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Holland J, Grigoryan G. Structure‐conditioned amino‐acid couplings: how contact geometry affects pairwise sequence preferences. Protein Sci 2022; 31:900-917. [PMID: 35060221 PMCID: PMC8927866 DOI: 10.1002/pro.4280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/11/2022]
Abstract
Relating a protein's sequence to its conformation is a central challenge for both structure prediction and sequence design. Statistical contact potentials, as well as their more descriptive versions that account for side‐chain orientation and other geometric descriptors, have served as simplistic but useful means of representing second‐order contributions in sequence–structure relationships. Here we ask what happens when a pairwise potential is conditioned on the fully defined geometry of interacting backbones fragments. We show that the resulting structure‐conditioned coupling energies more accurately reflect pair preferences as a function of structural contexts. These structure‐conditioned energies more reliably encode native sequence information and more highly correlate with experimentally determined coupling energies. Clustering a database of interaction motifs by structure results in ensembles of similar energies and clustering them by energy results in ensembles of similar structures. By comparing many pairs of interaction motifs and showing that structural similarity and energetic similarity go hand‐in‐hand, we provide a tangible link between modular sequence and structure elements. This link is applicable to structural modeling, and we show that scoring CASP models with structured‐conditioned energies results in substantially higher correlation with structural quality than scoring the same models with a contact potential. We conclude that structure‐conditioned coupling energies are a good way to model the impact of interaction geometry on second‐order sequence preferences.
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Affiliation(s)
- Jack Holland
- Department of Computer Science Dartmouth College Hanover New Hampshire USA
| | - Gevorg Grigoryan
- Department of Computer Science Dartmouth College Hanover New Hampshire USA
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Kataria R, Kaundal R. Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets. FRONTIERS IN PLANT SCIENCE 2022; 13:895480. [PMID: 35800602 PMCID: PMC9253690 DOI: 10.3389/fpls.2022.895480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/31/2022] [Indexed: 05/04/2023]
Abstract
Triticum aestivum (wheat), a major staple food grain, is affected by various biotic stresses. Among these, fungal diseases cause about 15-20% of yield loss, worldwide. In this study, we performed a comparative analysis of protein-protein interactions between two Puccinia graminis races (Pgt 21-0 and Pgt Ug99) that cause stem (black) rust in wheat. The available molecular techniques to study the host-pathogen interaction mechanisms are expensive and labor-intensive. We implemented two computational approaches (interolog and domain-based) for the prediction of PPIs and performed various functional analysis to determine the significant differences between the two pathogen races. The analysis revealed that T. aestivum-Pgt 21-0 and T. aestivum-Pgt Ug99 interactomes consisted of ∼90M and ∼56M putative PPIs, respectively. In the predicted PPIs, we identified 115 Pgt 21-0 and 34 Pgt Ug99 potential effectors that were highly involved in pathogen virulence and development. Functional enrichment analysis of the host proteins revealed significant GO terms and KEGG pathways such as O-methyltransferase activity (GO:0008171), regulation of signal transduction (GO:0009966), lignin metabolic process (GO:0009808), plastid envelope (GO:0009526), plant-pathogen interaction pathway (ko04626), and MAPK pathway (ko04016) that are actively involved in plant defense and immune signaling against the biotic stresses. Subcellular localization analysis anticipated the host plastid as a primary target for pathogen attack. The highly connected host hubs in the protein interaction network belonged to protein kinase domain including Ser/Thr protein kinase, MAPK, and cyclin-dependent kinase. We also identified 5,577 transcription factors in the interactions, associated with plant defense during biotic stress conditions. Additionally, novel host targets that are resistant to stem rust disease were also identified. The present study elucidates the functional differences between Pgt 21-0 and Pgt Ug99, thus providing the researchers with strain-specific information for further experimental validation of the interactions, and the development of durable, disease-resistant crop lines.
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Affiliation(s)
- Raghav Kataria
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, Logan, UT, United States
- Department of Computer Science, College of Science, Utah State University, Logan, UT, United States
- *Correspondence: Rakesh Kaundal,
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Saha D, Kundu S. A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. Front Microbiol 2021; 12:613067. [PMID: 33679637 PMCID: PMC7930833 DOI: 10.3389/fmicb.2021.613067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is a leading cause of pneumonia and septicemia across the world. The rapid emergence of multidrug-resistant K. pneumoniae strains necessitates the discovery of effective drugs against this notorious pathogen. However, there is a dearth of knowledge on the mechanisms by which this deadly pathogen subverts host cellular machinery. To fill this knowledge gap, our study attempts to identify the potential mechanisms of host cell subversion by building a K. pneumoniae-human interactome based on rigorous computational methodology. The putative host targets inferred from the predicted interactome were found to be functionally enriched in the host's immune surveillance system and allied functions like apoptosis, hypoxia, etc. A multifunctionality-based scoring system revealed P53 as the most multifunctional protein among host targets accompanied by HIF1A and STAT1. Moreover, mining of host protein-protein interaction (PPI) network revealed that host targets interact among themselves to form a network (TTPPI), where P53 and CDC5L occupy a central position. The TTPPI is composed of several inter complex interactions which indicate that K. pneumoniae might disrupt functional coordination between these protein complexes through targeting of P53 and CDC5L. Furthermore, we identified four pivotal K. pneumoniae-targeted transcription factors (TTFs) that are part of TTPPI and are involved in generating host's transcriptional response to K. pneumoniae-mediated sepsis. In a nutshell, our study identifies some of the pivotal molecular targets of K. pneumoniae which primarily correlate to the physiological response of host during K. pneumoniae-mediated sepsis.
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Affiliation(s)
- Deeya Saha
- Department of Biophysics, Molecular Biology and Bioinformatics, Faculty of Science, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, Faculty of Science, University of Calcutta, Kolkata, India
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Kataria R, Duhan N, Kaundal R. Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. FRONTIERS IN PLANT SCIENCE 2021; 12:807354. [PMID: 35251063 PMCID: PMC8891223 DOI: 10.3389/fpls.2021.807354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Medicago sativa (also known as alfalfa), a forage legume, is widely cultivated due to its high yield and high-value hay crop production. Infectious diseases are a major threat to the crops, owing to huge economic losses to the agriculture industry, worldwide. The protein-protein interactions (PPIs) between the pathogens and their hosts play a critical role in understanding the molecular basis of pathogenesis. Pseudomonas syringae pv. syringae ALF3 suppresses the plant's innate immune response by secreting type III effector proteins into the host cell, causing bacterial stem blight in alfalfa. The alfalfa-P. syringae system has little information available for PPIs. Thus, to understand the infection mechanism, we elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two computational approaches: interolog-based and domain-based method. A total of ∼14 M putative PPIs were predicted between 50,629 alfalfa proteins and 2,932 P. syringae proteins by combining these approaches. Additionally, ∼0.7 M consensus PPIs were also predicted. The functional analysis revealed that P. syringae proteins are highly involved in nucleotide binding activity (GO:0000166), intracellular organelle (GO:0043229), and translation (GO:0006412) while alfalfa proteins are involved in cellular response to chemical stimulus (GO:0070887), oxidoreductase activity (GO:0016614), and Golgi apparatus (GO:0005794). According to subcellular localization predictions, most of the pathogen proteins targeted host proteins within the cytoplasm and nucleus. In addition, we discovered a slew of new virulence effectors in the predicted HPIs. The current research describes an integrated approach for deciphering genome-scale host-pathogen PPIs between alfalfa and P. syringae, allowing the researchers to better understand the pathogen's infection mechanism and develop pathogen-resistant lines.
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Affiliation(s)
- Raghav Kataria
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Bioinformatics Facility, Center for Integrated Biosystems, Utah State University, Logan, UT, United States
- Department of Computer Science, College of Science, Utah State University, Logan, UT, United States
- *Correspondence: Rakesh Kaundal, ;
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Mirzaie M. Identification of native protein structures captured by principal interactions. BMC Bioinformatics 2019; 20:604. [PMID: 31752663 PMCID: PMC6873546 DOI: 10.1186/s12859-019-3186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
Background Evaluation of protein structure is based on trustworthy potential function. The total potential of a protein structure is approximated as the summation of all pair-wise interaction potentials. Knowledge-based potentials (KBP) are one type of potential functions derived by known experimentally determined protein structures. Although several KBP functions with different methods have been introduced, the key interactions that capture the total potential have not studied yet. Results In this study, we seek the interaction types that preserve as much of the total potential as possible. We employ a procedure based on the principal component analysis (PCA) to extract the significant and key interactions in native protein structures. We call these interactions as principal interactions and show that the results of the model that considers only these interactions are very close to the full interaction model that considers all interactions in protein fold recognition. In fact, the principal interactions maintain the discriminative power of the full interaction model. This method was evaluated on 3 KBPs with different contact definitions and thresholds of distance and revealed that their corresponding principal interactions are very similar and have a lot in common. Additionally, the principal interactions consisted of 20 % of the full interactions on average, and they are between residues, which are considered important in protein folding. Conclusions This work shows that all interaction types are not equally important in discrimination of native structure. The results of the reduced model based on principal interactions that were very close to the full interaction model suggest that a new strategy is needed to capture the role of remaining interactions (non-principal interactions) to improve the power of knowledge-based potential functions.
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Affiliation(s)
- Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O.Box: 14115-134, Tehran, Iran.
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Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions. Molecules 2017; 22:molecules22101722. [PMID: 29027921 PMCID: PMC6151622 DOI: 10.3390/molecules22101722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 11/16/2022] Open
Abstract
Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.
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Liu Y, Zeng J, Gong H. Improving the orientation-dependent statistical potential using a reference state. Proteins 2014; 82:2383-93. [DOI: 10.1002/prot.24600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Yufeng Liu
- MOE Key Laboratory of Bioinformatics; School of Life Sciences, Tsinghua University; Beijing 100084 China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University; Beijing 100084 China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics; School of Life Sciences, Tsinghua University; Beijing 100084 China
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Zhou J, Yan W, Hu G, Shen B. SVR_CAF: An integrated score function for detecting native protein structures among decoys. Proteins 2013; 82:556-64. [DOI: 10.1002/prot.24421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/30/2013] [Accepted: 09/10/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Jianhong Zhou
- Center for Systems Biology; Soochow University; Suzhou Jiangsu 215006 China
| | - Wenying Yan
- Center for Systems Biology; Soochow University; Suzhou Jiangsu 215006 China
| | - Guang Hu
- Center for Systems Biology; Soochow University; Suzhou Jiangsu 215006 China
| | - Bairong Shen
- Center for Systems Biology; Soochow University; Suzhou Jiangsu 215006 China
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Using the unfolded state as the reference state improves the performance of statistical potentials. Biophys J 2013. [PMID: 23199923 DOI: 10.1016/j.bpj.2012.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Distance-dependent statistical potentials are an important class of energy functions extensively used in modeling protein structures and energetics. These potentials are obtained by statistically analyzing the proximity of atoms in all combinatorial amino-acid pairs in proteins with known structures. In model evaluation, the statistical potential is usually subtracted by the value of a reference state for better selectivity. An ideal reference state should include the general chemical properties of polypeptide chains so that only the unique factors stabilizing the native structures are retained after calibrating on reference state. However, reference states available as of this writing rarely model specific chemical constraints of peptide bonds and therefore poorly reflect the behavior of polypeptide chains. In this work, we proposed a statistical potential based on unfolded state ensemble (SPOUSE), where the reference state is summarized from the unfolded state ensembles of proteins produced according to the statistical coil model. Due to its better representation of the features of polypeptides, SPOUSE outperforms three of the most widely used distance-dependent potentials not only in native conformation identification, but also in the selection of close-to-native models and correlation coefficients between energy and model error. Furthermore, SPOUSE shows promising possibility of further improvement by integration with the orientation-dependent side-chain potentials.
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Kristiansson E, Österlund T, Gunnarsson L, Arne G, Larsson DGJ, Nerman O. A novel method for cross-species gene expression analysis. BMC Bioinformatics 2013; 14:70. [PMID: 23444967 PMCID: PMC3679856 DOI: 10.1186/1471-2105-14-70] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 02/13/2013] [Indexed: 12/27/2022] Open
Abstract
Background Analysis of gene expression from different species is a powerful way to identify evolutionarily conserved transcriptional responses. However, due to evolutionary events such as gene duplication, there is no one-to-one correspondence between genes from different species which makes comparison of their expression profiles complex. Results In this paper we describe a new method for cross-species meta-analysis of gene expression. The method takes the homology structure between compared species into account and can therefore compare expression data from genes with any number of orthologs and paralogs. A simulation study shows that the proposed method results in a substantial increase in statistical power compared to previously suggested procedures. As a proof of concept, we analyzed microarray data from heat stress experiments performed in eight species and identified several well-known evolutionarily conserved transcriptional responses. The method was also applied to gene expression profiles from five studies of estrogen exposed fish and both known and potentially novel responses were identified. Conclusions The method described in this paper will further increase the potential and reliability of meta-analysis of gene expression profiles from evolutionarily distant species. The method has been implemented in R and is freely available at
http://bioinformatics.math.chalmers.se/Xspecies/.
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Affiliation(s)
- Erik Kristiansson
- Department of Mathematical Statistics, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden.
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On the transferability of fractional contributions to the hydration free energy of amino acids. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1343-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Basu S, Bhattacharyya D, Banerjee R. Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J 2012; 102:2605-14. [PMID: 22713576 DOI: 10.1016/j.bpj.2012.04.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 01/09/2023] Open
Abstract
Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors.
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Affiliation(s)
- Sankar Basu
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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Lu WW, Huang RB, Wei YT, Meng JZ, Du LQ, Du QS. Statistical energy potential: reduced representation of Dehouck–Gilis–Rooman function by selecting against decoy datasets. Amino Acids 2012; 42:2353-61. [DOI: 10.1007/s00726-011-0977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 07/06/2011] [Indexed: 11/24/2022]
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Tian L, Wu A, Cao Y, Dong X, Hu Y, Jiang T. NCACO-score: an effective main-chain dependent scoring function for structure modeling. BMC Bioinformatics 2011; 12:208. [PMID: 21612673 PMCID: PMC3123610 DOI: 10.1186/1471-2105-12-208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background Development of effective scoring functions is a critical component to the success of protein structure modeling. Previously, many efforts have been dedicated to the development of scoring functions. Despite these efforts, development of an effective scoring function that can achieve both good accuracy and fast speed still presents a grand challenge. Results Based on a coarse-grained representation of a protein structure by using only four main-chain atoms: N, Cα, C and O, we develop a knowledge-based scoring function, called NCACO-score, that integrates different structural information to rapidly model protein structure from sequence. In testing on the Decoys'R'Us sets, we found that NCACO-score can effectively recognize native conformers from their decoys. Furthermore, we demonstrate that NCACO-score can effectively guide fragment assembly for protein structure prediction, which has achieved a good performance in building the structure models for hard targets from CASP8 in terms of both accuracy and speed. Conclusions Although NCACO-score is developed based on a coarse-grained model, it is able to discriminate native conformers from decoy conformers with high accuracy. NCACO is a very effective scoring function for structure modeling.
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Affiliation(s)
- Liqing Tian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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