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Moringo NA, Shen H, Tauzin LJ, Wang W, Landes CF. Polymer Free Volume Effects on Protein Dynamics in Polystyrene Revealed by Single-Molecule Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2330-2338. [PMID: 32078328 DOI: 10.1021/acs.langmuir.9b03535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein-polymer interactions are critical to applications ranging from biomedical devices to chromatographic separations. The mechanistic relationship between the microstructure of polymer chains and protein interactions is challenging to quantify and not well studied. Here, single-molecule microscopy is used to compare the dynamics of two model proteins, α-lactalbumin and lysozyme, at the interface of uncharged polystyrene with varied molecular weights. The two proteins exhibit different surface interaction mechanisms despite having a similar size and structure. α-Lactalbumin exhibits interfacial adsorption-desorption with residence times that depend on polymer molecular weight. Lysozyme undergoes a continuous time random walk at the polystyrene surface with residence times that also depend on the molecular weight of polystyrene. Single-molecule observables suggest that the hindered continuous time random walk dynamics displayed by lysozyme are determined by the polystyrene free volume, a finding supported by thermal annealing and solvent quality studies. Hindered dynamics are dominated by short-range hydrophobic interactions where the contributions of electrostatic forces are negligible. This work establishes a relationship between the microscale structure (i.e., free volume) of polystyrene polymer chains to nanoscale interfacial protein dynamics.
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L. S, Vasu P. In silico designing of therapeutic protein enriched with branched-chain amino acids for the dietary treatment of chronic liver disease. J Mol Graph Model 2017; 76:192-204. [DOI: 10.1016/j.jmgm.2017.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023]
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Design of bio-based supramolecular structures through self-assembly of α-lactalbumin and lysozyme. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2016.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Woods KN, Pfeffer J. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. Mol Biol Evol 2016; 33:40-61. [PMID: 26337549 PMCID: PMC4693973 DOI: 10.1093/molbev/msv178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function.
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Chakraborti S, Sarwar S, Chakrabarti P. The Effect of the Binding of ZnO Nanoparticle on the Structure and Stability of α-Lactalbumin: A Comparative Study. J Phys Chem B 2013; 117:13397-408. [DOI: 10.1021/jp404411b] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Shamila Sarwar
- Department of Biochemistry, Bose Institute, Kolkata 700054, India
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Smirnova E, Safenkova I, Stein-Margolina B, Shubin V, Gurvits B. L-arginine induces protein aggregation and transformation of supramolecular structures of the aggregates. Amino Acids 2013; 45:845-55. [PMID: 23744402 DOI: 10.1007/s00726-013-1528-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/29/2013] [Indexed: 12/14/2022]
Abstract
Protein misfolding, self-assembly, and aggregation are an essential problem in cell biology, biotechnology, and biomedicine. The protein aggregates are very different morphologically varying from soluble amorphous aggregates to highly ordered amyloid-like fibrils. The objective of this study was to elucidate the role of the amino acid L-arginine (Arg), a widely used suppressor of protein aggregation, in the regulation of transformations of soluble aggregation-prone proteins into supramolecular structures of higher order. However, a striking potential of Arg to govern the initial events in the process of protein aggregation has been revealed under environment conditions where the protein aggregation in its absence was not observed. Using dynamic light scattering we have demonstrated that Arg (10-100 mM) dramatically accelerated the dithiothreitol-induced aggregation of acidic model proteins. The inhibitory effect on the protein aggregation was revealed at higher concentrations of Arg. Using atomic force microscopy it was shown that aggregation of α-lactalbumin from bovine milk induced upon addition of Arg reached a state of formation of supramolecular structures of non-fibrillar species profoundly differing from those of the individual protein in type, size, and shape. The interaction of another positively charged amino acid L-lysine with α-lactalbumin also resulted in profound acceleration of the aggregation process and transformation of supramolecular structures of the aggregates.
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Affiliation(s)
- Ekaterina Smirnova
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, 119071, Moscow, Russia
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Artemova NV, Stein-Margolina VA, Bumagina ZM, Gurvits BY. Acceleration of protein aggregation by amphiphilic peptides: transformation of supramolecular structure of the aggregates. Biotechnol Prog 2011; 27:846-54. [PMID: 21365787 DOI: 10.1002/btpr.574] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 10/15/2010] [Indexed: 11/09/2022]
Abstract
Protein self-assembly and aggregation represent a special tool in biomedicine and biotechnology to produce biological materials for a wide range of applications. The protein aggregates are very different morphologically, varying from soluble amorphous aggregates to highly ordered amyloid-like fibrils, the latter being associated with molecular structures able to perform specific functions in living systems. Fabrication of novel biomaterials resembling natural protein assemblies has awakened interest in identification of low-molecular-weight biogenic agents as regulators of transformation of aggregation-prone proteins into fibrillar structures. Short amphiphilic peptides can be considered for this role. Using dynamic light scattering, turbidimetry, fluorescence spectroscopy, and transmission electron microscopy (TEM), we have demonstrated that the Arg-Phe dipeptide dramatically accelerates the aggregation of a model protein, α-lactalbumin, to generate morphologically different structures. TEM revealed transformation of spherical particles observed in the control samples into branched chains of fibril-like nanostructures in the presence of the peptide, suggesting that amphiphilic peptides can induce changes in the physicochemical properties of a protein substrate (net charge, hydrophobicity, and tendency to β-structure formation) resulting in accumulation of peptide-protein complexes competent to self-assembly into supramolecular structures. A number of other short amphiphilic peptides have also been shown to accelerate the aggregation process, using alternative complementary protein substrates for identification of molecular recognition modules. Peptide-protein assemblies are suggested to play the role of building blocks for formation of supramolecular structures profoundly differing from those of the individual protein substrate in type, size, and shape.
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Affiliation(s)
- N V Artemova
- AN Bakh Institute of Biochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
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8
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Kirberger M, Wang X, Zhao K, Tang S, Chen G, Yang JJ. Integration of Diverse Research Methods to Analyze and Engineer Ca-Binding Proteins: From Prediction to Production. Curr Bioinform 2010; 5:68-80. [PMID: 20802832 PMCID: PMC2927018 DOI: 10.2174/157489310790596358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In recent years, increasingly sophisticated computational and bioinformatics tools have evolved for the analyses of protein structure, function, ligand interactions, modeling and energetics. This includes the development of algorithms to recursively evaluate side-chain rotamer permutations, identify regions in a 3D structure that meet some set of search parameters, calculate and minimize energy values, and provide high-resolution visual tools for theoretical modeling. Here we discuss the interdependency between different areas of bioinformatics, the evolution of different algorithm design approaches, and finally the transition from theoretical models to real-world design and application as they relate to Ca(2+)-binding proteins. Within this context, it has become evident that significant pre-experimental design and calculations can be modeled through computational methods, thus eliminating potentially unproductive research and increasing our confidence in the correlation between real and theoretical models. Moving from prediction to production, it is anticipated that bioinformatics tools will play an increasingly significant role in research and development, improving our ability to both understand the physiological roles of Ca(2+) and other metals and to extend that knowledge to the design of function-specific synthetic proteins capable of fulfilling different roles in medical diagnostics and therapeutics.
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Affiliation(s)
- Michael Kirberger
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia
| | - Kun Zhao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Shen Tang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Guantao Chen
- Department of Computer Science, Georgia State University, Atlanta, Georgia
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Jenny J. Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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9
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Dynamic and supramolecular organisation of α-lactalbumin/lysozyme microspheres: A microscopic study. Biophys Chem 2010; 146:30-5. [DOI: 10.1016/j.bpc.2009.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/02/2009] [Accepted: 10/04/2009] [Indexed: 11/23/2022]
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10
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Li JH, Liu YQ, Lü P, Lin HF, Bai Y, Wang XC, Chen YL. A signaling pathway linking nitric oxide production to heterotrimeric G protein and hydrogen peroxide regulates extracellular calmodulin induction of stomatal closure in Arabidopsis. PLANT PHYSIOLOGY 2009; 150:114-24. [PMID: 19321706 PMCID: PMC2675720 DOI: 10.1104/pp.109.137067] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Accepted: 03/19/2009] [Indexed: 05/18/2023]
Abstract
Extracellular calmodulin (ExtCaM) regulates stomatal movement by eliciting a cascade of intracellular signaling events including heterotrimeric G protein, hydrogen peroxide (H(2)O(2)), and Ca(2+). However, the ExtCaM-mediated guard cell signaling pathway remains poorly understood. In this report, we show that Arabidopsis (Arabidopsis thaliana) NITRIC OXIDE ASSOCIATED1 (AtNOA1)-dependent nitric oxide (NO) accumulation plays a crucial role in ExtCaM-induced stomatal closure. ExtCaM triggered a significant increase in NO levels associated with stomatal closure in the wild type, but both effects were abolished in the Atnoa1 mutant. Furthermore, we found that ExtCaM-mediated NO generation is regulated by GPA1, the Galpha-subunit of heterotrimeric G protein. The ExtCaM-dependent NO accumulation was nullified in gpa1 knockout mutants but enhanced by overexpression of a constitutively active form of GPA1 (cGalpha). In addition, cGalpha Atnoa1 and gpa1-2 Atnoa1 double mutants exhibited a similar response as did Atnoa1. The defect in gpa1 was rescued by overexpression of AtNOA1. Finally, we demonstrated that G protein activation of NO production depends on H(2)O(2). Reduced H(2)O(2) levels in guard cells blocked the stomatal response of cGalpha lines, whereas exogenously applied H(2)O(2) rescued the defect in ExtCaM-mediated stomatal closure in gpa1 mutants. Moreover, the atrbohD/F mutant, which lacks the NADPH oxidase activity in guard cells, had impaired NO generation in response to ExtCaM, and H(2)O(2)-induced stomatal closure and NO accumulation were greatly impaired in Atnoa1. These findings have established a signaling pathway leading to ExtCaM-induced stomatal closure, which involves GPA1-dependent activation of H(2)O(2) production and subsequent AtNOA1-dependent NO accumulation.
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Affiliation(s)
- Jian-Hua Li
- Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang 050016, China
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11
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Ji HF, Shen L, Grandori R, Müller N. The effect of heme on the conformational stability of micro-myoglobin. FEBS J 2007; 275:89-96. [DOI: 10.1111/j.1742-4658.2007.06176.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Nigen M, Croguennec T, Madec MN, Bouhallab S. Apo alpha-lactalbumin and lysozyme are colocalized in their subsequently formed spherical supramolecular assembly. FEBS J 2007; 274:6085-93. [PMID: 17970750 DOI: 10.1111/j.1742-4658.2007.06130.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We have reported previously that the calcium-depleted form of bovine alpha-lactalbumin (apo alpha-LA) interacts with hen egg-white lysozyme (LYS) to form spherical supramolecular structures. These supramolecular structures contain an equimolar ratio of the two proteins. We further explore here the organization of these structures. The spherical morphology and size of the assembled LYS/apo alpha-LA supramolecular structures were demonstrated using confocal scanning laser microscopy and scanning electron microscopy. From confocal scanning laser microscopy experiments with labelled proteins, it was found that LYS and apo alpha-LA were perfectly colocalized and homogeneously distributed throughout the entire three-dimensional structure of the microspheres formed. The spatial colocalization of the two proteins was also confirmed by the occurrence of a fluorescence resonance energy transfer phenomenon between labelled apo alpha-LA and labelled LYS. Polarized light microscopy analysis revealed that the microspheres formed differ from spherulites, a higher order semicrystalline structure. As the molecular mechanism initiating the formation of these microspheres is still unknown, we discuss the potential involvement of a LYS/apo alpha-LA heterodimer as a starting block for such a supramolecular assembly.
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Ji HF, Zhang HY. A comparative molecular dynamics study on thermostability of human and chicken prion proteins. Biochem Biophys Res Commun 2007; 359:790-4. [PMID: 17560545 DOI: 10.1016/j.bbrc.2007.05.194] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 05/29/2007] [Indexed: 11/16/2022]
Abstract
To compare the thermostabilities of human and chicken normal cellular prion proteins (HuPrP(C) and CkPrP(C)), molecular dynamics (MD) simulations were performed for both proteins at an ensemble level (10 parallel simulations at 400 K and 5 parallel simulations at 300 K as a control). It is found that the thermostability of HuPrP(C) is comparable with that of CkPrP(C), which implicates that the non-occurrence of prion diseases in non-mammals cannot be completely attributed to the thermodynamic properties of non-mammalian PrP(C).
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Affiliation(s)
- Hong-Fang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
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14
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Bánó M, Marek J. How thick is the layer of thermal volume surrounding the protein? Biophys Chem 2005; 120:44-54. [PMID: 16242836 DOI: 10.1016/j.bpc.2005.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 09/23/2005] [Accepted: 09/25/2005] [Indexed: 10/25/2022]
Abstract
Investigation on the volume properties of protein hydration layers is reported. Presented results are based on combination of Monte Carlo modeling and available experimental data. Six globular proteins with known data are chosen for analysis. Analyzing the model and the experimental results we found that water molecules bound to proteins by hydrogen bond are preferentially located at the places with local depressions on the protein surface. Consequently, the hydration level is not strictly proportional to the area of charged and polar surfaces, but also depends on the shape of the molecular surface. The thickness of the thermal volume layer as calculated in the framework of the scaled particle theory is 0.6-0.65 A for chosen proteins. The obtained value is significantly lower than that presented for proteins in earlier papers (where proportionality between the hydration level and the area of charged and polar surfaces was assumed), but is close to the value published for small solute molecules. Discussion including the influence of protein size and the thermal motion of the surface is presented.
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Affiliation(s)
- Mikulás Bánó
- Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04353 Kosice, Slovak Republic.
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Ji HF, Zhang HY, Shen L. The Role of Electrostatic Interaction in Triggering the Unraveling of Stable Helix 1 in Normal Prion Protein. A Molecular Dynamics Simulation Investigation. J Biomol Struct Dyn 2005; 22:563-70. [PMID: 15702928 DOI: 10.1080/07391102.2005.10507026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The conversion of normal prion protein (PrPC) into scrapie isoform (PrPSc) is a key event in the pathogenesis of prion diseases. However, the conversion mechanism has given rise to much controversy. For instance, there is much debate on the behavior of helix 1 (H1) in the conversion. A series of experiments demonstrated that H1 in isolated state was very stable under a variety of conditions. But, other experiments indicated that helices 2 and 3 rather than H1 were retained in PrPSc. In this paper, molecular dynamics (MD) simulation is employed to investigate the dynamic behavior of H1. It is revealed that although the helix 1 of Human PrPC (HuPrPC) is very stable in the isolated state, it becomes unstable when incorporated into native HuPrPC, which likely results from the long-range electrostatic interaction between Asp147 and Arg208 located in the helices 1 and 3, respectively. This explanation is supported by experimental evaluation and MD simulation on D147N mutant of HuPrPC that the mutant becomes a little more stable than the wild type HuPrPC. This finding not only help to reconcile the existing debate on the role of helix 1 in the PrPC-->PrPSc transition, but also reveals a possible mechanism for triggering the PrPC-->PrPSc conversion.
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Affiliation(s)
- Hong-Fang Ji
- Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, PR China
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Liu HL, Shu YC, Wu YH. Molecular dynamics simulations to determine the optimal loop length in the helix-loop-helix motif. J Biomol Struct Dyn 2003; 20:741-5. [PMID: 12744703 DOI: 10.1080/07391102.2003.10506890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this study, 100 ps molecular dynamics simulations were conducted to determine the optimal length of the Gly loop in the helix-loop-helix motif. The results revealed that the length of the loop significantly affected the stability of the two alpha-helices. In addition, the optimal loop length to maintain the highest helicity of the target peptide was found to be the one corresponding to 7 Gly residues. Longer loop length resulted in structural destabilization due to the entropic effect, while shorter loop length was not suitable to achieve intrachain packing of the two alpha-helices.
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Affiliation(s)
- Hsuan-Liang Liu
- Department of Chemical Engineering, National Taipei University of Technology, No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei 10643, Taiwan.
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Joniau M, Haezebrouck P, Noyelle K, Van Dael H. Structural basis for the appearance of a molten globule state in chimeric molecules derived from lysozyme and ?-lactalbumin. Proteins 2001; 44:1-11. [PMID: 11354000 DOI: 10.1002/prot.1065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The problem as to why alpha-lactalbumin, in the absence of Ca(2+), forms a molten globule intermediate, in contrast to its structural homologue lysozyme, has been addressed by the construction of chimeras of human lysozyme in which either the Ca(2+)-binding loop or a part of helix C of bovine alpha-lactalbumin were transplanted. Previously, we have shown that the introduction of both structural elements together in the lysozyme matrix causes the apo form of the resulting chimera to display molten globule behavior during the course of thermal denaturation. In this article, we demonstrate that this molten globule character is not correlated with the Ca(2+)-binding loop. Also, the Del 101 mutant in which Arg101 was deleted to simulate the alpha-lactalbumin conformation of the connecting loop between helix C and helix D, does not show a stable equilibrium intermediate. Rather, the molten globule character of the chimeras has to be related with a specific part of helix C. More particularly, attention is drawn to the four hydrophobic side-chains I93, V96, I99, and L100, the lysozyme counterparts of which are constituted of less bulky valines and alanine. Our observations are discussed in terms of decreased stability of the native form and increased stability of the intermediate molten globule.
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Affiliation(s)
- M Joniau
- Interdisciplinary Research Centre, K.U. Leuven Campus Kortrijk, Kortrijk, Belgium
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