolytes also act as potential antioxidant and also help to prevent protein aggregation, amyloid formation or misfolding, and therefore are considered promising molecules for neurodegenerative and many other genetic diseases. Osmolytes are also known to be involved in the regulation of several key immunological processes. In the present review we discuss in detail the effect of these compounds on important aspects of vaccines i.e., increasing the efficiency, production and purification steps. The present review therefore will help researchers to make a better strategy in vaccine production to formulation by incorporating specific and appropriate osmolytes in the processes.
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Affiliation(s)
- Tauheed Hasan
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Kritika Kumari
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | | | - Jaya Handa
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Tabish Rehman
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Nasim Akhtar Ansari
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
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10
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Wang W, Roberts CJ. Protein aggregation – Mechanisms, detection, and control. Int J Pharm 2018; 550:251-268. [DOI: 10.1016/j.ijpharm.2018.08.043] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
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11
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Rydeen AE, Brustad EM, Pielak GJ. Osmolytes and Protein–Protein Interactions. J Am Chem Soc 2018; 140:7441-7444. [DOI: 10.1021/jacs.8b03903] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Rahman S, Ali SA, Islam A, Hassan MI, Ahmad F. Testing the dependence of stabilizing effect of osmolytes on the fractional increase in the accessible surface area on thermal and chemical denaturations of proteins. Arch Biochem Biophys 2016; 591:7-17. [DOI: 10.1016/j.abb.2015.11.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/04/2015] [Accepted: 11/21/2015] [Indexed: 11/28/2022]
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14
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Scherer TM. Role of Cosolute–Protein Interactions in the Dissociation of Monoclonal Antibody Clusters. J Phys Chem B 2015; 119:13027-38. [DOI: 10.1021/acs.jpcb.5b07568] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas M. Scherer
- Genentech (a Member of the Roche Group), Late Stage Pharmaceutical Development, 1 DNA Way, South San Francisco, California 94080, United States
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15
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Rahman S, Warepam M, Singh LR, Dar TA. A current perspective on the compensatory effects of urea and methylamine on protein stability and function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:129-36. [PMID: 26095775 DOI: 10.1016/j.pbiomolbio.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/16/2022]
Abstract
Urea is a strong denaturant and inhibits many enzymes but is accumulated intracellularly at very high concentrations (up to 3-4 M) in mammalian kidney and in many marine fishes. It is known that the harmful effects of urea on the macromolecular structure and function is offset by the accumulation of an osmolytic agent called methylamine. Intracellular concentration of urea to methylamines falls in the ratio of 2:1 to 3:2 (molar ratio). At this ratio, the thermodynamic effects of urea and methylamines on protein stability and function are believed to be algebraically additive. The mechanism of urea-methylamine counteraction has been widely investigated on various approaches including, thermodynamic, structural and functional aspects. Recent advances have also revealed atomic level insights of counteraction and various molecular dynamic simulation studies have yielded significant molecular level informations on the interaction between urea and methylamines with proteins. It is worthwhile that urea-methylamine system not only plays pivotal role for the survival and functioning of the renal medullary cells but also is a key osmoregulatory component of the marine elasmobranchs, holocephalans and coelacanths. Therefore, it is important to combine all discoveries and discuss the developments in context to physiology of the mammalian kidney and adaptation of the marine organisms. In this article we have for the first time reviewed all major developments on urea-counteraction systems to date. We have also discussed about other additional urea-counteraction systems discovered so far including urea-NaCl, urea-myoinsoitol and urea-molecular chaperone systems. Insights for the possible future research have also been highlighted.
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Affiliation(s)
- Safikur Rahman
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Laishram R Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Tanveer Ali Dar
- Clinical Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India.
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16
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Knowles DB, Shkel IA, Phan NM, Sternke M, Lingeman E, Cheng X, Cheng L, O'Connor K, Record MT. Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes. Biochemistry 2015; 54:3528-42. [PMID: 25962980 DOI: 10.1021/acs.biochem.5b00246] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we obtain the data needed to predict chemical interactions of polyethylene glycols (PEGs) and glycerol with proteins and related organic compounds and thereby interpret or predict chemical effects of PEGs on protein processes. To accomplish this, we determine interactions of glycerol and tetraEG with >30 model compounds displaying the major C, N, and O functional groups of proteins. Analysis of these data yields coefficients (α values) that quantify interactions of glycerol, tetraEG, and PEG end (-CH2OH) and interior (-CH2OCH2-) groups with these groups, relative to interactions with water. TetraEG (strongly) and glycerol (weakly) interact favorably with aromatic C, amide N, and cationic N, but unfavorably with amide O, carboxylate O, and salt ions. Strongly unfavorable O and salt anion interactions help make both small and large PEGs effective protein precipitants. Interactions of tetraEG and PEG interior groups with aliphatic C are quite favorable, while interactions of glycerol and PEG end groups with aliphatic C are not. Hence, tetraEG and PEG300 favor unfolding of the DNA-binding domain of lac repressor (lacDBD), while glycerol and di- and monoethylene glycol are stabilizers. Favorable interactions with aromatic and aliphatic C explain why PEG400 greatly increases the solubility of aromatic hydrocarbons and steroids. PEG400-steroid interactions are unusually favorable, presumably because of simultaneous interactions of multiple PEG interior groups with the fused ring system of the steroid. Using α values reported here, chemical contributions to PEG m-values can be predicted or interpreted in terms of changes in water-accessible surface area (ΔASA) and separated from excluded volume effects.
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Affiliation(s)
- D B Knowles
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Noel M Phan
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Matt Sternke
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Emily Lingeman
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Lixue Cheng
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Kevin O'Connor
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- †Department of Biochemistry, ‡Department of Chemistry, and §Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
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17
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Yan S, Tang Y, Yu M. Resonance Rayleigh scattering detection of heparin with concanavalin A. RSC Adv 2015. [DOI: 10.1039/c5ra11700c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stepwise macromolecular interactions observed between conA and heparin, which are accompanied by RRS changes.
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Affiliation(s)
- Shuguang Yan
- College of Energy Resources
- Chengdu University of Technology
- Chengdu 610059
- China
| | - Yurong Tang
- College of Material and Chemistry & Chemical Engineering
- Chengdu University of Technology
- Chengdu 610059
- China
| | - Mengling Yu
- College of Material and Chemistry & Chemical Engineering
- Chengdu University of Technology
- Chengdu 610059
- China
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18
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Reddy PM, Taha M, Sharma YVRK, Venkatesu P, Lee MJ. Quantifying the co-solvent effects on trypsin from the digestive system of carp Catla catla by biophysical techniques and molecular dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c5ra01302j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urea molecules locate within 0.5 nm of the surface of trypsin.
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Affiliation(s)
- P. Madhusudhana Reddy
- Department of Chemistry
- University of Delhi
- Delhi – 110 007
- India
- Department of Chemical Engineering
| | - M. Taha
- CICECO
- Departamento de Química
- Universidade de Aveiro
- 3810-193 Aveiro
- Portugal
| | | | | | - Ming-Jer Lee
- Department of Chemical Engineering
- National Taiwan University of Science & Technology
- Taipei 10607
- Taiwan
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19
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Feng C, Luo YJ, Krueger F. Neural signatures of fairness-related normative decision making in the ultimatum game: a coordinate-based meta-analysis. Hum Brain Mapp 2014; 36:591-602. [PMID: 25327760 DOI: 10.1002/hbm.22649] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 01/10/2023] Open
Abstract
The willingness to incur personal costs to enforce prosocial norms represents a hallmark of human civilization. Although recent neuroscience studies have used the ultimatum game to understand the neuropsychological mechanisms that underlie the enforcement of fairness norms; however, a precise characterization of the neural systems underlying fairness-related norm enforcement remains elusive. In this study, we used a coordinate-based meta-analysis on functional magnetic resonance imaging (fMRI) studies using the ultimatum game with the goal to provide an additional level of evidence for the refinement of the underlying neural architecture of this human puzzling behavior. Our results demonstrated a convergence of reported activation foci in brain networks associated with psychological components of fairness-related normative decision making, presumably reflecting a reflexive and intuitive system (System 1) and a reflective and deliberate system (System 2). System 1 (anterior insula, ventromedial prefrontal cortex [PFC]) may be associated with the reflexive and intuitive responses to norm violations, representing a motivation to punish norm violators. Those intuitive responses conflict with economic self-interest, encoded in the dorsal anterior cingulate cortex (ACC), which may engage cognitive control from a reflective and deliberate System 2 to resolve the conflict by either suppressing (ventrolateral PFC, dorsomedial PFC, left dorsolateral PFC, and rostral ACC) the intuitive responses or over-riding self-interest (right dorsolateral PFC). Taken together, we suggest that fairness-related norm enforcement recruits an intuitive system for rapid evaluation of norm violations and a deliberate system for integrating both social norms and self-interest to regulate the intuitive system in favor of more flexible decision making.
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Affiliation(s)
- Chunliang Feng
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
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Hatori K, Iwasaki T, Wada R. Effect of urea and trimethylamine N-oxide on the binding between actin molecules. Biophys Chem 2014; 193-194:20-6. [DOI: 10.1016/j.bpc.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/14/2014] [Accepted: 07/14/2014] [Indexed: 01/20/2023]
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Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron-electron resonance. Proc Natl Acad Sci U S A 2014; 111:E1201-10. [PMID: 24707053 DOI: 10.1073/pnas.1403179111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron-electron resonance (DEER) provides long-range (20-80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0-3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter.
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