1
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Biswal S, Agmon N. Collagen Structured Hydration. Biomolecules 2023; 13:1744. [PMID: 38136615 PMCID: PMC10742079 DOI: 10.3390/biom13121744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer of water molecules hydrogen bonded to the backbone carbonyl (bb-CO) oxygen atoms. This originates from the following observations. The radius of gyration attests that the PPG triplets are organized along a straight line, so that all triplets (excepting the ends) are equivalent. The solvent-accessible surface area (SASA) for the bb-CO oxygens shows a repetitive regularity for every triplet. This leads to water occupancy of the bb-CO sites following a similar regularity. In the crystal-phase X-ray data, as well as in our 100 K simulations, we observe a 0-2-1 water occupancy in the P-P-G triplet. Surprisingly, a similar (0-1.7-1) regularity is maintained in the liquid phase, in spite of the sub-nsec water exchange rates, because the bb-CO sites rarely remain vacant. The manifested ordered first-shell water molecules are expected to produce a cylindrical electrostatic potential around the peptide, to be investigated in future work.
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Affiliation(s)
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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2
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Amano KI, Furukawa S, Kubo Y, Nakamura Y, Ishii R, Tanase A, Maebayashi M, Hayashi T, Nishi N, Sakka T. Nonadditivities of the Particle Sizes Hidden in Model Pair Potentials and Their Effects on Physical Adsorptions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12999-13007. [PMID: 37658821 DOI: 10.1021/acs.langmuir.3c00968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
It is important to understand the mechanism of colloidal particle assembly near a substrate for development of drug delivery systems, micro-/nanorobots, batteries, heterogeneous catalysts, paints, and cosmetics. Understanding the mechanism is also important for crystallization of the colloidal particles and proteins. In this study, we calculated the physical adsorption of colloidal particles on a flat wall mainly using the integral equation theory, wherein small and large colloidal particles were employed. In the calculation system, like-charged electric double-layer potentials were used as pair potentials. In some cases, it was found that the small particles are more easily adsorbed. This result is unusual from the viewpoint of the Asakura-Oosawa theory, and we call it a "reversal phenomenon". Theoretical analysis revealed that the reversal phenomenon originates from the nonadditivities of the particle sizes. Using the knowledge obtained from this study, we invented a method to analyze the size nonadditivity hidden in model pair potentials. The method will be useful for confirmation of various simulation results regarding the adsorption and development of force fields for colloidal particles, proteins, and solutes.
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Affiliation(s)
- Ken-Ichi Amano
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Satoshi Furukawa
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuto Kubo
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata 950-2181, Japan
| | - Yuka Nakamura
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata 950-2181, Japan
| | - Rina Ishii
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Ayane Tanase
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Masahiro Maebayashi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata 950-2181, Japan
| | - Naoya Nishi
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Tetsuo Sakka
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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3
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Arakawa T, Tomioka Y, Kurosawa Y, Akuta T. Elucidating the mechanisms of additive effects at high concentrations on hydrophobic interaction chromatography. J Chromatogr A 2023; 1702:464091. [PMID: 37269642 DOI: 10.1016/j.chroma.2023.464091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/05/2023]
Abstract
Hydrophobic interaction chromatography (HIC) is a commonly used chromatography technique for purifying proteins. It utilizes salting-out salts to facilitate the binding of native proteins to weakly hydrophobic ligands. There have been three proposed mechanisms for the promoting effects of salting-out salts, which include the dehydration of proteins by salts, cavity theory, and salt exclusion. To evaluate the above three mechanisms, an HIC study was conducted on Phenyl Sepharose using four different additives. These additives included a salting-out salt (NH4)2SO4, sodium phosphate that increases the surface tension of water, a salting-in salt MgCl2, and an amphiphilic protein-precipitant polyethylene glycol (PEG). Results indicated that the first two salts resulted in protein binding, while MgCl2 and PEG led to flow-through. These findings were then used to interpret the three proposed mechanisms, which showed that MgCl2 and PEG deviated from the dehydration mechanism, and MgCl2 also deviated from the cavity theory. The observed effects of these additives on HIC were reasonably well explained for the first time by their interactions with proteins.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
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4
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New Insight into the Effects of Various Parameters on the Crystallization of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO) from Alcaligenes eutrophus. CRYSTALS 2022. [DOI: 10.3390/cryst12020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of proteins. Many parameters influence the complexity of protein crystallization. Therefore, it is not easy to systematically examine all of these parameters individually during crystallization because of a limited quantity of purified protein. We studied several factors that influence crystallization including protein concentration, pH, temperature, age, volume of crystallization, inhibitors, metal ions, seeding, and precipitating agents on RuBisCO samples from Alcaligenes eutrophus which are not only freshly purified, but are also dissolved both individually and in combination from microcrystals and precipitated droplets of recycled RuBisCO. Single-, twin-, and/or microcrystals are dependent upon the concentration of RuBisCO by both RuBisCO samples. The morphology, either orthorhombic- or monoclinic-space group, depends upon pH. Furthermore, ammonium sulfate((NH4)2SO4) concentration at 20 °C (22% saturated) and/or at 4 °C (28% saturated) affected the crystallization of RuBisCO differently from one another. Finally, the age of RuBisCO also affected more uniformity and forming sharp edge during crystallization. Unexpected surprising monoclinic RuBisCO crystals were grown from dissolved microcrystals and precipitated droplets recycled RuBisCO samples. This quaternary RuBisCO single crystal, which contained Mg2+ and HCO3 for an activated ternary complex and is inhibited with a transition substrate analogue, CABP (2-carboxyarabinitol-1,5-bisphosphate)−, diffracts better than 2.2 Å. It is different from Hansen S. et al. reported RuBisCO crystals which were grown ab initio in absence of Mg2+, HCO3− and CABP, a structure which was determined at 2.7 Å resolution.
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5
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Cheng R, Li J, Ríos de Anda I, Taylor TWC, Faers MA, Anderson JLR, Seddon AM, Royall CP. Protein-polymer mixtures in the colloid limit: Aggregation, sedimentation, and crystallization. J Chem Phys 2021; 155:114901. [PMID: 34551522 DOI: 10.1063/5.0052122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality, the situation is rather more complex. A simple step toward higher complexity is to treat the proteins as non-spherical particles and that is the approach we pursue here. We investigate the phase behavior of the enhanced green fluorescent protein (eGFP) under the addition of a non-adsorbing polymer, polyethylene glycol. From small angle x-ray scattering, we infer that the eGFP undergoes dimerization and we treat the dimers as spherocylinders with aspect ratio L/D - 1 = 1.05. Despite the complex nature of the proteins, we find that the phase behavior is similar to that of hard spherocylinders with an ideal polymer depletant, exhibiting aggregation and, in a small region of the phase diagram, crystallization. By comparing our measurements of the onset of aggregation with predictions for hard colloids and ideal polymers [S. V. Savenko and M. Dijkstra, J. Chem. Phys. 124, 234902 (2006) and Lo Verso et al., Phys. Rev. E 73, 061407 (2006)], we find good agreement, which suggests that the behavior of the eGFP is consistent with that of hard spherocylinders and ideal polymers.
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Affiliation(s)
- Rui Cheng
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - Jingwen Li
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | | | - Thomas W C Taylor
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | | | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Annela M Seddon
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - C Patrick Royall
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
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6
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Lynch ML, Dudek MF, Bowman SE. A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. PATTERNS (NEW YORK, N.Y.) 2020; 1:100024. [PMID: 32776019 PMCID: PMC7409820 DOI: 10.1016/j.patter.2020.100024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 03/30/2020] [Indexed: 10/26/2022]
Abstract
Nearly 90% of structural models in the Protein Data Bank (PDB), the central resource worldwide for three-dimensional structural information, are currently derived from macromolecular crystallography (MX). A major bottleneck in determining MX structures is finding conditions in which a biomolecule will crystallize. Here, we present a searchable database of the chemicals associated with successful crystallization experiments from the PDB. We use these data to examine the relationship between protein secondary structure and average molecular weight of polyethylene glycol and to investigate patterns in crystallization conditions. Our analyses reveal striking patterns of both redundancy of chemical compositions in crystallization experiments and extreme sparsity of specific chemical combinations, underscoring the challenges faced in generating predictive models for de novo optimal crystallization experiments.
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Affiliation(s)
- Miranda L. Lynch
- High-Throughput Crystallization Screening Center, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Max F. Dudek
- University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sarah E.J. Bowman
- High-Throughput Crystallization Screening Center, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, NY 14203, USA
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7
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Schiefner A, Walser R, Gebauer M, Skerra A. Proline/alanine-rich sequence (PAS) polypeptides as an alternative to PEG precipitants for protein crystallization. Acta Crystallogr F Struct Biol Commun 2020; 76:320-325. [PMID: 32627748 PMCID: PMC7336357 DOI: 10.1107/s2053230x20008328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/22/2020] [Indexed: 11/11/2022] Open
Abstract
Proline/alanine-rich sequence (PAS) polypeptides represent a novel class of biosynthetic polymers comprising repetitive sequences of the small proteinogenic amino acids L-proline, L-alanine and/or L-serine. PAS polymers are strongly hydrophilic and highly soluble in water, where they exhibit a natively disordered conformation without any detectable secondary or tertiary structure, similar to polyethylene glycol (PEG), which constitutes the most widely applied precipitant for protein crystallization to date. To investigate the potential of PAS polymers for structural studies by X-ray crystallography, two proteins that were successfully crystallized using PEG in the past, hen egg-white lysozyme and the Fragaria × ananassa O-methyltransferase, were subjected to crystallization screens with a 200-residue PAS polypeptide. The PAS polymer was applied as a precipitant using a vapor-diffusion setup that allowed individual optimization of the precipitant concentration in the droplet in the reservoir. As a result, crystals of both proteins showing high diffraction quality were obtained using the PAS precipitant. The genetic definition and precise macromolecular composition of PAS polymers, both in sequence and in length, distinguish them from all natural and synthetic polymers that have been utilized for protein crystallization so far, including PEG, and facilitate their adaptation for future applications. Thus, PAS polymers offer potential as novel precipitants for biomolecular crystallography.
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Affiliation(s)
- André Schiefner
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Rebecca Walser
- XL-protein GmbH, Lise-Meitner-Strasse 30, 85354 Freising, Germany
| | - Michaela Gebauer
- XL-protein GmbH, Lise-Meitner-Strasse 30, 85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
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8
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Newman J, van Raaij MJ. Innovation versus practice in biological crystallization. Acta Crystallogr F Struct Biol Commun 2020; 76:290-291. [PMID: 32627743 PMCID: PMC7336356 DOI: 10.1107/s2053230x20008869] [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] [Indexed: 11/10/2022] Open
Abstract
Improving biological crystallization by innovation and publication.
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Affiliation(s)
- Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052 Australia
| | - Mark J. van Raaij
- Department of Molecular Structure, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, E-28049, Spain
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9
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Wilson J, Ristic M, Kirkwood J, Hargreaves D, Newman J. Predicting the Effect of Chemical Factors on the pH of Crystallization Trials. iScience 2020; 23:101219. [PMID: 32540772 PMCID: PMC7298652 DOI: 10.1016/j.isci.2020.101219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 01/13/2023] Open
Abstract
In macromolecular crystallization, success is often dependent on the pH of the experiment. However, little is known about the pH of reagents used, and it is generally assumed that the pH of the experiment will closely match that of any buffering chemical in the solution. We use a large dataset of experimentally measured solution pH values to show that this assumption can be very wrong and generate a model that can be used to successfully predict the overall solution pH of a crystallization experiment. Furthermore, we investigate the time dependence of the pH of some polyethylene glycol polymers widely used in protein crystallization under different storage conditions. The overall pH of crystallization solutions can be modeled The model was trained and tested on a set of more than 40,000 measured pH values A pH value can be assigned to a non-buffered crystallization cocktail A 12-month stability study of polyethylene glycol suggests ways to store PEGs
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Affiliation(s)
- Julie Wilson
- Department of Mathematics, University of York, York, UK.
| | - Marko Ristic
- Collaborative Crystallisation Centre, CSIRO, Parkville, VIC, Australia
| | | | - David Hargreaves
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge, UK
| | - Janet Newman
- Collaborative Crystallisation Centre, CSIRO, Parkville, VIC, Australia.
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10
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Santos RD, Iria I, Manuel AM, Leandro AP, Madeira CAC, Goncalves J, Carvalho AL, Roque ACA. Magnetic Precipitation: A New Platform for Protein Purification. Biotechnol J 2020; 15:e2000151. [PMID: 32578939 DOI: 10.1002/biot.202000151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/03/2020] [Indexed: 01/01/2023]
Abstract
One of the trends in downstream processing comprises the use of "anything-but-chromatography" methods to overcome the current downfalls of standard packed-bed chromatography. Precipitation and magnetic separation are two techniques already proven to accomplish protein purification from complex media, yet never used in synergy. With the aim to capture antibodies directly from crude extracts, a new approach combining precipitation and magnetic separation is developed and named as affinity magnetic precipitation. A precipitation screening, based on the Hofmeister series, and a commercial precipitation kit are tested with affinity magnetic particles to assess the best condition for antibody capture from human serum plasma and clarified cell supernatant. The best conditions are obtained when using PEG3350 as precipitant at 4 °C for 1 h, reaching 80% purity and 50% recovery of polyclonal antibodies from plasma, and 99% purity with 97% recovery yield of anti-TNFα mAb from cell supernatants. These results show that the synergetic use of precipitation and magnetic separation can represent an alternative for the efficient capture of antibodies.
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Affiliation(s)
- Raquel Dos Santos
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Caparica, 2829-516, Portugal
| | - Inês Iria
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Avenida Prof. Gama Pinto, Lisbon, 1649-003, Portugal
| | - Ana M Manuel
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Avenida Prof. Gama Pinto, Lisbon, 1649-003, Portugal
| | - Ana P Leandro
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Avenida Prof. Gama Pinto, Lisbon, 1649-003, Portugal
| | - Catarina A C Madeira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Avenida Prof. Gama Pinto, Lisbon, 1649-003, Portugal
| | - Joao Goncalves
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Avenida Prof. Gama Pinto, Lisbon, 1649-003, Portugal
| | - Ana Luísa Carvalho
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Caparica, 2829-516, Portugal
| | - Ana Cecília A Roque
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Caparica, 2829-516, Portugal
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11
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Seraj Z, Seyedarabi A. The role of Cinnamaldehyde and Phenyl ethyl alcohol as two types of precipitants affecting protein hydration levels. Int J Biol Macromol 2020; 146:705-715. [PMID: 31887389 DOI: 10.1016/j.ijbiomac.2019.12.204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 10/25/2022]
Abstract
Release of water is the main force which drives proteins towards crystallisation (giving rise to protein crystals for crystallography) and aggregation (main cause of neurodegenerative diseases), and as such it is possible to make changes in the crystallisation/aggregation process by using compounds which are able to reduce the amount of water molecules around proteins. Cinnamaldehyde and Phenyl ethyl alcohol are the active constituents of cinnamon and rose flower, respectively. Traditional Iranian Medicine (TIM) suggests the use of cinnamon and rose flower for the reduction of excess coldness and wetness from the brain of patients suffering from Dementia. Using crystallisation as a model system and X-ray crystallography, we tested whether Cinnamaldehyde or Phenyl ethyl alcohol can mimic the role of precipitants resulting in the formation of crystals of HEWL (as a model protein) by releasing water from the surrounding protein environment. Results have revealed that both Cinnamaldehyde and Phenyl ethyl alcohol, in particular, were capable to adequately act as 'precipitants' but in the presence of NaCl (as a salt), resulting in better crystals of HEWL by changing the amount of charge and/or making water molecules unavailable in the symmetry related position, in line with the role suggested for these compounds by TIM.
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Affiliation(s)
- Zahra Seraj
- Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran
| | - Arefeh Seyedarabi
- Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614411, Iran.
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12
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Enhancement of stratification of colloidal particles near a substrate induced by addition of non-adsorbing polymers. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Debnath B, Das B. Ion-Solvation and Ion-Association Behavior of Tetraphenylphosphonium Chloride, Sodium Tetraphenylborate and Sodium Chloride in Polyethylene Glycol + Water Mixtures at 298.15 K. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00891-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Yilmaz E, Bier D, Guillory X, Briels J, Ruiz-Blanco YB, Sanchez-Garcia E, Ottmann C, Kaiser M. Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry 2018; 24:13807-13814. [PMID: 29924885 DOI: 10.1002/chem.201801074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/15/2018] [Indexed: 12/26/2022]
Abstract
Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling complexation of the amino group by the ether oxygen residues. The resulting biochemical binding affinity and thus biological relevance of this supramolecular interaction however remains unclear so far. Here, we report that OEG-containing phosphophenol ether inhibitors of 14-3-3 proteins also display such a "lysine-wrapping" binding mode. For better investigating the biochemical relevance of this binding mode, we made use of the dimeric nature of 14-3-3 proteins and designed as well as synthesized a set of bivalent 14-3-3 inhibitors for biochemical and X-ray crystallography-based structural studies. We found that all synthesized derivatives adapted the "lysine-wrapping" binding mode in the crystal structures; in solution, a different binding mode is however observed, most probably as the "lysine-wrapping" binding mode turned out to be a rather weak interaction. Accordingly, our studies demonstrate that structural studies of OEG-lysine interactions are difficult to interpret and their presence in structural studies may not automatically be correlated with a relevant interaction also in solution but requires further biochemical studies.
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Affiliation(s)
- Elvan Yilmaz
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - David Bier
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Xavier Guillory
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen Briels
- Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christian Ottmann
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Markus Kaiser
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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15
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16
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Apparent and Transfer Molar Volumes for Aqueous Solution Containing Polyethylene Glycols and Amino Acid Ionic Liquids at 298.15 K. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0780-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Ibanez ACS, Marji E, Luk YY. Cromoglycate mesogen forms isodesmic assemblies promoted by peptides and induces aggregation of a range of proteins. RSC Adv 2018; 8:29598-29606. [PMID: 35547307 PMCID: PMC9085300 DOI: 10.1039/c8ra05226c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/05/2018] [Indexed: 11/21/2022] Open
Abstract
Disodium cromoglycate (5′DSCG) belongs to a class of nonamphiphilic molecules that form nematic chromonic liquid crystals in aqueous solutions. As the concentration increases, it is believed that the molecules first form isodesmic assemblies in water, which further align to form liquid crystal phases. However, the reports on isodesmic assemblies of 5′DSCG have been scarce. Herein, we show that the presence of peptides can promote the isodesmic assembly of 5′DSCG over a broad range of concentrations before reaching the liquid crystal phase. The presence of peptides can lower the 5′DSCG concentration in the aqueous solution to ∼1.5 wt% (from 11–12 wt%, forming a nematic liquid crystal phase) for isodesmic assembly formation. This result indicates a demixing between 5′DSCG and peptides in aqueous solution. We further explored this demixing mechanism to precipitate a wide range of proteins, namely, lectin A, esterase, lipase, bovine serum albumin, trypsin, and a pilin protein from bacterium Pseudomonas aeruginosa. We found that 5′DSCG caused the aggregation of all these proteins except trypsin. These results, along with past findings, suggest that 5′DSCG isodesmic assemblies have the potential to assist in protein purification and crystallization. 5′DSCG molecules form isodesmic assembly in the presence of peptides, and cause a wide range of proteins to aggregate.![]()
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Affiliation(s)
| | - Elaine Marji
- Chemistry Department
- Syracuse University
- Syracuse
- USA
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18
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Daley KR, Kubarych KJ. An “Iceberg” Coating Preserves Bulk Hydration Dynamics in Aqueous PEG Solutions. J Phys Chem B 2017; 121:10574-10582. [DOI: 10.1021/acs.jpcb.7b08030] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberly R. Daley
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
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19
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Chudoba R, Heyda J, Dzubiella J. Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution. J Chem Theory Comput 2017; 13:6317-6327. [DOI: 10.1021/acs.jctc.7b00560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Richard Chudoba
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstraße
15, D-12489 Berlin, Germany
- Institut
für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Jan Heyda
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-16628 Praha 6, Czech Republic
| | - Joachim Dzubiella
- Institut
für Physik, Humboldt-Universität zu Berlin, Newtonstraße
15, D-12489 Berlin, Germany
- Institut
für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
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20
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Abstract
Controlling interactions between proteins and nanoparticles in electrolyte solutions is crucial for advancing biological sciences and biotechnology. The assembly of charged nanoparticles (NPs) and proteins in aqueous solutions can be directed by modifying the salt concentration. High concentrations of monovalent salt can induce the solubilization or crystallization of NPs and proteins. By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic correlations in the electrolyte, NPs pairs at high monovalent salt concentrations interact via remarkably strong long-range attractions or repulsions, which can be split into three regimes depending on the surface charge densities of the NPs. NPs with zero-to-low surface charge densities interact via a long-range attraction that is stronger and has a similar range to the depletion attraction induced by polymers with radius of gyrations comparable to the NP diameter. On the other hand, moderately charged NPs with smooth surfaces as well as DNA-functionalized NPs with no possibility of hybridization between them interact via a strong repulsion of range and strength larger than the repulsion predicted by models that neglect ionic correlations, including the Derjaguin-Landau-Vervey-Overbeek (DLVO) model. Interactions between strongly charged NPs (>2 e/nm2), both types smooth and DNA-functionalized NPs, show an attractive potential well at intermediate-to-high salt concentrations, which demonstrates that electrolytes can induce aggregation of strongly charged NPs. Our work provides an improved understanding of the role of ionic correlations in NP assembly and design rules to utilize the salting-out process to crystallize NPs.
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21
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Pereira JH, McAndrew RP, Tomaleri GP, Adams PD. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. J Appl Crystallogr 2017; 50:1352-1358. [PMID: 29021733 PMCID: PMC5627680 DOI: 10.1107/s1600576717011347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/01/2017] [Indexed: 01/29/2023] Open
Abstract
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.
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Affiliation(s)
- Jose H. Pereira
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Ryan P. McAndrew
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | | | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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22
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Belime A, Gravel E, Brenet S, Ancelet S, Caneiro C, Hou Y, Thielens N, Doris E, Ling WL. Mode of PEG Coverage on Carbon Nanotubes Affects Binding of Innate Immune Protein C1q. J Phys Chem B 2017; 122:757-763. [PMID: 28915042 DOI: 10.1021/acs.jpcb.7b06596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface modification of nanoparticles with poly(ethylene glycol) (PEG) is used in biomedicine to increase the circulation time of the particles after intravenous injection. Here, we study the interaction of PEG-covered carbon nanotubes (CNTs) with the serum complement protein C1q. Besides being the target-recognizing unit of the initiating complex for the classical pathway of complement in our innate immune system, C1q is involved in a range of important physiological processes. We modified the surface of multiwalled CNTs with covalently grafted PEG and physically adsorbed PEG. Transmission electron microscopy revealed the interaction of these PEG-coated CNTs with C1q. We found abundant C1q coverage on the PEG-grafted CNTs but not on the CNTs with adsorbed PEG. We tested the ability of these CNTs to activate the complement system using in vitro complement activation assays. None of the CNTs studied activated the C1q-dependent classical complement pathway. These findings are pertinent to the safe design and novel biomedical applications of PEGylated CNTs.
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Affiliation(s)
- Agathe Belime
- Service de Chimie Bioorganique et de Marquage (SCBM), CEA, Université Paris-Saclay , 91191 Gif-sur-Yvette, France
| | - Edmond Gravel
- Service de Chimie Bioorganique et de Marquage (SCBM), CEA, Université Paris-Saclay , 91191 Gif-sur-Yvette, France
| | - Sophie Brenet
- Univ. Grenoble Alpes , CNRS, CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Sarah Ancelet
- Univ. Grenoble Alpes , CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Yanxia Hou
- Univ. Grenoble Alpes , CNRS, CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Nicole Thielens
- Univ. Grenoble Alpes , CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Eric Doris
- Service de Chimie Bioorganique et de Marquage (SCBM), CEA, Université Paris-Saclay , 91191 Gif-sur-Yvette, France
| | - Wai Li Ling
- Univ. Grenoble Alpes , CEA, CNRS, IBS, F-38000 Grenoble, France
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23
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Fu Z, BeMiller JN. Effect of hydrocolloids and salts on retrogradation of native and modified maize starch. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2017.01.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Alfano C, Sanfelice D, Martin SR, Pastore A, Temussi PA. An optimized strategy to measure protein stability highlights differences between cold and hot unfolded states. Nat Commun 2017; 8:15428. [PMID: 28516908 PMCID: PMC5454340 DOI: 10.1038/ncomms15428] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
Macromolecular crowding ought to stabilize folded forms of proteins, through an excluded volume effect. This explanation has been questioned and observed effects attributed to weak interactions with other cell components. Here we show conclusively that protein stability is affected by volume exclusion and that the effect is more pronounced when the crowder's size is closer to that of the protein under study. Accurate evaluation of the volume exclusion effect is made possible by the choice of yeast frataxin, a protein that undergoes cold denaturation above zero degrees, because the unfolded form at low temperature is more expanded than the corresponding one at high temperature. To achieve optimum sensitivity to changes in stability we introduce an empirical parameter derived from the stability curve. The large effect of PEG 20 on cold denaturation can be explained by a change in water activity, according to Privalov's interpretation of cold denaturation.
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Affiliation(s)
- Caterina Alfano
- Department of Basic and Clinical Neurosciences, King's College London, London SE5 9RX, UK
| | - Domenico Sanfelice
- Department of Basic and Clinical Neurosciences, King's College London, London SE5 9RX, UK
| | - Stephen R. Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Annalisa Pastore
- Department of Basic and Clinical Neurosciences, King's College London, London SE5 9RX, UK
- Department of Molecular Medicine, University of Pavia, Pavia 27100, Italy
| | - Piero Andrea Temussi
- Department of Basic and Clinical Neurosciences, King's College London, London SE5 9RX, UK
- Dipartimento di Scienze Chimiche, Universita' di Napoli Federico II, Napoli 80126, Italy
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25
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Hofmann M, Winzer M, Weber C, Gieseler H. Limitations of polyethylene glycol-induced precipitation as predictive tool for protein solubility during formulation development. J Pharm Pharmacol 2017; 70:648-654. [DOI: 10.1111/jphp.12699] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/29/2016] [Indexed: 11/27/2022]
Abstract
Abstract
Objective
Polyethylene glycol (PEG)-induced protein precipitation is often used to extrapolate apparent protein solubility at specific formulation compositions. The procedure was used for several fields of application such as protein crystal growth but also protein formulation development. Nevertheless, most studies focused on applicability in protein crystal growth. In contrast, this study focuses on applicability of PEG-induced precipitation during high-concentration protein formulation development.
Methods
In this study, solubility of three different model proteins was investigated over a broad range of pH. Solubility values predicted by PEG-induced precipitation were compared to real solubility behaviour determined by either turbidity or content measurements.
Key findings
Predicted solubility by PEG-induced precipitation was confirmed for an Fc fusion protein and a monoclonal antibody. In contrast, PEG-induced precipitation failed to predict solubility of a single-domain antibody construct. Applicability of PEG-induced precipitation as indicator of protein solubility during formulation development was found to be not valid for one of three model molecules.
Conclusions
Under certain conditions, PEG-induced protein precipitation is not valid for prediction of real protein solubility behaviour. The procedure should be used carefully as tool for formulation development, and the results obtained should be validated by additional investigations.
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Affiliation(s)
- Melanie Hofmann
- Division of Pharmaceutics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Merck KGaA, Darmstadt, Germany
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26
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Renaissance of protein crystallization and precipitation in biopharmaceuticals purification. Biotechnol Adv 2017; 35:41-50. [DOI: 10.1016/j.biotechadv.2016.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
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27
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Abstract
Protein crystallization was discovered by chance nearly 200 years ago and was developed in the late nineteenth century as a powerful purification tool, and a demonstration of chemical purity. The crystallization of proteins, nucleic acids, and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule, but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by manipulation of various parameters that include temperature, ionic strength, and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors, or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch, and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years due to the advent of practical, easy-to-use screening kits, and the application of laboratory robotics.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
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28
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Naschberger A, Fürnrohr BG, Lenac Rovis T, Malic S, Scheffzek K, Dieplinger H, Rupp B. The N14 anti-afamin antibody Fab: a rare V L1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling. Acta Crystallogr D Struct Biol 2016; 72:1267-1280. [PMID: 27917827 PMCID: PMC5137224 DOI: 10.1107/s205979831601723x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/26/2016] [Indexed: 12/31/2022] Open
Abstract
The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.
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Affiliation(s)
- Andreas Naschberger
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Barbara G. Fürnrohr
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Tihana Lenac Rovis
- Center for Proteomics, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
| | - Suzana Malic
- Center for Proteomics, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
| | - Klaus Scheffzek
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Hans Dieplinger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
- Vitateq Biotechnology GmbH, Innrain 66, 6020 Innsbruck, Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
- CVMO, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
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29
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Gupta S, Biehl R, Sill C, Allgaier J, Sharp M, Ohl M, Richter D. Protein Entrapment in Polymeric Mesh: Diffusion in Crowded Environment with Fast Process on Short Scales. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sudipta Gupta
- Juelich Centre
for Neutron Science (JCNS), outstation at SNS, PO Box
2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory (ORNL), PO Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Ralf Biehl
- Juelich Centre for
Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Clemens Sill
- Juelich Centre for
Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jürgen Allgaier
- Juelich Centre for
Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Melissa Sharp
- Institute Laue-Langevin
(ILL), 71 rue des Martyrs, 38042 Grenoble, Cedex 9, France
- European Spallation
Source (ESS), PO Box 176, SE-221 00 Lund, Sweden
| | - Michael Ohl
- Juelich Centre
for Neutron Science (JCNS), outstation at SNS, PO Box
2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory (ORNL), PO Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Dieter Richter
- Juelich Centre for
Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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30
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Kirkwood J, Hargreaves D, O’Keefe S, Wilson J. Analysis of crystallization data in the Protein Data Bank. Acta Crystallogr F Struct Biol Commun 2015; 71:1228-34. [PMID: 26457511 PMCID: PMC4601584 DOI: 10.1107/s2053230x15014892] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein was investigated and the possibility of predicting whether a protein will crystallize was explored.
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Affiliation(s)
- Jobie Kirkwood
- Department of Chemistry, University of York, York YO10 5DD, England
| | - David Hargreaves
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge CB4 0WG, England
| | - Simon O’Keefe
- Department of Computer Science, University of York, York YO10 5DD, England
| | - Julie Wilson
- Department of Chemistry, University of York, York YO10 5DD, England
- Department of Mathematics, University of York, York YO10 5DD, England
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31
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Structure of a PEGylated protein reveals a highly porous double-helical assembly. Nat Chem 2015; 7:823-8. [DOI: 10.1038/nchem.2342] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/31/2015] [Indexed: 12/14/2022]
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32
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Effects of PEG molecular weight on its interaction with albumin. CHINESE JOURNAL OF POLYMER SCIENCE 2015. [DOI: 10.1007/s10118-015-1687-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Chaikuad A, Knapp S, von Delft F. Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1627-39. [PMID: 26249344 PMCID: PMC4528798 DOI: 10.1107/s1399004715007968] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/22/2015] [Indexed: 11/10/2022]
Abstract
The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.
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Affiliation(s)
- Apirat Chaikuad
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Building N240 Room 3.03, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Frank von Delft
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
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34
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35
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Liu Y, Zhang XF, Zhang CY, Guo YZ, Xie SX, Zhou RB, Cheng QD, Yan EK, Liu YL, Lu XL, Lu QQ, Lu HM, Ye YJ, Yin DC. A protein crystallisation screening kit designed using polyethylene glycol as major precipitant. CrystEngComm 2015. [DOI: 10.1039/c5ce00779h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Baumgartner K, Galm L, Nötzold J, Sigloch H, Morgenstern J, Schleining K, Suhm S, Oelmeier SA, Hubbuch J. Determination of protein phase diagrams by microbatch experiments: exploring the influence of precipitants and pH. Int J Pharm 2014; 479:28-40. [PMID: 25541147 DOI: 10.1016/j.ijpharm.2014.12.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/13/2014] [Indexed: 12/01/2022]
Abstract
Knowledge of protein phase behavior is essential for downstream process design in the biopharmaceutical industry. Proteins can either be soluble, crystalline or precipitated. Additionally liquid-liquid phase separation, gelation and skin formation can occur. A method to generate phase diagrams in high throughput on an automated liquid handling station in microbatch scale was developed. For lysozyme from chicken egg white, human lysozyme, glucose oxidase and glucose isomerase phase diagrams were generated at four different pH values – pH 3, 5, 7 and 9. Sodium chloride, ammonium sulfate, polyethylene glycol 300 and polyethylene glycol 1000 were used as precipitants. Crystallizing conditions could be found for lysozyme from chicken egg white using sodium chloride, for human lysozyme using sodium chloride or ammonium sulfate and glucose isomerase using ammonium sulfate. PEG caused destabilization of human lysozyme and glucose oxidase solutions or a balance of stabilizing and destabilizing effects for glucose isomerase near the isoelectric point. This work presents a systematic generation and extensive study of phase diagrams of proteins. Thus, it adds to the general understanding of protein behavior in liquid formulation and presents a convenient methodology applicable to any protein solution.
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Affiliation(s)
- Kai Baumgartner
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Lara Galm
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Juliane Nötzold
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Heike Sigloch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Josefine Morgenstern
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Kristina Schleining
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Susanna Suhm
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Stefan A Oelmeier
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, Karlsruhe 76131, Germany.
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Senske M, Törk L, Born B, Havenith M, Herrmann C, Ebbinghaus S. Protein stabilization by macromolecular crowding through enthalpy rather than entropy. J Am Chem Soc 2014; 136:9036-41. [PMID: 24888734 DOI: 10.1021/ja503205y] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dilute solution. Macromolecular crowding is commonly understood in terms of an entropic volume exclusion effect based on hardcore repulsions among the macromolecules. We studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, urea). Our results show that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temperature dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by the excluded volume theory, we observed an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromolecular crowder dextran was similar to the enthalpic stabilization mechanism of its monomeric building block glucose. In the case of poly(ethylene glycol), entropy is dominating over enthalpy leading to an overall destabilization. We propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability.
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Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II, Ruhr-Universität Bochum , 44780 Bochum, Germany
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Gao J, Ye K, He M, Xiong WW, Cao W, Lee ZY, Wang Y, Wu T, Huo F, Liu X, Zhang Q. Tuning metal–carboxylate coordination in crystalline metal–organic frameworks through surfactant media. J SOLID STATE CHEM 2013. [DOI: 10.1016/j.jssc.2013.07.031] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Petrov A, Lombardo S, Audette GF. Fibril-mediated oligomerization of pilin-derived protein nanotubes. J Nanobiotechnology 2013; 11:24. [PMID: 23829476 PMCID: PMC3704941 DOI: 10.1186/1477-3155-11-24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/01/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Self-assembling protein nanotubes (PNTs) are an intriguing alternative to carbon nanotubes for applications in bionanotechnology, in part due to greater inherent biocompatibility. The type IV pilus of the gram negative bacteria Pseudomonas aeruginosa is a protein-based fibre composed of a single subunit, the type IV pilin. Engineered pilin monomers from P. aeruginosa strain K122-4 (ΔK122) have been shown to oligomerize into PNTs both in solution and at surfaces. In order to fully exploit PNTs in bionanotechonological settings, an in-depth understanding of their assembly, physical characteristics and robustness, both in solution and when constrained to surfaces, is required. RESULTS This study details the effectiveness of multiple initiators of ΔK122-derived PNT oligomerization and characterize the formation of PNTs in solution. The optimal initiator for the oligomerization of ΔK122 in solution was observed to be 2-methyl-2,4-pentanediol (MPD). Conversely, larger PEG molecules do not trigger oligomerization. Multi-angle light scattering analysis indicates that the pilin protein exists in a monomer-dimer equilibrium in solution, and that an intermediate species forms within three hours that then coalesces over time into high molecular weight PNTs. Transmission Electron Microscopic analysis was used to observe the formation of oligomerized ΔK122 fibrils prior to assembly into full-length PNTs. CONCLUSIONS The oligomerization of ΔK122 pilin derived PNTs is a fibril mediated process. The optimal trigger for PNT oligomerization in solution is MPD, and the observation that PEGs do not induce oligomerization may enable the oligomerization of pilin-derived PNTs on PEG-functionalized surfaces for implantable bionanodevices.
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Affiliation(s)
- Anna Petrov
- Department of Chemistry, York University, Toronto, ON M3J1P3, Canada
| | | | - Gerald F Audette
- Department of Chemistry, York University, Toronto, ON M3J1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Canada
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Gorrec F. The current approach to initial crystallization screening of proteins is under-sampled. J Appl Crystallogr 2013; 46:795-797. [PMID: 23682195 PMCID: PMC3654315 DOI: 10.1107/s0021889813008030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/23/2013] [Indexed: 11/20/2022] Open
Abstract
Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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Huang W, Bardaro MF, Varani G, Drobny GP. Preparation of RNA samples with narrow line widths for solid state NMR investigations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:51-54. [PMID: 22967888 DOI: 10.1016/j.jmr.2012.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/19/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
Solid state NMR can provide detailed structural and dynamic information on biological systems that cannot be studied under solution conditions, and can investigate motions which occur with rates that cannot be fully studied by solution NMR. This approach has successfully been used to study proteins, but the application of multidimensional solid state NMR to RNA has been limited because reported line widths have been too broad to execute most multidimensional experiments successfully. A reliable method to generate spectra with narrow line widths is necessary to apply the full range of solid state NMR spectroscopic approaches to RNA. Using the HIV-1 transactivation response (TAR) RNA as a model, we present an approach based on precipitation with polyethylene glycol that improves the line width of (13)C signals in TAR from >6 ppm to about 1 ppm, making solid state 2D NMR studies of selectively enriched RNAs feasible at ambient temperature.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA
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Tomita S, Nagasaki Y, Shiraki K. Different mechanisms of action of poly(ethylene glycol) and arginine on thermal inactivation of lysozyme and ribonuclease A. Biotechnol Bioeng 2012; 109:2543-52. [DOI: 10.1002/bit.24531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/27/2012] [Accepted: 04/09/2012] [Indexed: 01/07/2023]
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Zobnina VG, Kosevich MV, Chagovets VV, Boryak OA, Vékey K, Gömöry Á, Kulyk AN. Interactions of oligomers of organic polyethers with histidine amino acid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:532-540. [PMID: 22302493 DOI: 10.1002/rcm.5342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Knowledge on noncovalent intermolecular interactions of organic polyethers with amino acids is essential to gain a better understanding on how polymers assemble in organic nanoparticles which are promising for drug delivery and cryoprotection. The main objective of the present study was to determine how polyethers assemble around ionizable amino acids such as histidine. METHODS Electrospray mass spectrometry was applied to probe the interactions in model systems consisting of polyethylene glycol PEG-400 or oxyethylated glycerol OEG-5 and amino acid histidine hydrochloride. Molecular dynamics simulation was utilized to visualize the structure of complexes of polyether oligomers with histidine in different charge states. RESULTS Stable gas-phase clusters composed of polyether oligomers (PEG(n), OEG(n)) with protonated histidine--PEG(n)•His•H(+), OEG(n)•His•H(+), OEG(n)•OEG(m)•His•H(+) and chlorine counterion--PEG(n)•Cl(-), OEG(n)•Cl(-), were observed under electrospray conditions. Molecular dynamics simulation of representative polyether-histidine complexes revealed the stabilization of oligomers by multiple hydrogen and coordination bonds whereby charged groups are wrapped by the polymeric chains. CONCLUSIONS The self-organization of polyether chains around the protonated imidazole group of histidine was revealed. This finding should be considered when modelling a pegylated protein structure and polyether-based organic nanoparticles.
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Affiliation(s)
- Valentina G Zobnina
- B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Avenue 47, Kharkov, 61103, Ukraine
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Priya MH, Ashbaugh HS, Paulaitis ME. Cosolvent Preferential Molecular Interactions in Aqueous Solutions. J Phys Chem B 2011; 115:13633-42. [DOI: 10.1021/jp2083067] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Hamsa Priya
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - H. S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - M. E. Paulaitis
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
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Gorrec F, Palmer CM, Lebon G, Warne T. Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:463-70. [PMID: 21543849 PMCID: PMC3087625 DOI: 10.1107/s0907444911008754] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 03/07/2011] [Indexed: 11/29/2022]
Abstract
The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting `Pi screens' have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, England.
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Ruangprasert A, Craven SH, Neidle EL, Momany C. Full-Length Structures of BenM and Two Variants Reveal Different Oligomerization Schemes for LysR-Type Transcriptional Regulators. J Mol Biol 2010; 404:568-86. [DOI: 10.1016/j.jmb.2010.09.053] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/21/2010] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
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Skálová T, Dušková J, Hašek J, Kolenko P, Štěpánková A, Dohnálek J. Alternative polymer precipitants for protein crystallization. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810014317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A set of 16 inexpensive and commercially available polymer precipitants were tested for protein crystallization. Eight of them were found suitable: polyethylene glycol dimethyl ether of molecular weight (MW) 500, 1000 and 2000; di[poly(ethylene glycol)] adipate, MW 900; poly(ethylene glycol-ran-propylene glycol), MW 2500 and 12000; poly(acrylic acid) sodium salt, MW 2100; and polyethylene glycol methyl ether methacrylate, MW 1100. Two new crystallization screens, PolyA and PolyB, were formulated using these eight polymers, each containing 96 solutions – four polymers in combination with 24 common salts and buffers, covering pH values from 4.5 to 9.0. The screens were tested on 29 proteins, 21 of which were crystallized. The tests confirmed the applicability of the eight polymers as precipitants for protein crystallization.
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Grimm C, Chari A, Reuter K, Fischer U. A crystallization screen based on alternative polymeric precipitants. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:685-97. [PMID: 20516621 DOI: 10.1107/s0907444910009005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 03/09/2010] [Indexed: 11/10/2022]
Abstract
Most commercially available crystallization screens are sparse-matrix screens with a predominance of inorganic salts and polyethylene glycols (PEGs) as precipitants. It was noted that commercially available screens are largely unsatisfactory for the purpose of the crystallization of multimeric protein and protein-nucleic acid complexes. This was reasoned to be a consequence of the redundancy in screening crystallization parameter space by the predominance of PEG as a precipitant in standard screens and it was suggested that this limitation could be overcome by introducing a variety of other organic polymers. Here, a set of 288 crystallization conditions was devised based on alternative polymeric precipitants and tested against a set of 20 different proteins/complexes; finally, a screen comprising the 96 most promising conditions designed to complement PEG- and salt-based commercial screens was proposed.
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Affiliation(s)
- Clemens Grimm
- Lehrstuhl für Biochemie, Biozentrum der Universität Würzburg, 97074 Würzburg, Germany.
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50
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Chapter 1 Introduction to the Crystallization of Biological Macromolecules. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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