Helical ensembles outperform ideal helices in molecular replacement

The conventional approach in molecular replacement (MR) is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterised families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high albeit local structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolution. Here we explore the performance of libraries of helical ensembles created by clustering helical segments. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. We observed a 30% increase in the number of solutions obtained by AMPLE when using this new set of ensembles compared to performance with ideal helices. The boost of performance was notable across three different folds: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction of the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the “helical ensembles” mode.

[1]  Kathrin Meindl,et al.  Exploiting tertiary structure through local folds for crystallographic phasing , 2013, Nature Methods.

[2]  D. Rigden,et al.  Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling , 2020, Acta Crystallographica Section D: Structural Biology.

[3]  R. Read,et al.  Improved estimates of coordinate error for molecular replacement , 2013, Acta crystallographica. Section D, Biological crystallography.

[4]  G J Barton,et al.  Application of multiple sequence alignment profiles to improve protein secondary structure prediction , 2000, Proteins.

[5]  M. J. Jedrzejas,et al.  Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity. , 2002, Journal of molecular biology.

[6]  C. Millán,et al.  ARCIMBOLDO on coiled coils , 2018, Acta crystallographica. Section D, Structural biology.

[7]  O. Mayans,et al.  Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds , 2016, IUCrJ.

[8]  Ronan M Keegan,et al.  Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment , 2018, Acta crystallographica. Section D, Structural biology.

[9]  N. Oppenheimer,et al.  Structure and mechanism , 1989 .

[10]  Huw T Jenkins,et al.  Fragon: rapid high-resolution structure determination from ideal protein fragments , 2018, Acta crystallographica. Section D, Structural biology.

[11]  Randy J Read,et al.  On the application of the expected log-likelihood gain to decision making in molecular replacement , 2018, Acta crystallographica. Section D, Structural biology.

[12]  Isabel Usón,et al.  ALIXE: a phase-combination tool for fragment-based molecular replacement , 2020, Acta crystallographica. Section D, Structural biology.

[13]  Robert Preissner,et al.  Structural features of transmembrane helices , 2004, FEBS letters.

[14]  M. Woolfson,et al.  ACORN: a review. , 2006, Acta crystallographica. Section D, Biological crystallography.

[15]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[16]  Massimo D Sammito,et al.  ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation , 2020, Acta crystallographica. Section D, Structural biology.

[17]  Martyn D. Winn,et al.  Routine phasing of coiled-coil protein crystal structures with AMPLE , 2015, IUCrJ.

[18]  Evgeny Krissinel,et al.  Enhanced fold recognition using efficient short fragment clustering. , 2012, Journal of molecular biochemistry.

[19]  Martyn D. Winn,et al.  Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models , 2015, Acta crystallographica. Section D, Biological crystallography.

[20]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[21]  Philip Evans,et al.  An introduction to molecular replacement , 2007, Acta crystallographica. Section D, Biological crystallography.

[22]  Andrea Thorn,et al.  Extending molecular-replacement solutions with SHELXE , 2013, Acta crystallographica. Section D, Biological crystallography.

[23]  J. Gough,et al.  The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures , 2019, Nucleic Acids Res..

[24]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[25]  Richard Axel,et al.  Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 Å resolution , 1992, Cell.

[26]  R J Read,et al.  Pushing the boundaries of molecular replacement with maximum likelihood. , 2003, Acta crystallographica. Section D, Biological crystallography.

[27]  Ronan M Keegan,et al.  Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE , 2018, Acta crystallographica. Section D, Structural biology.

[28]  Ronan M Keegan,et al.  AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. , 2012, Acta crystallographica. Section D, Biological crystallography.

[29]  U. Pieper,et al.  Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. , 1998, Structure.

[30]  D. Baker,et al.  Principles for designing ideal protein structures , 2012, Nature.

[31]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[32]  Christopher J. Williams,et al.  Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix , 2019, Acta crystallographica. Section D, Structural biology.

[33]  G. Sheldrick,et al.  Crystallographic ab initio protein structure solution below atomic resolution , 2009, Nature Methods.

[34]  O. Mayans,et al.  Approaches to ab initio molecular replacement of α-helical transmembrane proteins , 2017, Acta crystallographica. Section D, Structural biology.

[35]  Felix Simkovic,et al.  Using Phaser and ensembles to improve the performance of SIMBAD , 2020, Acta crystallographica. Section D, Structural biology.

[36]  Jia‐xing Yao.  ACORN in CCP4 and its applications. , 2002, Acta crystallographica. Section D, Biological crystallography.

[37]  M G Rossmann,et al.  The molecular replacement method. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[38]  E J Dodson,et al.  Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures. , 2000, Structure.

[39]  玉一 芦田,et al.  Acta Crystallographica Section D (Biological Crystallography) の発刊に際して , 1993 .

[40]  Dániel Kozma,et al.  PDBTM: Protein Data Bank of transmembrane proteins after 8 years , 2012, Nucleic Acids Res..