1
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Soltani M, Hunt JP, Smith AK, Zhao EL, Knotts TA, Bundy BC. Assessing the predictive capabilities of design heuristics and coarse-grain simulation toward understanding and optimizing site-specific covalent immobilization of β-lactamase. Biotechnol J 2022; 17:e2100535. [PMID: 35189031 DOI: 10.1002/biot.202100535] [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: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 11/12/2022]
Abstract
For industrial applications, covalent immobilization of enzymes provides minimum leakage, recoverability, reusability, and high stability. Yet, the suitability of a given site on the enzyme for immobilization remains a trial-and-error procedure. Here, we investigate the reliability of design heuristics and a coarse-grain molecular simulation in predicting the optimum sites for covalent immobilization of TEM-1 β-lactamase. We utilized E. coli-lysate-based cell-free protein synthesis (CFPS) to produce variants containing a site-specific incorporated unnatural amino acid with a unique moiety to facilitate site directed covalent immobilization. To constrain the number of potential immobilization sites, we investigated the predictive capability of several design heuristics. The suitability of immobilization sites was determined by analyzing expression yields, specific activity, immobilization efficiency, and stability of variants. These experimental findings are compared with coarse-grain simulation of TEM-1 domain stability and thermal stability and analyzed for a priori predictive capabilities. This work demonstrates that the design heuristics successfully identify a subset of locations for experimental validation. Specifically, the nucleotide following amber stop codon and domain stability correlate well with the expression yield and specific activity of the variants, respectively. Our approach highlights the advantages of combining coarse-grain simulation and high-throughput experimentation using CFPS to identify optimal enzyme immobilization sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Addison K Smith
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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2
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Xu Y, Kang R, Ren L, Yang L, Yue T. Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. Biomolecules 2021; 11:biom11111688. [PMID: 34827686 PMCID: PMC8615548 DOI: 10.3390/biom11111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The knot is one of the most remarkable topological features identified in an increasing number of proteins with important functions. However, little is known about how the knot is formed during protein folding, and untied or maintained in protein unfolding. By means of all-atom molecular dynamics simulation, here we employ methyltransferase YbeA as the knotted protein model to analyze changes of the knotted conformation coupled with protein unfolding under thermal and mechanical denaturing conditions. Our results show that the trefoil knot in YbeA is occasionally untied via knot loosening rather than sliding under enhanced thermal fluctuations. Through correlating protein unfolding with changes in the knot position and size, several aspects of barriers that jointly suppress knot untying are revealed. In particular, protein unfolding is always prior to knot untying and starts preferentially from separation of two α-helices (α1 and α5), which protect the hydrophobic core consisting of β-sheets (β1–β4) from exposure to water. These β-sheets form a loop through which α5 is threaded to form the knot. Hydrophobic and hydrogen bonding interactions inside the core stabilize the loop against loosening. In addition, residues at N-terminal of α5 define a rigid turning to impede α5 from sliding out of the loop. Site mutations are designed to specifically eliminate these barriers, and easier knot untying is achieved under the same denaturing conditions. These results provide new molecular level insights into the folding/unfolding of knotted proteins.
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Affiliation(s)
- Yan Xu
- College of Electronic Engineering and Automation, Shandong University of Science and Technology, Qingdao 266590, China;
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Runshan Kang
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Luyao Ren
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Lin Yang
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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3
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Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. J Mol Model 2021; 27:261. [PMID: 34432183 DOI: 10.1007/s00894-021-04882-2] [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: 01/25/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.
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Affiliation(s)
- Armen H Poghosyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia.
| | - Aram A Shahinyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia
| | - Gayane R Kirakosyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | - Naira M Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | | | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
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4
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Zegarra FC, Homouz D, Wittung-Stafshede P, Cheung MS. The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico. J Phys Chem B 2021; 125:3501-3509. [PMID: 33818090 DOI: 10.1021/acs.jpcb.1c00219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the role of a zero-order loop in the folding process of a protein, here we used coarse-grained molecular dynamics (CGMD) simulations in silico to compare two variants of apoazurin: one named "loop" which contained the disulfide, and another named "open" in which the disulfide bond between residues 3 and 26 was removed. CGMD simulations were performed to probe the stability and unfolding pathway of the two apoazurin variants at different urea concentrations and temperatures. Our results show that the covalent loop plays a prominent role in the unfolding mechanism of apoazurin; its removal alters both the folding-transition state and the unfolded-state ensemble of conformations. We propose that modulation of azurin's folding landscape by the disulfide bridge may be related to both copper capturing and redox sensing.
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Affiliation(s)
- Fabio C Zegarra
- Laboratorio de Sistemas Inteligentes, EPIME, Universidad Nacional Tecnológica de Lima Sur (UNTELS), Lima 15834, Peru.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, 127788 United Arab Emirates.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Margaret S Cheung
- Pacific Northwest National Laboratory, Research Science Center, Seattle, Washington 98109, United States.,Department of Physics, University of Washington, Seattle, Washington 98195, United States.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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5
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Xu Y, Li S, Yan Z, Ge B, Huang F, Yue T. Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations. J Phys Chem Lett 2019; 10:5815-5822. [PMID: 31525988 DOI: 10.1021/acs.jpclett.9b02209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1-α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure-function relationship of dimerization in knotted proteins.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
- College of Electronic Engineering and Automation , Shandong University of Science and Technology , Qingdao 266590 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
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6
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Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder. Biomolecules 2019; 9:biom9090477. [PMID: 31547256 PMCID: PMC6769620 DOI: 10.3390/biom9090477] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.
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7
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Narayan A, Bhattacharjee K, Naganathan AN. Thermally versus Chemically Denatured Protein States. Biochemistry 2019; 58:2519-2523. [PMID: 31083972 DOI: 10.1021/acs.biochem.9b00089] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein unfolding thermodynamic parameters are conventionally extracted from equilibrium thermal and chemical denaturation experiments. Despite decades of work, the degree of structure and the compactness of denatured states populated in these experiments are still open questions. Here, building on previous works, we show that thermally and chemically denatured protein states are distinct from the viewpoint of far-ultraviolet circular dichroism experiments that report on the local conformational status of peptide bonds. The differences identified are independent of protein length, structural class, or experimental conditions, highlighting the presence of two sub-ensembles within the denatured states. The sub-ensembles, UT and UD for thermally induced and denaturant-induced unfolded states, respectively, can exclusively exchange populations as a function of temperature at high chemical denaturant concentrations. Empirical analysis suggests that chemically denatured states are ∼50% more expanded than the thermally denatured chains of the same protein. Our observations hint that the strength of protein backbone-backbone interactions and identity versus backbone-solvent/co-solvent interactions determine the conformational distributions. We discuss the implications for protein folding mechanisms, the heterogeneity in relaxation rates, and folding diffusion coefficients.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Kabita Bhattacharjee
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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8
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Zegarra FC, Homouz D, Gasic AG, Babel L, Kovermann M, Wittung-Stafshede P, Cheung MS. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico. J Phys Chem B 2019; 123:3607-3617. [PMID: 30963769 DOI: 10.1021/acs.jpcb.9b00782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
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Affiliation(s)
- Fabio C Zegarra
- Department of Physics , University of Houston , Houston 77204 , United States
| | - Dirar Homouz
- Department of Physics , University of Houston , Houston 77204 , United States.,Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Andrei G Gasic
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Lucas Babel
- Department of Physics , University of Houston , Houston 77204 , United States
| | | | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
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9
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Xu Y, Li S, Yan Z, Luo Z, Ren H, Ge B, Huang F, Yue T. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations. Biophys J 2018; 115:1681-1689. [PMID: 30314655 PMCID: PMC6225051 DOI: 10.1016/j.bpj.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/11/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022] Open
Abstract
A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot. One protein is YbeA from Escherichia coli, containing a deep trefoil knot within the sequence, and the other is the modified protein with the knot of YbeA being removed. Under certain chemical denaturing conditions, the unknotted protein fully unfolds whereas the knotted protein does not, suggesting a higher intrinsic stability for the protein having a knot. Both proteins unfold under enhanced thermal fluctuations but at different rates and with distinct pathways. Opening the hydrophobic core via separation between two α-helices is identified as a crucial step initiating the protein unfolding, which, however, is restrained for the knotted protein by topological and geometrical frustrations. Energy barriers for denaturing the protein are reduced by removing the knot, as evidenced by mechanical unfolding simulations. Finally, yet importantly, no obvious change in size or location of the knot was observed during denaturing processes, indicating that YbeA may remain knotted for a relatively long time during and after denaturation.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Shixin Li
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zengshuai Yan
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zhen Luo
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Hao Ren
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China; Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China.
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10
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Mohan V, Sengupta B, Acharyya A, Yadav R, Das N, Sen P. Region-Specific Double Denaturation of Human Serum Albumin: Combined Effects of Temperature and GnHCl on Structural and Dynamical Responses. ACS OMEGA 2018; 3:10406-10417. [PMID: 31459168 PMCID: PMC6645044 DOI: 10.1021/acsomega.8b00967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/08/2018] [Indexed: 05/30/2023]
Abstract
In this work, we have investigated the effects of denaturing agents, guanidine hydrochloride (GnHCl) and temperature, on the overall structure, domain-I, and domain-III of human serum albumin (HSA) using circular dichroism (CD) spectroscopy and steady-state, time-resolved fluorescence spectroscopy. We have tagged Cys-34 of HSA, located at domain-I, using N-(7-dimethylamino-4-methylcoumarin-3-yl)iodoacetamide and Tyr-411 of HSA, located at domain-III, using p-nitrophenyl coumarin ester, for this purpose. The CD spectroscopy studies reveal the overall denaturation of the protein. The denaturation follows the expected direction in which the protein is denatured with an increase in the concentration of GnHCl or temperature. The α-helicity of the native state of HSA was found to be 64.2%, and the minimum value of α-helicity was found to be 14.8% in the presence of 6 M GnHCl at room temperature. Steady-state emission studies were carried out on domain-I and domain-III of the protein using site-specific fluorescent tags. The degree of folding of the two domains at different combinations of temperature and GnHCl concentration was calculated and was found to follow a slightly different course of denaturation. Solvation dynamics was found to be quite different for these two domains. The domain-I of HSA has a maximum solvation time of 0.39 ns, and the solvation time tends to decrease with the action of either temperature or GnHCl. On the other hand, the domain-III of HSA showed a much higher solvation time (1.42 ns) and does not show any regular change at higher temperatures or in the presence of GnHCl. This difference could be attributed to the different microenvironment inside the protein cores of the two domains.
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11
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Cheung MS, Gasic AG. Towards developing principles of protein folding and dynamics in the cell. Phys Biol 2018; 15:063001. [PMID: 29939151 DOI: 10.1088/1478-3975/aaced2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Proteins must fold and function in the immensely complex environment of a cell, i.e. the cytoplasm-this is far from the ideal test-tube setting of a dilute solution. Here we review the advances in protein folding and dynamics inside the cell. In developing principles of protein behavior in vivo, we also begin to understand the organization and dynamics of the cytoplasm, unifying the single protein scale with the many-protein architectures at the subcellular scale. Our group has significantly contributed to this frontier by characterizing the effect of macromolecular crowding on the distribution of protein conformations. Additionally, we provide a personal perspective on becoming a theoretical biological physicist in the era of interdisciplinary research that has been greatly influenced by Dr Kamal Shukla. We also share our view on the future direction of protein folding inside a cell.
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Affiliation(s)
- Margaret S Cheung
- Department of Physics, University of Houston, United States of America. Center for Theoretical Biological Physics, Rice University, United States of America. Author to whom any correspondence should be addressed
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12
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Zhu R, Zhou S, Peng W, Huang Y, Mirzaei P, Donohoo K, Mechref Y. Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent. J Proteome Res 2018; 17:2668-2678. [PMID: 29745666 DOI: 10.1021/acs.jproteome.8b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is a common protein post-translational modification (PTM) in living organisms and has been shown to associate with multiple diseases, and thus may potentially be a biomarker of such diseases. Efficient protein/glycoprotein extraction is a crucial step in the preparation of N-glycans derived from glycoproteins prior to LC-MS analysis. Convenient, efficient and unbiased sample preparation protocols are needed. Herein, we evaluated the use of sodium deoxycholate (SDC) acidic labile detergent to release N-glycans of glycoproteins derived from biological samples such as cancer cell lines. Compared to the filter-aided sample preparation approach, the sodium deoxycholate (SDC) assisted approach was determined to be more efficient and unbiased. SDC removal was determined to be more efficient when using acidic precipitation rather than ethyl acetate phase transfer. Efficient extraction of proteins/glycoproteins from biological samples was achieved by combining SDC lysis buffer and beads beating cell disruption. This was suggested by a significant overall increase in the intensities of N-glycans released from cancer cell lines. Additionally, the use of SDC approach was also shown to be more reproducible than those methods that do not use SDC.
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Affiliation(s)
- Rui Zhu
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
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13
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Shirke AN, White C, Englaender JA, Zwarycz A, Butterfoss GL, Linhardt RJ, Gross RA. Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis. Biochemistry 2018; 57:1190-1200. [PMID: 29328676 DOI: 10.1021/acs.biochem.7b01189] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cutinases are polyester hydrolases that show a remarkable capability to hydrolyze polyethylene terephthalate (PET) to its monomeric units. This revelation has stimulated research aimed at developing sustainable and green cutinase-catalyzed PET recycling methods. Leaf and branch compost cutinase (LCC) is particularly suited toward these ends given its relatively high PET hydrolysis activity and thermostability. Any practical enzymatic PET recycling application will require that the protein have kinetic stability at or above the PET glass transition temperature (Tg, i.e., 70 °C). This paper elucidates the thermodynamics and kinetics of LCC conformational and colloidal stability. Aggregation emerged as a major contributor that reduces LCC kinetic stability. In its native state, LCC is prone to aggregation owing to electrostatic interactions. Further, with increasing temperature, perturbation of LCC's tertiary structure and corresponding exposure of hydrophobic domains leads to rapid aggregation. Glycosylation was employed in an attempt to impede LCC aggregation. Owing to the presence of three putative N-glycosylation sites, expression of native LCC in Pichia pastoris resulted in the production of glycosylated LCC (LCC-G). LCC-G showed improved stability to native state aggregation while increasing the temperature for thermal induced aggregation by 10 °C. Furthermore, stabilization against thermal aggregation resulted in improved catalytic PET hydrolysis both at its optimum temperature and concentration.
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Affiliation(s)
- Abhijit N Shirke
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Christine White
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jacob A Englaender
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Allison Zwarycz
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi , Abu Dhabi, UAE
| | - Robert J Linhardt
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Richard A Gross
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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14
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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15
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Schroeder F, McIntosh AL, Martin GG, Huang H, Landrock D, Chung S, Landrock KK, Dangott LJ, Li S, Kaczocha M, Murphy EJ, Atshaves BP, Kier AB. Fatty Acid Binding Protein-1 (FABP1) and the Human FABP1 T94A Variant: Roles in the Endocannabinoid System and Dyslipidemias. Lipids 2016; 51:655-76. [PMID: 27117865 PMCID: PMC5408584 DOI: 10.1007/s11745-016-4155-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/11/2016] [Indexed: 01/01/2023]
Abstract
The first discovered member of the mammalian FABP family, liver fatty acid binding protein (FABP1, L-FABP), occurs at high cytosolic concentration in liver, intestine, and in the case of humans also in kidney. While the rat FABP1 is well studied, the extent these findings translate to human FABP1 is not clear-especially in view of recent studies showing that endocannabinoids and cannabinoids represent novel rat FABP1 ligands and FABP1 gene ablation impacts the hepatic endocannabinoid system, known to be involved in non-alcoholic fatty liver (NAFLD) development. Although not detectable in brain, FABP1 ablation nevertheless also impacts brain endocannabinoids. Despite overall tertiary structure similarity, human FABP1 differs significantly from rat FABP1 in secondary structure, much larger ligand binding cavity, and affinities/specificities for some ligands. Moreover, while both mouse and human FABP1 mediate ligand induction of peroxisome proliferator activated receptor-α (PPARα), they differ markedly in pattern of genes induced. This is critically important because a highly prevalent human single nucleotide polymorphism (SNP) (26-38 % minor allele frequency and 8.3 ± 1.9 % homozygous) results in a FABP1 T94A substitution that further accentuates these species differences. The human FABP1 T94A variant is associated with altered body mass index (BMI), clinical dyslipidemias (elevated plasma triglycerides and LDL cholesterol), atherothrombotic cerebral infarction, and non-alcoholic fatty liver disease (NAFLD). Resolving human FABP1 and the T94A variant's impact on the endocannabinoid and cannabinoid system is an exciting challenge due to the importance of this system in hepatic lipid accumulation as well as behavior, pain, inflammation, and satiety.
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Affiliation(s)
- Friedhelm Schroeder
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA.
| | - Avery L McIntosh
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Gregory G Martin
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Huan Huang
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Danilo Landrock
- Department of Pathobiology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Sarah Chung
- Department of Pathobiology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Kerstin K Landrock
- Department of Pathobiology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Lawrence J Dangott
- Department of Biochemistry and Biophysics, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
| | - Shengrong Li
- Avanti Polar Lipids, 700 Industrial Park Dr., Alabaster, AL, 35007-9105, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Eric J Murphy
- Department of Pharmacology, Physiology, and Therapeutics and Chemistry, University of North Dakota, Grand Forks, ND, 58202-9037, USA
| | - Barbara P Atshaves
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ann B Kier
- Department of Pathobiology, Texas A&M University, TVMC, College Station, TX, 77843-4466, USA
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16
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Shahid S, Ahmad F, Hassan MI, Islam A. Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture: An insight into stability-activity trade-off. Arch Biochem Biophys 2015; 584:42-50. [PMID: 26325080 DOI: 10.1016/j.abb.2015.08.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/19/2015] [Accepted: 08/23/2015] [Indexed: 12/25/2022]
Abstract
The cellular environment is crowded with different kinds of molecules with varying sizes, shapes and compositions. Most of the experiments studying the nature and behaviour of a protein have been done on the isolated protein in dilute buffer solutions which actually do not imitate the in vivo situation. To understand the consequences of such crowded environment, we investigated the effect of macromolecular crowding on the stability and activity of hen egg white lysozyme. Two crowding agents, dextran 70 and ficoll 70 which have different shapes and composition, have been employed in this study. To mimic the cellular condition from physiological point of view, the effect of mixtures of both the crowding agents has been also studied. The results indicate that owing to volume exclusion, lysozyme is stabilized while its activity decays with the increasing concentration of both the crowders elucidating the hypothesis of stability-activity trade-off. Mixed macromolecular crowding exerts greater effect than the sum of constituent crowding agents (dextran 70 and ficoll 70).
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Affiliation(s)
- Sumra Shahid
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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17
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Huang H, McIntosh AL, Martin GG, Landrock KK, Landrock D, Gupta S, Atshaves BP, Kier AB, Schroeder F. Structural and functional interaction of fatty acids with human liver fatty acid-binding protein (L-FABP) T94A variant. FEBS J 2014; 281:2266-83. [PMID: 24628888 DOI: 10.1111/febs.12780] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/17/2014] [Accepted: 03/11/2014] [Indexed: 12/13/2022]
Abstract
The human liver fatty acid-binding protein (L-FABP) T94A variant, the most common in the FABP family, has been associated with elevated liver triglyceride levels. How this amino acid substitution elicits these effects is not known. This issue was addressed using human recombinant wild-type (WT) and T94A variant L-FABP proteins as well as cultured primary human hepatocytes expressing the respective proteins (genotyped as TT, TC and CC). The T94A substitution did not alter or only slightly altered L-FABP binding affinities for saturated, monounsaturated or polyunsaturated long chain fatty acids, nor did it change the affinity for intermediates of triglyceride synthesis. Nevertheless, the T94A substitution markedly altered the secondary structural response of L-FABP induced by binding long chain fatty acids or intermediates of triglyceride synthesis. Finally, the T94A substitution markedly decreased the levels of induction of peroxisome proliferator-activated receptor α-regulated proteins such as L-FABP, fatty acid transport protein 5 and peroxisome proliferator-activated receptor α itself meditated by the polyunsaturated fatty acids eicosapentaenoic acid and docosahexaenoic acid in cultured primary human hepatocytes. Thus, although the T94A substitution did not alter the affinity of human L-FABP for long chain fatty acids, it significantly altered human L-FABP structure and stability, as well as the conformational and functional response to these ligands.
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Affiliation(s)
- Huan Huang
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX, USA
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18
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Boone CD, Habibzadegan A, Tu C, Silverman DN, McKenna R. Structural and catalytic characterization of a thermally stable and acid-stable variant of human carbonic anhydrase II containing an engineered disulfide bond. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1414-22. [PMID: 23897465 PMCID: PMC3727326 DOI: 10.1107/s0907444913008743] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/30/2013] [Indexed: 11/10/2022]
Abstract
The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration of CO2 to bicarbonate and a proton. Recently, there has been industrial interest in utilizing CAs as biocatalysts for carbon sequestration and biofuel production. The conditions used in these processes, however, result in high temperatures and acidic pH. This unfavorable environment results in rapid destabilization and loss of catalytic activity in CAs, ultimately resulting in cost-inefficient high-maintenance operation of the system. In order to negate these detrimental industrial conditions, cysteines at residues 23 (Ala23Cys) and 203 (Leu203Cys) were engineered into a wild-type variant of human CA II (HCAII) containing the mutation Cys206Ser. The X-ray crystallographic structure of the disulfide-containing HCAII (dsHCAII) was solved to 1.77 Å resolution and revealed that successful oxidation of the cysteine bond was achieved while also retaining desirable active-site geometry. Kinetic studies utilizing the measurement of (18)O-labeled CO2 by mass spectrometry revealed that dsHCAII retained high catalytic efficiency, and differential scanning calorimetry showed acid stability and thermal stability that was enhanced by up to 14 K compared with native HCAII. Together, these studies have shown that dsHCAII has properties that could be used in an industrial setting to help to lower costs and improve the overall reaction efficiency.
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Affiliation(s)
- Christopher D. Boone
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
| | - Andrew Habibzadegan
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
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19
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Dynamics and unfolding pathway of chimeric azurin variants: insights from molecular dynamics simulation. J Biol Inorg Chem 2013; 18:739-49. [DOI: 10.1007/s00775-013-1017-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/22/2013] [Indexed: 10/26/2022]
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20
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Larini L, Shea JE. Double Resolution Model for Studying TMAO/Water Effective Interactions. J Phys Chem B 2013; 117:13268-77. [DOI: 10.1021/jp403635g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Larini
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
| | - Joan-Emma Shea
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
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21
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Where soft matter meets living matter--protein structure, stability, and folding in the cell. Curr Opin Struct Biol 2013; 23:212-7. [PMID: 23474325 DOI: 10.1016/j.sbi.2013.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/08/2013] [Accepted: 02/13/2013] [Indexed: 01/06/2023]
Abstract
A protein is a biopolymer that self-assembles through the process of protein folding. A cell is a crowded space where the surrounding macromolecules of a protein can limit the number of ways of folding. These crowding macromolecules can also affect the shape and the size of a physically malleable, or 'soft, squishy', protein with regulatory purposes. In this review, we focus on the in silico approaches of coarse-grained molecular simulations that enable the investigation of protein folding in a cell-like environment. When these simulation results were compared with experimentally measured properties of a protein, such joint effort has yielded new ideas on the specific function of a protein in cells. We also highlighted the recent developments of computer modeling and simulations that encompass the importance of the shape of a macromolecule, the interactions between macromolecules, and the hydrodynamic interactions on the kinetics and thermodynamics of a protein in a high concentration of protein solution and in cytoplasmic environments.
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22
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Aggarwal M, Boone CD, Kondeti B, McKenna R. Structural annotation of human carbonic anhydrases. J Enzyme Inhib Med Chem 2012; 28:267-77. [DOI: 10.3109/14756366.2012.737323] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Mayank Aggarwal
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida,
Gainesville, FL, USA
| | - Christopher D. Boone
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida,
Gainesville, FL, USA
| | - Bhargav Kondeti
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida,
Gainesville, FL, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida,
Gainesville, FL, USA
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23
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Fisher Z, Boone CD, Biswas SM, Venkatakrishnan B, Aggarwal M, Tu C, Agbandje-McKenna M, Silverman D, McKenna R. Kinetic and structural characterization of thermostabilized mutants of human carbonic anhydrase II. Protein Eng Des Sel 2012; 25:347-55. [PMID: 22691706 DOI: 10.1093/protein/gzs027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous enzymes that catalyze the reversible hydration/dehydration of carbon dioxide/bicarbonate. As such, there is enormous industrial interest in using CA as a bio-catalyst for carbon sequestration and biofuel production. However, to ensure cost-effective use of the enzyme under harsh industrial conditions, studies were initiated to produce variants with enhanced thermostability while retaining high solubility and catalytic activity. Kinetic and structural studies were conducted to determine the structural and functional effects of these mutations. X-ray crystallography revealed that a gain in surface hydrogen bonding contributes to stability while retaining proper active site geometry and electrostatics to sustain catalytic efficiency. The kinetic profiles determined under a variety of conditions show that the surface mutations did not negatively impact the carbon dioxide hydration or proton transfer activity of the enzyme. Together these results show that it is possible to enhance the thermal stability of human carbonic anhydrase II by specific replacements of surface hydrophobic residues of the enzyme. In addition, combining these stabilizing mutations with strategic active site changes have resulted in thermostable mutants with desirable kinetic properties.
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Affiliation(s)
- Zoë Fisher
- Bioscience Division, TA-53 Bldg 622, Mailstop H805, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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24
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Samiotakis A, Cheung MS. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. J Chem Phys 2012; 135:175101. [PMID: 22070323 DOI: 10.1063/1.3656691] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.
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