1
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Helmick H, Tonner T, Hauersperger D, Okos M, Kokini JL. Comparison of the specific mechanical energy, specific thermal energy, and functional properties of cold and hot extruded pea protein isolate. Food Res Int 2023; 174:113603. [PMID: 37986466 DOI: 10.1016/j.foodres.2023.113603] [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: 08/09/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/22/2023]
Abstract
Pea protein is a popular source of plant-based protein, though its application in meat and dairy analog products is still lacking. This is particularly true in the development of products with fatty and creamy textures. Cold denaturation may be a way to induce these types of textures in food since this is a universal phenomenon in protein that occurs due to a weakening of hydrophobic interactions at cold temperatures. This work utilizes a single screw extruder to systematically study the impacts of moisture content (50-65 %) and pH (2,4.5,8) on the outlet temperatures, specific mechanical energy, specific thermal energy, and texture of cold-extruded pea protein. It was found that at pH 2 and moistures of 60 % and greater, the temperature of the product exiting the extruder is <5.5 °C, and also produced 13.7 %-36.5 % more specific thermal energy, indicating the occurrence of cold denaturation in these products. Based on these findings, a comparison of hot and cold extrusion was conducted as a function of pH and oil content. It was found that cold extrusion imparts 43.0 %-56.2 % more mechanical energy into the protein than hot extrusion, and the cold extruded protein had higher values of Young's modulus and breaking stress. The protein extruded at low temperatures was also able to bind 32.93 % more oil than hot extruded proteins when extruded with 10 % added oil, which may aid in the formation of protein-based fat memetics for the food industry.
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Affiliation(s)
- Harrison Helmick
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN 47907, United States
| | - Troy Tonner
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Daniel Hauersperger
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Martin Okos
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907, United States
| | - Jozef L Kokini
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN 47907, United States.
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2
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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3
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Engstler J, Giovambattista N. Different Temperature- and Pressure-Effects on the Water-Mediated Interactions between Hydrophobic, Hydrophilic, and Hydrophobic-Hydrophilic Nanoscale Surfaces. J Chem Phys 2022; 157:064701. [DOI: 10.1063/5.0097908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water-mediated interactions (WMI) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic-hydrophilic) interactions have been mostly overlooked. Here we study the role of T and P of the WMI between nanoscale (i) hydrophobic-hydrophobic, (ii) hydrophilic-hydrophilic, and (iii) hydrophilic-hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic and hybrid interactions are all sensitive to P. However, while hydrophobic interactions [case (i)] are sensitive to T-variations, hydrophilic [case (ii)] and hybrid interactions [case (iii)] are practically T-independent. An analysis of the entropic and enthalpic contributions to the PMF for cases (i)-(iii) is also presented. Our results are important in understanding T- and P-induced protein denaturation, and the interactions of biomolecules in solution, including protein aggregation andphase separation processes. From the computational point of view, the results presented here are relevant in the design of implicit water models for the study of molecular and colloidal/nanoparticle systems at different thermodynamic conditions.
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4
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Khuri RR, Phan TV, Austin RH. Protein dynamics implications of the low- and high-temperature denaturation of myoglobin. Phys Rev E 2021; 104:034414. [PMID: 34654144 DOI: 10.1103/physreve.104.034414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 08/19/2021] [Indexed: 11/07/2022]
Abstract
We reinvestigate a simple model used in the literature concerning the thermodynamic analysis of protein cold denaturation. We derive an exact thermodynamic expression for cold denaturation and give a better approximation than exists in the literature for predicting cold denaturation temperatures in the two-state model. We discuss the "dark-side" implications of this work for previous temperature-dependent protein dynamics experiments and discuss microfluidic experimental technologies, which could explore the thermal stability range of proteins below the bulk freezing point of water.
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Affiliation(s)
- Ramzi R Khuri
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York 10010, USA
| | - Trung V Phan
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
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5
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Parui S, Jana B. Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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Arsiccio A, Shea JE. Pressure Unfolding of Proteins: New Insights into the Role of Bound Water. J Phys Chem B 2021; 125:8431-8442. [PMID: 34310136 DOI: 10.1021/acs.jpcb.1c04398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
High pressures can be detrimental for protein stability, resulting in unfolding and loss of function. This phenomenon occurs because the unfolding transition is accompanied by a decrease in volume, which is typically attributed to the elimination of cavities that are present within the native state as a result of packing defects. We present a novel computational approach that enables the study of pressure unfolding in atomistically detailed protein models in implicit solvent. We include the effect of pressure using a transfer free energy term that allows us to decouple the effect of protein residues and bound water molecules on the volume change upon unfolding. We discuss molecular dynamics simulations results using this protocol for two model proteins, Trp-cage and staphylococcal nuclease (SNase). We find that the volume reduction of bound water is the key energetic term that drives protein denaturation under the effect of pressure, for both Trp-cage and SNase. However, we note differences in unfolding mechanisms between the smaller Trp-cage and the larger SNase protein. Indeed, the unfolding of SNase, but not Trp-cage, is seen to be further accompanied by a reduction in the volume of internal cavities. Our results indicate that, for small peptides, like Trp-cage, pressure denaturation is driven by the increase in solvent accessibility upon unfolding, and the subsequent increase in the number of bound water molecules. For larger proteins, like SNase, the cavities within the native fold act as weak spots, determining the overall resistance to pressure denaturation. Our simulations display a striking agreement with the pressure-unfolding profile experimentally obtained for SNase and represent a promising approach for a computationally efficient and accurate exploration of pressure-induced denaturation of proteins.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, California 93106, United States
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7
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Arsiccio A, Shea JE. Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. J Phys Chem B 2021; 125:5222-5232. [DOI: 10.1021/acs.jpcb.1c01694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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8
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The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Comput Biol 2020; 16:e1007767. [PMID: 32365068 PMCID: PMC7282669 DOI: 10.1371/journal.pcbi.1007767] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 03/02/2020] [Indexed: 11/19/2022] Open
Abstract
Many proteins have the potential to aggregate into amyloid fibrils, protein polymers associated with a wide range of human disorders such as Alzheimer’s and Parkinson’s disease. The thermodynamic stability of amyloid fibrils, in contrast to that of folded proteins, is not well understood: the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using a combination of theory, in vitro experiments, simulations of a coarse-grained protein model and meta-data analysis, we delineate the enthalpic and entropic contributions that dominate amyloid fibril elongation. Our prediction of a characteristic temperature-dependent enthalpic signature is confirmed by the performed calorimetric experiments and a meta-analysis over published data. From these results we are able to define the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability. Most proteins fold in the cell into stable, compact structures. Nevertheless, many proteins also have the ability to stick together, forming long fibrillar structures that are associated with a wide range of human disorders including Alzheimer’s and Parkinson’s disease. The exact nature of the amyloid-causing stickiness is not well understood, nevertheless amyloid fibrils show some very specific thermodynamic characteristics. Some fibrils even destabilise at low temperatures. In this work we translate hydrophobic theory previously used to model protein folding to fibril formation. We combine this theory with experimental measurements, simulations and meta-data analysis of different types of fibrils. This allowed us to unravel the nature of the stickiness in amyloid fibrils by observing the effect of temperature changes, specifically at low temperatures, on hydrophobicity.
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9
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Gasic AG, Cheung MS. A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure. J Phys Chem B 2020; 124:1619-1627. [DOI: 10.1021/acs.jpcb.9b10734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrei G. Gasic
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S. Cheung
- 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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10
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Gasic AG, Boob MM, Prigozhin MB, Homouz D, Wirth AJ, Daugherty CM, Gruebele M, Cheung MS. Critical phenomena in the temperature-pressure-crowding phase diagram of a protein. PHYSICAL REVIEW. X 2019; 9:041035. [PMID: 32642303 PMCID: PMC7343146 DOI: 10.1103/physrevx.9.041035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural integrity. These apparently conflicting behaviors are exhibited by systems near a critical point, where distinct phases merge-a concept beyond previous studies indicating proteins have a well-defined folded/unfolded phase boundary in the pressure-temperature plane. Here, by modeling the protein phosphoglycerate kinase (PGK) on the temperature (T), pressure (P), and crowding volume-fraction (ϕ) phase diagram, we demonstrate a critical transition where phases merge, and PGK exhibits large structural fluctuations. Above the critical point, the difference between the intermediate and unfolded phases disappears. When ϕ increases, the critical point moves to lower T c. We verify the calculations with experiments mapping the T-P-ϕ space, which likewise reveal a critical point at 305 K and 170 MPa that moves to lower T c as ϕ increases. Crowding places PGK near a critical line in its natural parameter space, where large conformational changes can occur without costly free energy barriers. Specific structures are proposed for each phase based on simulation.
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Affiliation(s)
- Andrei G. Gasic
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
| | - Mayank M. Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Maxim B. Prigozhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Dirar Homouz
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
- Khalifa University of Science and Technology, Department of Physics, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Anna Jean Wirth
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Caleb M. Daugherty
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Margaret S. Cheung
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
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11
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Hata H, Nishiyama M, Kitao A. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129395. [PMID: 31302180 DOI: 10.1016/j.bbagen.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan.
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12
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Engstler J, Giovambattista N. Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes. J Phys Chem B 2019; 123:1116-1128. [PMID: 30592598 DOI: 10.1021/acs.jpcb.8b10296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.
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Affiliation(s)
- Justin Engstler
- Department of Physics , Brooklyn College of the City University of New York , Brooklyn , New York 11210 , United States
| | - Nicolas Giovambattista
- Department of Physics , Brooklyn College of the City University of New York , Brooklyn , New York 11210 , United States.,Ph.D. Programs in Chemistry and Physics , The Graduate Center of the City University of New York , New York , New York 10016 , United States
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13
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Schneider S, Paulsen H, Reiter KC, Hinze E, Schiene-Fischer C, Hübner CG. Single molecule FRET investigation of pressure-driven unfolding of cold shock protein A. J Chem Phys 2018; 148:123336. [DOI: 10.1063/1.5009662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sven Schneider
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Hauke Paulsen
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Kim Colin Reiter
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Erik Hinze
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Halle/Saale D-06120, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale D-06120, Germany
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14
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Zheng W, Tsai MY, Wolynes PG. Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40). J Am Chem Soc 2017; 139:16666-16676. [PMID: 29057654 PMCID: PMC5805378 DOI: 10.1021/jacs.7b08089] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Using a predictive coarse-grained protein force field, we compute and compare the free energy landscapes and relative stabilities of amyloid-β protein (1-42) and amyloid-β protein (1-40) in their monomeric and oligomeric forms up to the octamer. At the same concentration, the aggregation free energy profile of Aβ42 is more downhill, with a computed solubility that is about 10 times smaller than that of Aβ40. At a concentration of 40 μM, the clear free energy barrier between the pre-fibrillar tetramer form and the fibrillar pentamer in the Aβ40 aggregation landscape disappears for Aβ42, suggesting that the Aβ42 tetramer has a more diverse structural range. To further compare the landscapes, we develop a cluster analysis based on the structural similarity between configurations and use it to construct an oligomerization map that captures the paths of easy interconversion between different but structurally similar states of oligomers for both species. A taxonomy of the oligomer species based on β-sheet stacking topologies is proposed. The comparison of the two oligomerization maps highlights several key differences in the landscapes that can be attributed to the two additional C-terminal residues that Aβ40 lacks. In general, the two terminal residues strongly stabilize the oligomeric structures for Aβ42 relative to Aβ40, and greatly facilitate the conversion from pre-fibrillar trimers to fibrillar tetramers.
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Affiliation(s)
- Weihua Zheng
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Min-Yeh Tsai
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Peter G. Wolynes
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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15
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Reddy G, Thirumalai D. Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. J Phys Chem B 2017; 121:995-1009. [DOI: 10.1021/acs.jpcb.6b13100] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Govardhan Reddy
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - D. Thirumalai
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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16
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Pucci F, Rooman M. Improved insights into protein thermal stability: from the molecular to the structurome scale. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0141. [PMID: 27698032 PMCID: PMC5052726 DOI: 10.1098/rsta.2016.0141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/09/2016] [Indexed: 05/18/2023]
Abstract
Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability-at the structurome level-contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Fabrizio Pucci
- Department of BioModeling, BioInformatics and BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Avenue 50, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Boulevard, 1050 Brussels, Belgium
| | - Marianne Rooman
- Department of BioModeling, BioInformatics and BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Avenue 50, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Boulevard, 1050 Brussels, Belgium
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17
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Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. J Phys Chem B 2016; 121:3473-3482. [PMID: 27797194 DOI: 10.1021/acs.jpcb.6b09347] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For α helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of α/β proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure prediction and makes the free energy profile more funneled toward native configurations. We explore the use of clustering analyses as a way of evaluating the confidence in various structure prediction models. Clustering using a local relative order parameter (mutual Q) of the predicted structural ensemble turns out to be optimal. The tightest cluster according to mutual Q generally has the most correctly folded structure. Since there is no bioinformatic input, AAWSEM amounts to an ab initio protein structure prediction method that combines the efficiency of coarse-grained simulations with the local structural accuracy that can be achieved from all-atom simulations.
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Affiliation(s)
- Mingchen Chen
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Bioengineering, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Xingcheng Lin
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Chemistry, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Biosciences, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Chemistry, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Biosciences, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
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18
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Krobath H, Chen T, Chan HS. Volumetric Physics of Polypeptide Coil–Helix Transitions. Biochemistry 2016; 55:6269-6281. [DOI: 10.1021/acs.biochem.6b00802] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Heinrich Krobath
- Departments of Biochemistry
and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tao Chen
- Departments of Biochemistry
and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Departments of Biochemistry
and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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19
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Kim SB, Palmer JC, Debenedetti PG. Computational investigation of cold denaturation in the Trp-cage miniprotein. Proc Natl Acad Sci U S A 2016; 113:8991-6. [PMID: 27457961 PMCID: PMC4987839 DOI: 10.1073/pnas.1607500113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544;
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20
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Camilloni C, Bonetti D, Morrone A, Giri R, Dobson CM, Brunori M, Gianni S, Vendruscolo M. Towards a structural biology of the hydrophobic effect in protein folding. Sci Rep 2016; 6:28285. [PMID: 27461719 PMCID: PMC4962056 DOI: 10.1038/srep28285] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/03/2016] [Indexed: 11/09/2022] Open
Abstract
The hydrophobic effect is a major driving force in protein folding. A complete understanding of this effect requires the description of the conformational states of water and protein molecules at different temperatures. Towards this goal, we characterise the cold and hot denatured states of a protein by modelling NMR chemical shifts using restrained molecular dynamics simulations. A detailed analysis of the resulting structures reveals that water molecules in the bulk and at the protein interface form on average the same number of hydrogen bonds. Thus, even if proteins are 'large' particles (in terms of the hydrophobic effect, i.e. larger than 1 nm), because of the presence of complex surface patterns of polar and non-polar residues their behaviour can be compared to that of 'small' particles (i.e. smaller than 1 nm). We thus find that the hot denatured state is more compact and richer in secondary structure than the cold denatured state, since water at lower temperatures can form more hydrogen bonds than at high temperatures. Then, using Φ-value analysis we show that the structural differences between the hot and cold denatured states result in two alternative folding mechanisms. These findings thus illustrate how the analysis of water-protein hydrogen bonds can reveal the molecular origins of protein behaviours associated with the hydrophobic effect.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Angela Morrone
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Rajanish Giri
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | | | - Maurizio Brunori
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
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21
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van Dijk E, Varilly P, Knowles TPJ, Frenkel D, Abeln S. Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation. PHYSICAL REVIEW LETTERS 2016; 116:078101. [PMID: 26943560 DOI: 10.1103/physrevlett.116.078101] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 05/04/2023]
Abstract
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavorable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here, we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
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Affiliation(s)
- Erik van Dijk
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
| | - Patrick Varilly
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sanne Abeln
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
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22
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Bianco V, Franzese G. Contribution of Water to Pressure and Cold Denaturation of Proteins. PHYSICAL REVIEW LETTERS 2015; 115:108101. [PMID: 26382703 DOI: 10.1103/physrevlett.115.108101] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 05/28/2023]
Abstract
The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.
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Affiliation(s)
- Valentino Bianco
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Giancarlo Franzese
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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