1
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Banayan NE, Loughlin BJ, Singh S, Forouhar F, Lu G, Wong K, Neky M, Hunt HS, Bateman LB, Tamez A, Handelman SK, Price WN, Hunt JF. Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution. Protein Sci 2024; 33:e4898. [PMID: 38358135 PMCID: PMC10868448 DOI: 10.1002/pro.4898] [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: 06/18/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.
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Affiliation(s)
- Nooriel E. Banayan
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Blaine J. Loughlin
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Shikha Singh
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Farhad Forouhar
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Guanqi Lu
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Kam‐Ho Wong
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Vaccine Research and DevelopmentPfizer Inc.Pearl RiverNew YorkUSA
| | - Matthew Neky
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Columbia UniversityNew YorkNew YorkUSA
| | - Henry S. Hunt
- Department of PhysicsStanford UniversityStanfordCaliforniaUSA
| | | | | | - Samuel K. Handelman
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Department of Pain & Neuronal HealthEli Lily & Co.893 Delaware StIndianapolisIndianaUSA
| | - W. Nicholson Price
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
University of Michigan Law SchoolAnn ArborMichiganUSA
| | - John F. Hunt
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
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2
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Zalar M, Bye J, Curtis R. Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme. J Am Chem Soc 2023; 145:929-943. [PMID: 36608272 PMCID: PMC9853864 DOI: 10.1021/jacs.2c09615] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Adenosine tripolyphosphate (ATP) is a small polyvalent anion that has recently been shown to interact with proteins and have a major impact on assembly processes involved in biomolecular condensate formation and protein aggregation. However, the nature of non-specific protein-ATP interactions and their effects on protein solubility are largely unknown. Here, the binding of ATP to the globular model protein is characterized in detail using X-ray crystallography and nuclear magnetic resonance (NMR). Using NMR, we identified six ATP binding sites on the lysozyme surface, with one known high-affinity nucleic acid binding site and five non-specific previously unknown sites with millimolar affinities that also bind tripolyphosphate (TPP). ATP binding occurs primarily through the polyphosphate moiety, which was confirmed by the X-ray structure of the lysozyme-ATP complex. Importantly, ATP binds preferentially to arginine over lysine in non-specific binding sites. ATP and TPP have similar effects on solution-phase protein-protein interactions. At low salt concentrations, ion binding to lysozyme causes precipitation, while at higher salt concentrations, redissolution occurs. The addition of an equimolar concentration of magnesium to ATP does not alter ATP binding affinities but prevents lysozyme precipitation. These findings have important implications for both protein crystallization and cell biology. Crystallization occurs readily in ATP solutions outside the well-established crystallization window. In the context of cell biology, the findings suggest that ATP binds non-specifically to folded proteins in physiological conditions. Based on the nature of the binding sites identified by NMR, we propose several mechanisms for how ATP binding can prevent the aggregation of natively folded proteins.
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3
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Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022; 61:785-794. [PMID: 35420793 DOI: 10.1021/acs.biochem.2c00127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many bacteria possess type-II immunity against invading phages or plasmids known as the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system to detect and degrade the foreign DNA sequences. The Cas9 protein has two endonucleases responsible for double-strand breaks (the HNH domain for cleaving the target strand of DNA duplexes and RuvC domain for the nontarget strand, respectively) and a single-guide RNA-binding domain where the RNA and target DNA strands are base-paired. Three engineered single Lys-to-Ala HNH mutants (K810A, K848A, and K855A) exhibit an enhanced substrate specificity for cleavage of the target DNA strand. We report in this study that in the wild-type (wt) enzyme, D835, Y836, and D837 within the Y836-containing loop (comprising E827-D837) adjacent to the catalytic site have uncharacterizable broadened 1H15N nuclear magnetic resonance (NMR) features, whereas remaining residues in the loop have different extents of broadened NMR spectra. We find that this loop in the wt enzyme exhibits three distinct conformations over the duration of the molecular dynamics simulations, whereas the three Lys-to-Ala mutants retain only one conformation. The versatility of multiple alternate conformations of this loop in the wt enzyme could help to recruit noncognate DNA substrates into the HNH active site for cleavage, thereby reducing its substrate specificity relative to the three mutants. Our study provides further experimental and computational evidence that Lys-to-Ala substitutions reduce dynamics of proteins and thus increase their stability.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521-9800, United States
| | - Federica Maschietto
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521-9800, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
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4
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Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr D Struct Biol 2017; 73:757-766. [PMID: 28876239 PMCID: PMC5586248 DOI: 10.1107/s2059798317010932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/25/2017] [Indexed: 11/13/2023] Open
Abstract
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a β-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for β-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for β-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a β-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.
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Affiliation(s)
- Kazunori D. Yamada
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Koshiro Nakai
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Fukasawa
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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5
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Austerberry JI, Dajani R, Panova S, Roberts D, Golovanov AP, Pluen A, van der Walle CF, Uddin S, Warwicker J, Derrick JP, Curtis R. The effect of charge mutations on the stability and aggregation of a human single chain Fv fragment. Eur J Pharm Biopharm 2017; 115:18-30. [DOI: 10.1016/j.ejpb.2017.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/14/2017] [Accepted: 01/15/2017] [Indexed: 01/10/2023]
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6
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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7
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Kang K, Choi JM, Fox JM, Snyder PW, Moustakas DT, Whitesides GM. Acetylation of Surface Lysine Groups of a Protein Alters the Organization and Composition of Its Crystal Contacts. J Phys Chem B 2016; 120:6461-8. [DOI: 10.1021/acs.jpcb.6b01105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyungtae Kang
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Department
of Applied Chemistry, Kyung Hee University, 1732 Deogyeong-daero, Giheung, Yongin, Gyeonggi 17104, Republic of Korea
| | - Jeong-Mo Choi
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Jerome M. Fox
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Phillip W. Snyder
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Demetri T. Moustakas
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Wyss
Institute of Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
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8
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Abstract
A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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9
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Parmar AS, James JK, Grisham DR, Pike DH, Nanda V. Dissecting Electrostatic Contributions to Folding and Self-Assembly Using Designed Multicomponent Peptide Systems. J Am Chem Soc 2016; 138:4362-7. [PMID: 26966815 DOI: 10.1021/jacs.5b10304] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate formation of nano- to microscale peptide fibers and sheets where assembly requires association of two distinct collagen mimetic peptides (CMPs). The multicomponent nature of these designs allows the decoupling of amino acid contributions to peptide folding versus higher-order assembly. While both arginine and lysine containing CMP sequences can favor triple-helix folding, only arginine promotes rapid supramolecular assembly in each of the three two-component systems examined. Unlike lysine, the polyvalent guanidyl group of arginine is capable of both intra- and intermolecular contacts, promoting assembly. This is consistent with the supramolecular diversity of CMP morphologies observed throughout the literature. It also connects CMP self-assembly with a broad range of biomolecular interaction phenomena, providing general principles for modeling and design.
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Affiliation(s)
- Avanish S Parmar
- Department of Physics, Indian Institute of Technology (Banaras Hindu University) , Varanasi 221005, Uttar Pradesh, India
| | - Jose K James
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University , 679 Hoes Lane West, Piscataway, New Jersey 08854, United States
| | - Daniel R Grisham
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University , 679 Hoes Lane West, Piscataway, New Jersey 08854, United States
| | - Douglas H Pike
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University , 679 Hoes Lane West, Piscataway, New Jersey 08854, United States
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University , 679 Hoes Lane West, Piscataway, New Jersey 08854, United States
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10
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Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
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Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
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11
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Devedjiev YD. The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis. Acta Crystallogr F Struct Biol Commun 2015; 71:157-62. [PMID: 25664789 PMCID: PMC4321469 DOI: 10.1107/s2053230x14027861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/21/2014] [Indexed: 11/10/2022] Open
Abstract
Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.
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Affiliation(s)
- Yancho D. Devedjiev
- Department of Anesthesiology, University of Virginia Medical Center, 1215 Lee Street, PO Box 800634, Charlottesville, VA 22908-0634, USA
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12
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Warwicker J, Charonis S, Curtis RA. Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design. Mol Pharm 2013; 11:294-303. [PMID: 24283752 PMCID: PMC3885198 DOI: 10.1021/mp4004749] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prediction and engineering of protein solubility is an important but imprecise area. While some features are routinely used, such as the avoidance of extensive non-polar surface area, scope remains for benchmarking of sequence and structural features with experimental data. We study properties in the context of experimental solubilities, protein gene expression levels, and families of abundant proteins (serum albumin and myoglobin) and their less abundant paralogues. A common feature that emerges for proteins with elevated solubility and at higher expression and abundance levels is an increased ratio of lysine content to arginine content. We suggest that the same properties of arginine that give rise to its recorded propensity for specific interaction surfaces also lead to favorable interactions at nonspecific contacts, and thus lysine is favored for proteins at relatively high concentration. A survey of protein therapeutics shows that a significant subset possesses a relatively low lysine to arginine ratio, and therefore may not be favored for high protein concentration. We conclude that modulation of lysine and arginine content could prove a useful and relatively simple addition to the toolkit available for engineering protein solubility in biotechnological applications.
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Affiliation(s)
- Jim Warwicker
- Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, U.K
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13
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Vekilov PG. Phase diagrams and kinetics of phase transitions in protein solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:193101. [PMID: 22495288 DOI: 10.1088/0953-8984/24/19/193101] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The phase behavior of proteins is of interest for fundamental and practical reasons. The nucleation of new phases is one of the last major unresolved problems of nature. The formation of protein condensed phases (crystals, polymers, and other solid aggregates, as well as dense liquids and gels) underlies pathological conditions, plays a crucial role in the biological function of the respective protein, or is an essential part of laboratory and industrial processes. In this review, we focus on phase transitions of proteins in their properly folded state. We first summarize the recently acquired understanding of physical processes underlying the phase diagrams of the protein solutions and the thermodynamics of protein phase transitions. Then we review recent findings on the kinetics of nucleation of dense liquid droplets and crystals. We explore the transition from nucleation to spinodal decomposition for liquid-liquid separation and introduce the new concept of solution-to-crystal spinodal. We review the two-step mechanism of protein crystal nucleation, in which mesoscopic metastable protein clusters serve as precursors to the ordered crystal nuclei. The concepts and mechanisms reviewed here provide powerful tools for control of the nucleation process by varying the solution thermodynamic parameters.
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical and Biomolecular Engineering and Department of Chemistry, University of Houston, Houston, TX 77204-4004, USA.
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14
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Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PLoS One 2012; 7:e30296. [PMID: 22279578 PMCID: PMC3261180 DOI: 10.1371/journal.pone.0030296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.
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15
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Sledz P, Zheng H, Murzyn K, Chruszcz M, Zimmerman MD, Chordia MD, Joachimiak A, Minor W. New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization. Protein Sci 2010; 19:1395-404. [PMID: 20506323 DOI: 10.1002/pro.420] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Surface lysine methylation (SLM) is a technique for improving the rate of success of protein crystallization by chemically methylating lysine residues. The exact mechanism by which SLM enhances crystallization is still not clear. To study these mechanisms, and to analyze the conditions where SLM will provide the optimal benefits for rescuing failed crystallization experiments, we compared 40 protein structures containing N,N-dimethyl-lysine (dmLys) to a nonredundant set of 18,972 nonmethylated structures from the PDB. By measuring the relative frequency of intermolecular contacts (where contacts are defined as interactions between the residues in proximity with a distance of 3.5 A or less) of basic residues in the methylated versus nonmethylated sets, dmLys-Glu contacts are seen more frequently than Lys-Glu contacts. Based on observation of the 10 proteins with both native and methylated structures, we propose that the increased rate of contact for dmLys-Glu is due to both a slight increase in the number of amine-carboxyl H-bonds and to the formation of methyl C--H...O interactions. By comparing the relative contact frequencies of dmLys with other residues, the mechanism by which methylation of lysines improves the formation of crystal contacts appears to be similar to that of Lys to Arg mutation. Moreover, analysis of methylated structures with the surface entropy reduction (SER) prediction server suggests that in many cases SLM of predicted SER sites may contribute to improved crystallization. Thus, tools that analyze protein sequences and mark residues for SER mutation may identify proteins with good candidate sites for SLM.
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Affiliation(s)
- Pawel Sledz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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16
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Abstract
A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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17
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Zurbriggen A, Schneider P, Bähler P, Baumann U, Erni B. Expression, purification, crystallization and preliminary X-ray analysis of the EIICGlc domain of the Escherichia coli glucose transporter. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:684-8. [PMID: 20516600 DOI: 10.1107/s1744309110013102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/08/2010] [Indexed: 11/11/2022]
Abstract
The glucose-import system of Escherichia coli consists of a hydrophilic EIIA(Glc) subunit and a transmembrane EIICB(Glc) subunit. EIICB(Glc) (UniProt P69786) contains two domains: the transmembrane EIIC(Glc) domain (40.6 kDa) and the cytoplasmic EIIB(Glc) domain (8.0 kDa), which are fused by a linker that is strongly conserved among its orthologues. The EIICB(Glc) subunit can be split within this motif by trypsin. Here, the crystallization of the tryptic EIIC(Glc) domain is described. A complete data set was collected to 4.5 A resolution at 100 K.
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Affiliation(s)
- Andreas Zurbriggen
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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18
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Kurpiewska K, Font J, Ribó M, Vilanova M, Lewiński K. X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability. Proteins 2010; 77:658-69. [PMID: 19544568 DOI: 10.1002/prot.22480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule.
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Affiliation(s)
- Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, Kraków 30-060, Poland
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19
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Wine Y, Cohen-Hadar N, Lamed R, Freeman A, Frolow F. Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity. Biotechnol Bioeng 2009; 104:444-57. [PMID: 19575413 DOI: 10.1002/bit.22427] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Bioinspired nano-scale biotemplating for the development of novel composite materials has recently culminated in several demonstrations of nano-structured hybrid materials. Protein crystals, routinely prepared for the elucidation of protein 3D structures by X-ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein "building blocks" in the crystal, a complementary 3D array of interconnected cavities--voids array, exhibiting highly ordered porosity is formed. The porous arrays of protein crystal may serve as a nano-structured, accurate biotemplate by a "filling" process. These cavities arrays are shaped by the mode of protein packing throughout the crystallization process. Here we propose and demonstrate feasibility of targeting site specific mutations to modify protein's surface to affect protein crystal packing, enabling the generation of a series of protein crystal "biotemplates" all originating from same parent protein. The selection of these modification sites was based on in silico analysis of protein-protein interface contact areas in the parent crystal. The model protein selected for this study was the N-terminal type II cohesin from the cellulosomal scaffold in ScaB subunit of Acetivibrio cellulolyticus and mutations were focused on lysine residues involved in protein packing as prime target. The impact of systematically mutating these lysine residues on protein packing and its resulting interconnected cavities array were found to be most significant when surface lysine residues were substituted to tryptophan residues. Our results demonstrate the feasibility of using pre-designed site directed mutations for the generation of a series of protein crystal biotemplates from a "parent" protein.
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Affiliation(s)
- Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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20
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Vetting MW, Hegde SS, Blanchard JS. Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:462-9. [PMID: 19390151 DOI: 10.1107/s0907444909008324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/06/2009] [Indexed: 11/10/2022]
Abstract
The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane-dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 A resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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21
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Ho C, Shanmugasundararaj S, Miller KW, Malinowski SA, Cook AC, Slater SJ. Interaction of anesthetics with the Rho GTPase regulator Rho GDP dissociation inhibitor. Biochemistry 2008; 47:9540-52. [PMID: 18702520 DOI: 10.1021/bi800544d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physiological effects of anesthetics have been ascribed to their interaction with hydrophobic sites within functionally relevant CNS proteins. Studies have shown that volatile anesthetics compete for luciferin binding to the hydrophobic substrate binding site within firefly luciferase and inhibit its activity (Franks, N. P., and Lieb, W. R. (1984) Nature 310, 599-601). To assess whether anesthetics also compete for ligand binding to a mammalian signal transduction protein, we investigated the interaction of the volatile anesthetic, halothane, with the Rho GDP dissociation inhibitor (RhoGDIalpha), which binds the geranylgeranyl moiety of GDP-bound Rho GTPases. Consistent with the existence of a discrete halothane binding site, the intrinsic tryptophan fluorescence of RhoGDIalpha was quenched by halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) in a saturable, concentration-dependent manner. Bromine quenching of tryptophan fluorescence is short-range and W192 and W194 of the RhoGDIalpha are located within the geranylgeranyl binding pocket, suggesting that halothane binds within this region. Supporting this, N-acetyl-geranylgeranyl cysteine reversed tryptophan quenching by halothane. Short chain n-alcohols ( n < 6) also reversed tryptophan quenching, suggesting that RhoGDIalpha may also bind n-alkanols. Consistent with this, E193 was photolabeled by 3-azibutanol. This residue is located in the vicinity of, but outside, the geranylgeranyl chain binding pocket, suggesting that the alcohol binding site is distinct from that occupied by halothane. Supporting this, N-acetyl-geranylgeranyl cysteine enhanced E193 photolabeling by 3-azibutanol. Overall, the results suggest that halothane binds to a site within the geranylgeranyl chain binding pocket of RhoGDIalpha, whereas alcohols bind to a distal site that interacts allosterically with this pocket.
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Affiliation(s)
- Cojen Ho
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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22
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Sugahara M, Asada Y, Shimizu K, Yamamoto H, Lokanath NK, Mizutani H, Bagautdinov B, Matsuura Y, Taketa M, Kageyama Y, Ono N, Morikawa Y, Tanaka Y, Shimada H, Nakamoto T, Sugahara M, Yamamoto M, Kunishima N. High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. ACTA ACUST UNITED AC 2008; 9:21-8. [PMID: 18677553 DOI: 10.1007/s10969-008-9042-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
Abstract
A high-throughput crystallization-to-structure pipeline for structural genomics was recently developed at the Advanced Protein Crystallography Research Group of the RIKEN SPring-8 Center in Japan. The structure determination pipeline includes three newly developed technologies for automating X-ray protein crystallography: the automated crystallization and observation robot system "TERA", the SPring-8 Precise Automatic Cryosample Exchanger "SPACE" for automated data collection, and the Package of Expert Researcher's Operation Network "PERON" for automated crystallographic computation from phasing to model checking. During the 5 years following April, 2002, this pipeline was used by seven researchers to determine 138 independent crystal structures (resulting from 437 purified proteins, 234 cryoloop-mountable crystals, and 175 diffraction data sets). The protocols used in the high-throughput pipeline are described in this paper.
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Affiliation(s)
- Michihiro Sugahara
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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23
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Liu B, Luna VM, Chen Y, Stout CD, Fee JA. An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1029-34. [PMID: 18084085 PMCID: PMC2344090 DOI: 10.1107/s1744309107054176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 10/29/2007] [Indexed: 11/10/2022]
Abstract
Past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. Described here is a successful application of this approach to the integral membrane protein Thermus thermophilus cytochrome ba(3) oxidase. Two mutant forms of this enzyme (I-K258R and I-K258R/II-E4Q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. These mutant proteins had greatly shortened crystallization times, decreasing from approximately 30 d for the wild type to 1-3 d for the mutants, and crystallization was highly reproducible. Native-like proteins crystallize in space group P4(3)2(1)2, whereas the mutant proteins crystallize in space group P4(1)2(1)2 with a different packing arrangement. Crystals of the P4(3)2(1)2 form occasionally diffracted to 2.4-2.3 A resolution following controlled dehydration, while those of the P4(1)2(1)2 form routinely diffracted to between 3.0 and 2.6 A for crystals that had been cryoprotected but not dehydrated.
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Affiliation(s)
- Bin Liu
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - V. Mitch Luna
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Ying Chen
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - C. David Stout
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - James A. Fee
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
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24
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Nauli S, Farr S, Lee YJ, Kim HY, Faham S, Bowie JU. Polymer-driven crystallization. Protein Sci 2007; 16:2542-51. [PMID: 17962407 PMCID: PMC2211692 DOI: 10.1110/ps.073074207] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Obtaining well-diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.
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Affiliation(s)
- Sehat Nauli
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles 90095-1570, USA
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25
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Malawski GA, Hillig RC, Monteclaro F, Eberspaecher U, Schmitz AAP, Crusius K, Huber M, Egner U, Donner P, Müller-Tiemann B. Identifying protein construct variants with increased crystallization propensity--a case study. Protein Sci 2007; 15:2718-28. [PMID: 17132859 PMCID: PMC2242438 DOI: 10.1110/ps.062491906] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.
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26
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Roos G, Brosens E, Wahni K, Desmyter A, Spinelli S, Wyns L, Messens J, Loris R. Combining site-specific mutagenesis and seeding as a strategy to crystallize 'difficult' proteins: the case of Staphylococcus aureus thioredoxin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1255-8. [PMID: 17142910 PMCID: PMC2225371 DOI: 10.1107/s1744309106047075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2006] [Accepted: 11/07/2006] [Indexed: 11/10/2022]
Abstract
The P31T mutant of Staphylococcus aureus thioredoxin crystallizes spontaneously in space group P2(1)2(1)2(1), with unit-cell parameters a = 41.7, b = 49.5, c = 55.6 A. The crystals diffract to 2.2 A resolution. Isomorphous crystals of wild-type thioredoxin as well as of other point mutants only grow when seeded with the P31T mutant. These results suggest seeding as a valuable tool complementing surface engineering for proteins that are hard to crystallize.
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Affiliation(s)
- Goedele Roos
- Brussels Center for Redox Biology, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
- Algemene Chemie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Elke Brosens
- Brussels Center for Redox Biology, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
| | - Khadija Wahni
- Brussels Center for Redox Biology, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
| | - Aline Desmyter
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Universites d’Aix-Marseille I et II, Campus de Luminy, 163 Avenue de Luminy 13288 Marseille CEDEX 9, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Universites d’Aix-Marseille I et II, Campus de Luminy, 163 Avenue de Luminy 13288 Marseille CEDEX 9, France
| | - Lode Wyns
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
| | - Joris Messens
- Brussels Center for Redox Biology, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
| | - Remy Loris
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) at the Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium
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27
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Wang BC, Adams MWW, Dailey H, DeLucas L, Luo M, Rose J, Bunzel R, Dailey T, Habel J, Horanyi P, Jenney FE, Kataeva I, Lee HS, Li S, Li T, Lin D, Liu ZJ, Luan CH, Mayer M, Nagy L, Newton MG, Ng J, Poole FL, Shah A, Shah C, Sugar FJ, Xu H. Protein production and crystallization at SECSG -- an overview. ACTA ACUST UNITED AC 2006; 6:233-43. [PMID: 16211524 DOI: 10.1007/s10969-005-2462-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2004] [Accepted: 02/15/2005] [Indexed: 11/27/2022]
Abstract
Using a high degree of automation, the Southeast Collaboratory for Structural Genomics (SECSG) has developed high throughput pipelines for protein production, and crystallization using a two-tiered approach. Primary, or tier-1, protein production focuses on producing proteins for members of large Pfam families that lack a representative structure in the Protein Data Bank. Target genomes are Pyrococcus furiosus and Caenorhabditis elegans. Selected human proteins are also under study. Tier-2 protein production, or target rescue, focuses on those tier-1 proteins, which either fail to crystallize or give poorly diffracting crystals. This two tier approach is more efficient since it allows the primary protein production groups to focus on the production of new targets while the tier-2 efforts focus on providing additional sample for further studies and modified protein for structure determination. Both efforts feed the SECSG high throughput crystallization pipeline, which is capable of screening over 40 proteins per week. Details of the various pipelines in use by the SECSG for protein production and crystallization, as well as some examples of target rescue are described.
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Affiliation(s)
- Bi-Cheng Wang
- Southeast Collaboratory for Structural Genomics, University of Georgia, Athens, GA 30602, USA
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28
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Anstrom DM, Colip L, Moshofsky B, Hatcher E, Remington SJ. Systematic replacement of lysine with glutamine and alanine in Escherichia coli malate synthase G: effect on crystallization. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1069-74. [PMID: 16511237 PMCID: PMC1978152 DOI: 10.1107/s1744309105036559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 11/08/2005] [Indexed: 01/19/2023]
Abstract
Two proposals recommend substitution of surface lysine residues as a means to improve the quality of protein crystals. In proposal I, substitution of lysine by alanine has been suggested to improve crystallization by reducing the entropic cost of ordering flexible side chains at crystal contacts. In proposal II, substitution of lysine by residues more commonly found in crystal contacts, such as glutamine, has been proposed to improve crystallization. 15 lysine residues on the surface of Escherichia coli malate synthase G, distributed over a variety of secondary structures, were individually mutated to both alanine and glutamine. For 28 variants, detailed studies of the effect on enzymatic activity and crystallization were conducted. This has permitted direct comparison of the relative effects of the two types of mutations. While none of the variants produced crystals suitable for X-ray structural determination, small crystals were obtained in a wide variety of conditions, in support of the general approach. Glutamine substitutions were found to be more effective than alanine in producing crystals, in support of proposal II. Secondary structure at the site of mutation does not appear to play a major role in determining the rate of success.
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Affiliation(s)
| | - Leslie Colip
- Institute of Molecular Biology, University of Oregon, USA
| | | | - Eric Hatcher
- Institute of Molecular Biology, University of Oregon, USA
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29
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Abstract
Small GTP-binding proteins of the Rho/Rac/Cdc42 family combine their GDP/GTP cycle, regulated by guanine nucleotide-exchange factors and GTPase-activating proteins, to a cytosol/membrane cycle, regulated by guanine nucleotide dissociation inhibitors (rhoGDIs). RhoGDIs are endowed with dual functions in the cytosol where they form soluble complexes with geranylgeranylated GDP-bound Rho proteins and at membrane interfaces where they monitor the delivery and extraction of Rho proteins to/from their site of action. They have little diversity compared with other Rho protein regulators and therefore have been regarded mostly as housekeeping regulators that distribute Rho proteins equally to any membranes. Recently, acquired data show that rhoGDIs, by interacting with candidate receptors/displacement factors or by phosphorylation, may in fact have active contributions to targeting Rho proteins to specific subcellular membranes and signaling pathways. In addition, the GDP/GTP and membrane/cytosol cycles can be uncoupled in certain cases, with Rho proteins either escaping the membrane/cytosol cycle or being regulated by rhoGDIs in their GTP-bound form. Here, we survey recent structure-function relationships and cellular studies on rhoGDIs and revisit their classical housekeeping role into novel and more specific functions. We also review their involvement in diseases.
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Affiliation(s)
- Estelle Dransart
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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30
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Derewenda ZS. Rational Protein Crystallization by Mutational Surface Engineering. Structure 2004; 12:529-35. [PMID: 15062076 DOI: 10.1016/j.str.2004.03.008] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 01/21/2004] [Accepted: 01/31/2004] [Indexed: 10/26/2022]
Abstract
Protein crystallization constitutes a limiting step in structure determination by X-ray diffraction. Even if single crystals are available, inadequate physical quality may seriously limit the resolution of the available data and consequently the accuracy of the atomic model. Recent studies show that targeted mutagenesis of surface patches containing residues with large flexible side chains and their replacement with smaller amino acids lead to effective preparation of X-ray quality crystals of proteins otherwise recalcitrant to crystallization. Furthermore, this technique can also be used to obtain crystals of superior quality as compared to those grown for the wild-type protein, sometimes increasing the effective resolution by as much as 1 A or more. Several recent examples of this new methodology suggest that the method has the potential to become a routine tool in protein crystallography.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA.
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