Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration
Stagg, Loren J.
Vassallo, David A.
Vega, Irving E.
Arold, Stefan T.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Structural Biology and Engineering
Permanent link to this recordhttp://hdl.handle.net/10754/325312
MetadataShow full item record
AbstractThe polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP domains for increasing the yield of fatty acids in bacterial cultures. 2013 Trujillo et al.
CitationTrujillo U, Vázquez-Rosa E, Oyola-Robles D, Stagg LJ, Vassallo DA, et al. (2013) Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration. PLoS ONE 8: e57859. doi:10.1371/journal.pone.0057859.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC3585217
- Expression of dehydratase domains from a polyunsaturated fatty acid synthase increases the production of fatty acids in Escherichia coli.
- Authors: Oyola-Robles D, Rullán-Lind C, Carballeira NM, Baerga-Ortiz A
- Issue date: 2014 Feb 5
- Tandem acyl carrier protein domains in polyunsaturated fatty acid synthases.
- Authors: Jiang H, Rajski SR, Shen B
- Issue date: 2009
- Loading of malonyl-CoA onto tandem acyl carrier protein domains of polyunsaturated fatty acid synthases.
- Authors: Santín O, Moncalián G
- Issue date: 2018 Aug 10
- Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production.
- Authors: Rullán-Lind C, Ortiz-Rosario M, García-González A, Stojanoff V, Chorna NE, Pietri RB, Baerga-Ortiz A
- Issue date: 2019 Nov 5
- Identification of novel protein domains required for the expression of an active dehydratase fragment from a polyunsaturated fatty acid synthase.
- Authors: Oyola-Robles D, Gay DC, Trujillo U, Sánchez-Parés JM, Bermúdez ML, Rivera-Díaz M, Carballeira NM, Baerga-Ortiz A
- Issue date: 2013 Jul
Showing items related by title, author, creator and subject.
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure predictionCui, Xuefeng; Lu, Zhiwu; wang, sheng; Wang, Jim Jing-Yan; Gao, Xin (Bioinformatics, Oxford University Press (OUP), 2016-06-15) [Article]Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.
QAUST: protein function prediction using structure similarity search, protein interaction and functional sequence motifsSmaili, Fatima Z.; Tian, Shuye; Roy, Ambrish; Alazmi, Meshari; Arold, Stefan T.; Mukherjee, Srayanta; Hefty, P. Scott; Chen, Wei; Gao, Xin (Accepted by Genomics, Proteomics, and Bioinformatics, Elsevier, 2020) [Article]The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how biological systems operate. We propose a novel method, QAUST, to infer protein functions, specifically Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. Our method uses three sources of information: structure information encoded by global and local structure similarity search, biological network information inferred by protein-protein interaction data, and sequence information extracted from functionally discriminative sequence motifs. The three pieces of information are combined by consensus averaging to make the final prediction. Our approach has been tested on 500 protein targets from the CAFA benchmark set. The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading. We further demonstrate that a previously unknown function of TRIM22 protein predicted by QAUST can be experimentally validated. Availability: http://www.cbrc.kaust.edu.sa/qaust/submit/.
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact MapsOliva, Romina; Chermak, Edrisse; Cavallo, Luigi (Molecules, MDPI AG, 2015-07-01) [Article]In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.