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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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Geerds C, Bleymüller WM, Meyer T, Widmann C, Niemann HH. A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:310-320. [PMID: 35234145 PMCID: PMC8900821 DOI: 10.1107/s2059798322000432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022]
Abstract
InlB, a bacterial agonist of the human receptor tyrosine kinase MET, consists of an N-terminal internalin domain, a central B repeat and three C-terminal GW domains. In all previous structures of full-length InlB or an InlB construct lacking the GW domains (InlB392), there was no interpretable electron density for the B repeat. Here, three InlB392 crystal structures in which the B repeat is resolved are described. These are the first structures to reveal the relative orientation of the internalin domain and the B repeat. A wild-type structure and two structures of the T332E variant together contain five crystallographically independent molecules. Surprisingly, the threonine-to-glutamate substitution in the B repeat substantially improved the crystallization propensity and crystal quality of the T332E variant. The internalin domain and B repeat are quite rigid internally, but are flexibly linked to each other. The new structures show that inter-domain flexibility is the most likely cause of the missing electron density for the B repeat in previous InlB structures. A potential binding groove between B-repeat strand β2 and an adjacent loop forms an important crystal contact in all five crystallographically independent chains. This region may represent a hydrophobic `sticky patch' that supports protein–protein interactions. This assumption agrees with the previous finding that all known inactivating point mutations in the B repeat lie within strand β2. The groove formed by strand β2 and the adjacent loop may thus represent a functionally important protein–protein interaction site in the B repeat.
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3
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Guo Y, Nishida N, Hoshino T. Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization. J Chem Inf Model 2021; 61:4571-4581. [PMID: 34565151 DOI: 10.1021/acs.jcim.1c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.
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Affiliation(s)
- Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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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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5
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Khabbazi A, Rahbar Kafshboran H, Nasiri Aghdam M, Nouri Nojadeh J, Daghagh H, Daneshmandpour Y, Kazemzadeh M, Hamzeiy H, Sakhinia E. A new report of autoinflammation and PLCG2-associated antibody deficiency and immune dysregulation (APLAID) with a homozygous pattern from Iran. Immunol Lett 2020; 221:27-32. [PMID: 32014489 DOI: 10.1016/j.imlet.2020.01.008] [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: 12/30/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 11/26/2022]
Abstract
Autoinflammation and PLCG2-associated antibody deficiency and immune dysregulation (APLAID) is an autosomal dominant autoinflammatory disease characterized by episodic skin, musculoskeletal, ophthalmic and gastrointestinal tract symptoms. Here we report an 11-year-old girl with a history of repeated episodes of fever, myalgia, arthralgia, abdominal pain, and urticarial rash in the trunk and limbs. Chest and pelvic X-Ray, sacroiliac joints MRI, brain MRI and abdominal CT scan were normal. Anti-nuclear antibody, Rheumatoid factor, cryoglobulin, ANCA/PR3, p-ANCA/MPO, anti-smooth muscle antibody and anti-mitochondrial antibody were negative. Serology for cytomegalovirus, Epstein-Barr, hepatitis B, hepatitis C, and HIV viruses was negative. Serum immunoglobulins were in the normal range. Genetic analysis for familial Mediterranean fever syndrome was negative. Whole exome sequencing was carried out to identify the genetic cause of our patient. We identified a homozygous missense variant (c.579C > G, p. His193Gln) in exon 7 of the PLCG2 gene. Bioinformatic analysis and clinical symptoms suggests this variant to be pathogenic in the homozygous state for APLAID and thus probably acting in an autosomal recessive manner. Our bioinformatic analysis also showed this novel mutation to have detrimental effects on the 3D structure of the PLCG2 protein, which is well conserved among many other similar species.
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Affiliation(s)
- Alireza Khabbazi
- Connective Tissue Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Maryam Nasiri Aghdam
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Nouri Nojadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Daghagh
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Kazemzadeh
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Hamzeiy
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Genomize Inc., Istanbul, Turkey
| | - Ebrahim Sakhinia
- Connective Tissue Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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6
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Dimova M, Devedjiev YD. Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase. IUCRJ 2018; 5:130-140. [PMID: 29765602 PMCID: PMC5947717 DOI: 10.1107/s2052252517017833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 12/13/2017] [Indexed: 05/03/2023]
Abstract
Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.
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Affiliation(s)
- Margarita Dimova
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
| | - Yancho D. Devedjiev
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
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7
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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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8
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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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9
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Altan I, Charbonneau P, Snell EH. Computational crystallization. Arch Biochem Biophys 2016; 602:12-20. [PMID: 26792536 DOI: 10.1016/j.abb.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/22/2015] [Accepted: 01/07/2016] [Indexed: 11/28/2022]
Abstract
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.
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Affiliation(s)
- Irem Altan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Physics, Duke University, Durham, NC 27708, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., NY 14203, USA; Department of Structural Biology, SUNY University of Buffalo, 700 Ellicott St., NY 14203, USA.
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10
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Fusco D, Charbonneau P. Soft matter perspective on protein crystal assembly. Colloids Surf B Biointerfaces 2016; 137:22-31. [DOI: 10.1016/j.colsurfb.2015.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/24/2023]
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11
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Pelz JP, Schindelin H, van Pee K, Kuper J, Kisker C, Diederichs K, Fischer U, Grimm C. Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project. ACTA ACUST UNITED AC 2015; 71:2040-53. [PMID: 26457428 DOI: 10.1107/s1399004715014832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/07/2015] [Indexed: 11/10/2022]
Abstract
The small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/6 and U5 are major constituents of the pre-mRNA processing spliceosome. They contain a common RNP core that is formed by the ordered binding of Sm proteins onto the single-stranded Sm site of the snRNA. Although spontaneous in vitro, assembly of the Sm core requires assistance from the PRMT5 and SMN complexes in vivo. To gain insight into the key steps of the assembly process, the crystal structures of two assembly intermediates of U snRNPs termed the 6S and 8S complexes have recently been reported. These multimeric protein complexes could only be crystallized after the application of various rescue strategies. The developed strategy leading to the crystallization and solution of the 8S crystal structure was subsequently used to guide a combination of rational crystal-contact optimization with surface-entropy reduction of crystals of the related 6S complex. Conversely, the resulting high-resolution 6S crystal structure was used during the restrained refinement of the 8S crystal structure.
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Affiliation(s)
- Jann Patrick Pelz
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Hermann Schindelin
- Rudolf-Virchow-Zentrum, DFG Research Centre for Experimental Medicine, University of Würzburg, Josef-Schneider-Strasse 2/Haus D15, 97080 Würzburg, Germany
| | - Katharina van Pee
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jochen Kuper
- Rudolf-Virchow-Zentrum, DFG Research Centre for Experimental Medicine, University of Würzburg, Josef-Schneider-Strasse 2/Haus D15, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Zentrum, DFG Research Centre for Experimental Medicine, University of Würzburg, Josef-Schneider-Strasse 2/Haus D15, 97080 Würzburg, Germany
| | - Kay Diederichs
- Protein Crystallography and Molecular Bioinformatics, University of Konstanz, 78457 Konstanz, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Clemens Grimm
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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12
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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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13
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Kalyoncu S, Hyun J, Pai JC, Johnson JL, Entzminger K, Jain A, Heaner DP, Morales IA, Truskett TM, Maynard JA, Lieberman RL. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments. Proteins 2014; 82:1884-95. [PMID: 24615866 PMCID: PMC4142072 DOI: 10.1002/prot.24542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 11/06/2022]
Abstract
Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts.
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Affiliation(s)
- Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Jeongmin Hyun
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer C. Pai
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer L. Johnson
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Kevin Entzminger
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Avni Jain
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - David P. Heaner
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Ivan A. Morales
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Jennifer A. Maynard
- McKetta Department of Chemical Engineering, University of Texas at Austin, MC0400, 1 University Station, Austin, TX 78712
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332-0400
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14
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Fusco D, Barnum TJ, Bruno AE, Luft JR, Snell EH, Mukherjee S, Charbonneau P. Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. PLoS One 2014; 9:e101123. [PMID: 24988076 PMCID: PMC4079662 DOI: 10.1371/journal.pone.0101123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.
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Affiliation(s)
- Diana Fusco
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
| | - Timothy J. Barnum
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew E. Bruno
- Center for Computational Research, State University of New York, Buffalo, New York, United States of America
| | - Joseph R. Luft
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
| | - Sayan Mukherjee
- Department of Statistical Science, Department of Computer Science and Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
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15
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Fusco D, Headd JJ, De Simone A, Wang J, Charbonneau P. Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study. SOFT MATTER 2014; 10:290-302. [PMID: 24489597 PMCID: PMC3907588 DOI: 10.1039/c3sm52175c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines have thus far prevented a comprehensive understanding of the phenomenon to emerge. We conduct a computational study of proteins from the rubredoxin family that bridges the two fields. Using atomistic simulations, we characterize the protein crystal contacts, and accordingly parameterize patchy particle models. Comparing the phase diagrams of these schematic models with experimental results enables us to critically examine the assumptions behind the two approaches. The study also reveals features of protein–protein interactions that can be leveraged to crystallize proteins more generally.
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Affiliation(s)
- Diana Fusco
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Jeffrey J. Headd
- Department of Biochemistry, Duke University, Durham, NC 27708, USA
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, South Kensington SW7 2AZ, UK
| | - Jun Wang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Patrick Charbonneau
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Physics, Duke University, Durham, NC 27708, USA
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16
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Goldschmidt L, Eisenberg D, Derewenda ZS. Salvage or recovery of failed targets by mutagenesis to reduce surface entropy. Methods Mol Biol 2014; 1140:201-9. [PMID: 24590720 DOI: 10.1007/978-1-4939-0354-2_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The success of macromolecular crystallization depends on the protein's ability to form specific, cohesive intermolecular interactions that serve as crystal contacts. In the cases where the protein lacks surface patches conducive to such interactions, crystallization may not occur. However, it is possible to enhance the likelihood of crystallization by engineering such patches through site-directed mutagenesis, targeting specifically residues with high side chain entropy and replacing them with small amino acids (i.e., surface entropy reduction, SER). This method has proven successful in hundreds of crystallographic analyses of proteins otherwise recalcitrant to crystallization. Three representative cases of the application of the SER strategy, assisted by the automated prediction of the mutation sites using the SER prediction (SERp) server are described.
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Affiliation(s)
- Lukasz Goldschmidt
- UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA
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17
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Levy ED, Teichmann S. Structural, evolutionary, and assembly principles of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:25-51. [PMID: 23663964 DOI: 10.1016/b978-0-12-386931-9.00002-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In the protein universe, 30-50% of proteins self-assemble to form symmetrical complexes consisting of multiple copies of themselves, called homomers. The prevalence of homomers motivates us to review many of their properties. In Section 1, we describe the methods and challenges associated with quaternary structure inference-these methods are indeed at the basis of any analysis on homomers. In Section 2, we describe the morphological properties of homomers, as well as the database 3DComplex, which provides a taxonomy for both homomeric and heteromeric protein complexes. In Section 3, we review interface properties of homomeric complexes. In Section 4, we then present recent findings on the evolution of homomer interfaces, which we link in Section 5 to the evolution of homomers as entire entities. In Section 6, we discuss mechanisms involved in their assembly and how these mechanisms can be linked to evolution.
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Affiliation(s)
- Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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Levy ED, De S, Teichmann SA. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A 2012; 109:20461-6. [PMID: 23184996 PMCID: PMC3528536 DOI: 10.1073/pnas.1209312109] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In living cells, functional protein-protein interactions compete with a much larger number of nonfunctional, or promiscuous, interactions. Several cellular properties contribute to avoiding unwanted protein interactions, including regulation of gene expression, cellular compartmentalization, and high specificity and affinity of functional interactions. Here we investigate whether other mechanisms exist that shape the sequence and structure of proteins to favor their correct assembly into functional protein complexes. To examine this question, we project evolutionary and cellular abundance information onto 397, 196, and 631 proteins of known 3D structure from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, respectively. On the basis of amino acid frequencies in interface patches versus the solvent-accessible protein surface, we define a propensity or "stickiness" scale for each of the 20 amino acids. We find that the propensity to interact in a nonspecific manner is inversely correlated with abundance. In other words, high abundance proteins have less sticky surfaces. We also find that stickiness constrains protein evolution, whereby residues in sticky surface patches are more conserved than those found in nonsticky patches. Finally, we find that the constraint imposed by stickiness on protein divergence is proportional to protein abundance, which provides mechanistic insights into the correlation between protein conservation and protein abundance. Overall, the avoidance of nonfunctional interactions significantly influences the physico-chemical and evolutionary properties of proteins. Remarkably, the effects observed are consistently larger in E. coli and S. cerevisiae than in H. sapiens, suggesting that promiscuous protein-protein interactions may be freer to accumulate in the human lineage.
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Affiliation(s)
- Emmanuel D. Levy
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada H3T 1J4
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Subhajyoti De
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045; and
- Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045
| | - Sarah A. Teichmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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19
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Krishnan S, Trievel RC. Structural and functional analysis of JMJD2D reveals molecular basis for site-specific demethylation among JMJD2 demethylases. Structure 2012; 21:98-108. [PMID: 23219879 DOI: 10.1016/j.str.2012.10.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/19/2012] [Accepted: 10/31/2012] [Indexed: 11/24/2022]
Abstract
JMJD2 lysine demethylases (KDMs) participate in diverse genomic processes. Most JMJD2 homologs display dual selectivity toward H3K9me3 and H3K36me3, with the exception of JMJD2D, which is specific for H3K9me3. Here, we report the crystal structures of the JMJD2D⋅2-oxoglutarate⋅H3K9me3 ternary complex and JMJD2D apoenzyme. Utilizing structural alignments with JMJD2A, molecular docking, and kinetic analysis with an array of histone peptide substrates, we elucidate the specific signatures that permit efficient recognition of H3K9me3 by JMJD2A and JMJD2D, and the residues in JMJD2D that occlude H3K36me3 demethylation. Surprisingly, these results reveal that JMJD2A and JMJD2D exhibit subtle yet important differences in H3K9me3 recognition, despite the overall similarity in the substrate-binding conformation. Further, we show that H3T11 phosphorylation abrogates demethylation by JMJD2 KDMs. Together, these studies reveal the molecular basis for JMJD2 site specificity and provide a framework for structure-based design of selective inhibitors of JMJD2 KDMs implicated in disease.
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Affiliation(s)
- Swathi Krishnan
- Department of Biological Chemistry, 1150 West Medical Center Drive, 5301 Medical Science Research Building III, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, 1150 West Medical Center Drive, 5301 Medical Science Research Building III, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Yan S, Wu G. Correlating dynamic amino acid properties with success rate of crystallization of proteins from Bacteroides vulgatus. CRYSTAL RESEARCH AND TECHNOLOGY 2012. [DOI: 10.1002/crat.201200007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Laganowsky A, Zhao M, Soriaga AB, Sawaya MR, Cascio D, Yeates TO. An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein Sci 2011; 20:1876-90. [PMID: 21898649 DOI: 10.1002/pro.727] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/17/2011] [Accepted: 08/17/2011] [Indexed: 12/31/2022]
Abstract
Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu²⁺, nickel (Ni²⁺), or zinc (Zn²⁺). The approach resulted in 16 new crystal structures--eight for T4L and eight for MBP--displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization-prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest.
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Affiliation(s)
- Arthur Laganowsky
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095-1570, USA
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22
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Derewenda ZS. It's all in the crystals…. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:243-8. [PMID: 21460442 PMCID: PMC3069739 DOI: 10.1107/s0907444911007797] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 03/01/2011] [Indexed: 02/07/2023]
Abstract
Macromolecular crystallography relies on the availability and quality of single crystals; these are typically obtained through extensive screening, which has a very low intrinsic success rate. Crystallization is not a completely stochastic process and many proteins do not succumb to crystallization because of specific microscopic features of their molecular surfaces. It follows that rational surface engineering through site-directed mutagenesis should allow a systematic and significant improvement in crystallization success rates. Here, one such established strategy, surface-entropy reduction (SER), is discussed, including its successes, limitations and possible future developments.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908-0793, USA.
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23
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Cieślik M, Derewenda ZS, Mura C. Abstractions, algorithms and data structures for structural bioinformatics in PyCogent. J Appl Crystallogr 2011; 44:424-428. [PMID: 22479120 PMCID: PMC3253748 DOI: 10.1107/s0021889811004481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 02/07/2011] [Indexed: 11/11/2022] Open
Abstract
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g.kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allowing sequence-based work to benefit from structure-derived data and, reciprocally, enabling structural studies to leverage PyCogent's versatile tools for phylogenetic and evolutionary analyses.
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Affiliation(s)
- Marcin Cieślik
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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24
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Leung DW, Borek D, Farahbakhsh M, Ramanan P, Nix JC, Wang T, Prins KC, Otwinowski Z, Honzatko RB, Helgeson LA, Basler CF, Amarasinghe GK. Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:689-92. [PMID: 20516601 PMCID: PMC2882771 DOI: 10.1107/s1744309110013266] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/10/2010] [Indexed: 11/10/2022]
Abstract
VP35 is one of seven structural proteins encoded by the Ebola viral genome and mediates viral replication, nucleocapsid formation and host immune suppression. The C-terminal interferon inhibitory domain (IID) of VP35 is critical for dsRNA binding and interferon inhibition. The wild-type VP35 IID structure revealed several conserved residues that are important for dsRNA binding and interferon antagonism. Here, the expression, purification and crystallization of recombinant Zaire Ebola VP35 IID mutants R312A, K319A/R322A and K339A in space groups P6(1)22, P2(1)2(1)2(1) and P2(1), respectively, are described. Diffraction data were collected using synchrotron sources at the Advanced Light Source and the Advanced Photon Source.
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Affiliation(s)
- Daisy W. Leung
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Dominika Borek
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Mina Farahbakhsh
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Undergraduate Program, Iowa State University, Ames, IA 50011, USA
| | - Parameshwaran Ramanan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Jay C. Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Kathleen C. Prins
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Zbyszek Otwinowski
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Luke A. Helgeson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Undergraduate Program, Iowa State University, Ames, IA 50011, USA
| | | | - Gaya K. Amarasinghe
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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25
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Derewenda ZS. Application of protein engineering to enhance crystallizability and improve crystal properties. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:604-15. [PMID: 20445236 PMCID: PMC3089013 DOI: 10.1107/s090744491000644x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 02/18/2010] [Indexed: 01/05/2023]
Abstract
Until recently, protein crystallization has mostly been regarded as a stochastic event over which the investigator has little or no control. With the dramatic technological advances in synchrotron-radiation sources and detectors and the equally impressive progress in crystallographic software, including automated model building and validation, crystallization has increasingly become the rate-limiting step in X-ray diffraction studies of macromolecules. However, with the advent of recombinant methods it has also become possible to engineer target proteins and their complexes for higher propensity to form crystals with desirable X-ray diffraction qualities. As most proteins that are under investigation today are obtained by heterologous overexpression, these techniques hold the promise of becoming routine tools with the potential to transform classical crystallization screening into a more rational high-success-rate approach. This article presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA.
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26
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Guo M, Shapiro R, Schimmel P, Yang XL. Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:243-50. [PMID: 20179335 PMCID: PMC2827346 DOI: 10.1107/s0907444909055462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 12/25/2009] [Indexed: 11/10/2022]
Abstract
Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an alpha-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered alpha-helix did not form a leucine zipper that interlocked with the same alpha-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization.
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Affiliation(s)
- Min Guo
- The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 2010; 462:808-12. [PMID: 20010690 PMCID: PMC2799227 DOI: 10.1038/nature08612] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 10/26/2009] [Indexed: 12/02/2022]
Abstract
Mistranslation from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences1-3. Throughout evolution, two editing-checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly1,2. One checkpoint is the AlaRS editing center, while the other is from widely distributed AlaXps—free-standing, genome-encoded editing proteins that clear Ser-tRNAAla. The paradox of misincorporating both a smaller (glycine) and a larger amino acid (serine) suggests a deep conflict for nature-designed AlaRS. To understand the chemical basis for this conflict, kinetic and mutational analysis, together with nine crystal structures, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the α–amino group of the bound amino acid using an acidic residue. This design, of more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently not able to find better architecture for recognition of alanine, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.
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