1
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Xiao-Qun Z, Xian-Li M, Ariffin NS. The potential of carbonic anhydrase enzymes as a novel target for anti-cancer treatment. Eur J Pharmacol 2024; 976:176677. [PMID: 38825301 DOI: 10.1016/j.ejphar.2024.176677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
Carbonic anhydrase (CA) is a zinc-dependent metal enzyme that maintains the pH and carbon dioxide (CO2) homeostasis in cells by catalyzing the reversible hydration and dehydration of CO2 and bicarbonate (HCO3-). In mammals, there are 16 isozymes of CA existed, namely CAI to CAXIV, but only 15 isozymes are found in humans except CAXV. Human CAs have highly conserved catalytic domains, all of which are distributed in different tissues and play important physiological roles. Changes in their functions may disrupt the typical distribution of CAs throughout human body and therefore CAs can be used as diagnostic biomarkers for many diseases. Furthermore, the expression of CAs is correlated to the progression of numerous tumors, therapeutic sensitivity and patient prognosis. In this review, we discuss thoroughly the structure of CAs, their functional activities in human physiology, dysregulations and diseases related to CAs, and different types of CA inhibitors that can reverse their dysregulation.
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Affiliation(s)
- Zhou Xiao-Qun
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300, Bandar Puncak Alam, Selangor, Malaysia; Guilin Medical University, GuiLin, China
| | | | - Nur Syamimi Ariffin
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300, Bandar Puncak Alam, Selangor, Malaysia.
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2
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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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3
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Maxwell M, Tan YJ, Lee R, Huber T, Otting G. Electrostatic Contribution to 19F Chemical Shifts in Fluorotryptophans in Proteins. Biochemistry 2023; 62:3255-3264. [PMID: 37934875 DOI: 10.1021/acs.biochem.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
DFT calculations indicate that the 19F chemical shifts of aromatic rings containing single fluorine substituents are sensitive to the electric fields and electric field gradients at the position of the fluorine atom. The present work explores whether long-range structure restraints can be gained from changes in 19F chemical shifts following mutations of charged to uncharged residues. 19F chemical shifts of fluorotryptophan residues were measured in two different proteins, GB1 and the NT* domain, following mutations of single asparagine residues to aspartic acid. Four different versions of fluorotryptophan were investigated, including 4-, 5-, 6-, and 7-fluorotryptophan, which were simultaneously installed by cell-free protein synthesis using 4-, 5-, 6-, and 7-fluoroindole as precursors for the tryptophan synthase present in the S30 extract. For comparison, the 1H chemical shifts of the corresponding nonfluorinated protein mutants produced with 13C-labeled tryptophan were also measured. The results show that the 19F chemical shifts respond more sensitively to the charge mutations than the 1H chemical shifts in the nonfluorinated references, but the chemical shift changes were much smaller than predicted by DFT calculations of fluoroindoles in the electric field of a partial charge in vacuum, indicating comprehensive dielectric shielding by water and protein. No straightforward correlation with the location of the charge mutation could be established.
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Affiliation(s)
- Michael Maxwell
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Yi Jiun Tan
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Richmond Lee
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong 2500, New South Wales, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Gottfried Otting
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
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4
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Sidhanta SPD, Sowdhamini R, Srinivasan N. Comparative analysis of permanent and transient domain-domain interactions in multi-domain proteins. Proteins 2023. [PMID: 37828826 DOI: 10.1002/prot.26581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 10/14/2023]
Abstract
Protein domains are structural, functional, and evolutionary units. These domains bring out the diversity of functionality by means of interactions with other co-existing domains and provide stability. Hence, it is important to study intra-protein inter-domain interactions from the perspective of types of interactions. Domains within a chain could interact over short timeframes or permanently, rather like protein-protein interactions (PPIs). However, no systematic study has been carried out between two classes, namely permanent and transient domain-domain interactions. In this work, we studied 263 two-domain proteins, belonging to either of these classes and their interfaces on the basis of several factors, such as interface area and details of interactions (number, strength, and types of interactions). We also characterized them based on residue conservation at the interface, correlation of residue motions across domains, its involvement in repeat formation, and their involvement in particular molecular processes. Finally, we could analyze the interactions arising from domains in two-domain monomeric proteins, and we observed significant differences between these two classes of domain interactions and a few similarities. This study will help to obtain a better understanding of structure-function and folding principles of multi-domain proteins.
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Affiliation(s)
| | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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5
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Oh J, Durai P, Kannan P, Park J, Yeon YJ, Lee WK, Park K, Seo MH. Domain-wise dissection of thermal stability enhancement in multidomain proteins. Int J Biol Macromol 2023; 237:124141. [PMID: 36958447 DOI: 10.1016/j.ijbiomac.2023.124141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]
Abstract
Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.
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Affiliation(s)
- Jisung Oh
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Prasannavenkatesh Durai
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Chungbuk 28160, South Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
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6
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Yin R, Feng BY, Varshney A, Pierce BG. Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants. Protein Sci 2022; 31:e4379. [PMID: 35900023 PMCID: PMC9278006 DOI: 10.1002/pro.4379] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/17/2022]
Abstract
High-resolution experimental structural determination of protein-protein interactions has led to valuable mechanistic insights, yet due to the massive number of interactions and experimental limitations there is a need for computational methods that can accurately model their structures. Here we explore the use of the recently developed deep learning method, AlphaFold, to predict structures of protein complexes from sequence. With a benchmark of 152 diverse heterodimeric protein complexes, multiple implementations and parameters of AlphaFold were tested for accuracy. Remarkably, many cases (43%) had near-native models (medium or high critical assessment of predicted interactions accuracy) generated as top-ranked predictions by AlphaFold, greatly surpassing the performance of unbound protein-protein docking (9% success rate for near-native top-ranked models), however AlphaFold modeling of antibody-antigen complexes within our set was unsuccessful. We identified sequence and structural features associated with lack of AlphaFold success, and we also investigated the impact of multiple sequence alignment input. Benchmarking of a multimer-optimized version of AlphaFold (AlphaFold-Multimer) with a set of recently released antibody-antigen structures confirmed a low rate of success for antibody-antigen complexes (11% success), and we found that T cell receptor-antigen complexes are likewise not accurately modeled by that algorithm, showing that adaptive immune recognition poses a challenge for the current AlphaFold algorithm and model. Overall, our study demonstrates that end-to-end deep learning can accurately model many transient protein complexes, and highlights areas of improvement for future developments to reliably model any protein-protein interaction of interest.
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Affiliation(s)
- Rui Yin
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
| | - Brandon Y. Feng
- Department of Computer ScienceUniversity of MarylandCollege ParkMarylandUSA
| | - Amitabh Varshney
- Department of Computer ScienceUniversity of MarylandCollege ParkMarylandUSA
| | - Brian G. Pierce
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMarylandUSA
- Marlene and Stewart Greenebaum Comprehensive Cancer CenterUniversity of Maryland School of MedicineBaltimoreMarylandUSA
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7
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From complete cross-docking to partners identification and binding sites predictions. PLoS Comput Biol 2022; 18:e1009825. [PMID: 35089918 PMCID: PMC8827487 DOI: 10.1371/journal.pcbi.1009825] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/09/2022] [Accepted: 01/11/2022] [Indexed: 11/19/2022] Open
Abstract
Proteins ensure their biological functions by interacting with each other. Hence, characterising protein interactions is fundamental for our understanding of the cellular machinery, and for improving medicine and bioengineering. Over the past years, a large body of experimental data has been accumulated on who interacts with whom and in what manner. However, these data are highly heterogeneous and sometimes contradictory, noisy, and biased. Ab initio methods provide a means to a "blind" protein-protein interaction network reconstruction. Here, we report on a molecular cross-docking-based approach for the identification of protein partners. The docking algorithm uses a coarse-grained representation of the protein structures and treats them as rigid bodies. We applied the approach to a few hundred of proteins, in the unbound conformations, and we systematically investigated the influence of several key ingredients, such as the size and quality of the interfaces, and the scoring function. We achieved some significant improvement compared to previous works, and a very high discriminative power on some specific functional classes. We provide a readout of the contributions of shape and physico-chemical complementarity, interface matching, and specificity, in the predictions. In addition, we assessed the ability of the approach to account for protein surface multiple usages, and we compared it with a sequence-based deep learning method. This work may contribute to guiding the exploitation of the large amounts of protein structural models now available toward the discovery of unexpected partners and their complex structure characterisation.
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8
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Van Wyk JC, Sewell BT, Danson MJ, Tsekoa TL, Sayed MF, Cowan DA. Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase. Curr Res Struct Biol 2022; 4:256-270. [PMID: 36106339 PMCID: PMC9465369 DOI: 10.1016/j.crstbi.2022.07.002] [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: 03/10/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022] Open
Abstract
Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4–7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15–1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising. Random mutagenesis yields a 15-fold increase in nitrile hydratase thermostability. Salt bridges and hydrogen bonds improves nitrile hydratase thermostability. Water-mediated hydrogen bonds improves protein thermostability.
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9
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de O Araújo J, Pinheiro S, Zamora WJ, Alves CN, Lameira J, Lima AH. Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9). Sci Rep 2021; 11:23003. [PMID: 34837010 PMCID: PMC8626507 DOI: 10.1038/s41598-021-02366-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. Besides, clustering results for the native dimer showed accessible cavities to drugs. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Jéssica de O Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Silvana Pinheiro
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - William J Zamora
- School of Chemistry & Faculty of Pharmacy, University of Costa Rica, San Pedro, San José, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT-CONARE), Pavas, San José, Costa Rica
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil.
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10
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Mukhopadhyay S, Das T, Bose M, Jain CK, Chakraborty M, Mukherjee S, Shikha K, Das AK, Ganguly A. Residues at the interface between zinc binding and winged helix domains of human RECQ1 play a significant role in DNA strand annealing activity. Nucleic Acids Res 2021; 49:11834-11854. [PMID: 34751402 PMCID: PMC8599812 DOI: 10.1093/nar/gkab968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 10/01/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
RECQ1 is the shortest among the five human RecQ helicases comprising of two RecA like domains, a zinc-binding domain and a RecQ C-terminal domain containing the winged-helix (WH). Mutations or deletions on the tip of a β-hairpin located in the WH domain are known to abolish the unwinding activity. Interestingly, the same mutations on the β-hairpin of annealing incompetent RECQ1 mutant (RECQ1T1) have been reported to restore its annealing activity. In an attempt to unravel the strand annealing mechanism, we have crystallized a fragment of RECQ1 encompassing D2–Zn–WH domains harbouring mutations on the β-hairpin. From our crystal structure data and interface analysis, we have demonstrated that an α-helix located in zinc-binding domain potentially interacts with residues of WH domain, which plays a significant role in strand annealing activity. We have shown that deletion of the α-helix or mutation of specific residues on it restores strand annealing activity of annealing deficient constructs of RECQ1. Our results also demonstrate that mutations on the α-helix induce conformational changes and affects DNA stimulated ATP hydrolysis and unwinding activity of RECQ1. Our study, for the first time, provides insight into the conformational requirements of the WH domain for efficient strand annealing by human RECQ1.
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Affiliation(s)
| | - Tulika Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Madhuparna Bose
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Chetan Kumar Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Mayukh Chakraborty
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Sunandan Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India.,International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Kumari Shikha
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Amit K Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Agneyo Ganguly
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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11
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Murali R, Zhang H, Cai Z, Lam L, Greene M. Rational Design of Constrained Peptides as Protein Interface Inhibitors. Antibodies (Basel) 2021; 10:antib10030032. [PMID: 34449551 PMCID: PMC8395526 DOI: 10.3390/antib10030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
The lack of progress in developing targeted therapeutics directed at protein–protein complexes has been due to the absence of well-defined ligand-binding pockets and the extensive intermolecular contacts at the protein–protein interface. Our laboratory has developed approaches to dissect protein–protein complexes focusing on the superfamilies of erbB and tumor necrosis factor (TNF) receptors by the combined use of structural biology and computational biology to facilitate small molecule development. We present a perspective on the development and application of peptide inhibitors as well as immunoadhesins to cell surface receptors performed in our laboratory.
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Affiliation(s)
- Ramachandran Murali
- Cedars-Sinai Medical Center, Department of Biomedical Science, Research Division of Immunology, Los Angeles, CA 90211, USA
- Correspondence: (R.M.); (M.G.)
| | - Hongtao Zhang
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Zheng Cai
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Lian Lam
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Mark Greene
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
- Correspondence: (R.M.); (M.G.)
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12
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Malhotra S, Joseph AP, Thiyagalingam J, Topf M. Assessment of protein-protein interfaces in cryo-EM derived assemblies. Nat Commun 2021; 12:3399. [PMID: 34099703 PMCID: PMC8184972 DOI: 10.1038/s41467-021-23692-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/14/2021] [Indexed: 02/05/2023] Open
Abstract
Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein-protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein-protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM.
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Affiliation(s)
- Sony Malhotra
- grid.4464.20000 0001 2161 2573Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK ,grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Agnel Praveen Joseph
- grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Jeyan Thiyagalingam
- grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Maya Topf
- grid.4464.20000 0001 2161 2573Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK ,grid.13648.380000 0001 2180 3484Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
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13
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Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA. Structural motifs in protein cores and at protein-protein interfaces are different. Protein Sci 2020; 30:381-390. [PMID: 33166001 DOI: 10.1002/pro.3996] [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: 07/17/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 11/10/2022]
Abstract
Structures of proteins and protein-protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time, there could be differences because in order to function, proteins interact with other molecules, undergo conformations changes, and so forth, which might impose different restraints on the tertiary versus quaternary structures. This study focuses on structural properties of protein-protein interfaces in comparison with the protein core, based on the wealth of currently available structural data and new structure-based approaches. The results showed that physicochemical characteristics, such as amino acid composition, residue-residue contact preferences, and hydrophilicity/hydrophobicity distributions, are similar in protein core and protein-protein interfaces. On the other hand, characteristics that reflect the evolutionary pressure, such as structural composition and packing, are largely different. The results provide important insight into fundamental properties of protein structure and function. At the same time, the results contribute to better understanding of the ways to dock proteins. Recent progress in predicting structures of individual proteins follows the advancement of deep learning techniques and new approaches to residue coevolution data. Protein core could potentially provide large amounts of data for application of the deep learning to docking. However, our results showed that the core motifs are significantly different from those at protein-protein interfaces, and thus may not be directly useful for docking. At the same time, such difference may help to overcome a major obstacle in application of the coevolutionary data to docking-discrimination of the intramolecular information not directly relevant to docking.
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Affiliation(s)
- Anna Hadarovich
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Devlina Chakravarty
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,Department of Chemistry, Rutgers University, Camden, New Jersey, USA
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Petras J Kundrotas
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
| | - Ilya A Vakser
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA.,Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
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14
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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15
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Upadhyayula RS. Computational Investigation of Structural Interfaces of Protein Complexes with Short Linear Motifs. J Proteome Res 2020; 19:3254-3263. [DOI: 10.1021/acs.jproteome.0c00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Raghavender Surya Upadhyayula
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, Rajasthan 302001, India
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16
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Ghosh DK, Kumar A, Ranjan A. T54R mutation destabilizes the dimer of superoxide dismutase 1T54R by inducing steric clashes at the dimer interface. RSC Adv 2020; 10:10776-10788. [PMID: 35492906 PMCID: PMC9050410 DOI: 10.1039/c9ra09870d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/28/2020] [Indexed: 11/29/2022] Open
Abstract
Mutations cause abnormalities in protein structure, function and oligomerization. Different mutations in the superoxide dismutase 1 (SOD1) protein cause its misfolding, loss of dimerization and aggravate its aggregation in the amyotrophic lateral sclerosis disease. In this study, we report the mechanistic details of how a threonine-to-arginine mutation at the 54th position (T54R) of SOD1 results in destabilization of the dimer interface of SOD1T54R. Using computational and experimental methods, we show that the T54R mutation increases fluctuation of the mutation-harboring loop (R54-loop) of SOD1T54R. Fluctuation of this loop causes steric clashes that involve arginine-54 (R54) and other residues of SOD1T54R, resulting in loss of inter-subunit contacts at the dimer interface. Since the T54 residue-containing loop is necessary for the dimerization of wild-type SOD1, fluctuation of the R54-loop, steric clashes involving R54 and loss of inter-subunit contacts give rise to the loss of SOD1T54R dimer stability. This correlates to energetically unfavorable tethering of the monomers of SOD1T54R. The outcome is gradual splitting of SOD1T54R dimers into monomers, thereby exposing the previously buried hydrophobic interface residues to the aqueous environment. This event finally leads to aggregation of SOD1T54R. T54R mutation has no effect in altering the relative positions of copper and zinc ion binding residues of SOD1T54R. The native SOD1 structure is stable, and there is no destabilizing effect at its dimer interface. Overall, our study reveals the intricate mechanism of T54R mutation-associated destabilization of the dimer of the SOD1T54R protein. T54R mutation destabilizes the dimer of SOD1T54R.![]()
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Affiliation(s)
- Debasish Kumar Ghosh
- Computational and Functional Genomics Group
- Centre for DNA Fingerprinting and Diagnostics
- Hyderabad 500039
- India
| | - Abhishek Kumar
- Computational and Functional Genomics Group
- Centre for DNA Fingerprinting and Diagnostics
- Hyderabad 500039
- India
- Graduate Studies
| | - Akash Ranjan
- Computational and Functional Genomics Group
- Centre for DNA Fingerprinting and Diagnostics
- Hyderabad 500039
- India
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17
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Abstract
Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Using single-molecule force spectroscopy, we have defined how stabilizing interfaces among the domains of elongation factor G (EF-G) shape its folding pathway. Contrary to the expectation that multidomain proteins fold sequentially as they emerge from the ribosome, we find that folding cannot be completed until the full protein has been synthesized. This posttranslational folding mechanism results in a propensity for misfolding. It is dictated by an energetic coupling among domains that enables conformational flexibility crucial for EF-G function. EF-G thus provides an example of how distinct biological ends—robust folding and functionally important flexibility—come into conflict during protein biogenesis. Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.
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18
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Smith J, McMullen P, Yuan Z, Pfaendtner J, Jiang S. Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules 2019; 21:435-443. [DOI: 10.1021/acs.biomac.9b01191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Josh Smith
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Patrick McMullen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Zhefan Yuan
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
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19
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Li Q, Scholl ZN, Marszalek PE. Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase. Biophys J 2019; 115:46-58. [PMID: 29972811 DOI: 10.1016/j.bpj.2018.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/31/2018] [Accepted: 05/21/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphoglycerate kinase (PGK) is a highly conserved enzyme that is crucial for glycolysis. PGK is a monomeric protein composed of two similar domains and has been the focus of many studies for investigating interdomain interactions within the native state and during folding. Previous studies used traditional biophysical methods (such as circular dichroism, tryptophan fluorescence, and NMR) to measure signals over a large ensemble of molecules, which made it difficult to observe transient changes in stability or structure during unfolding and refolding of single molecules. Here, we unfold single molecules of PGK using atomic force spectroscopy and steered molecular dynamic computer simulations to examine the conformational dynamics of PGK during its unfolding process. Our results show that after the initial forced separation of its domains, yeast PGK (yPGK) does not follow a single mechanical unfolding pathway; instead, it stochastically follows two distinct pathways: unfolding from the N-terminal domain or unfolding from the C-terminal domain. The truncated yPGK N-terminal domain unfolds via a transient intermediate, whereas the structurally similar isolated C-terminal domain has no detectable intermediates throughout its mechanical unfolding process. The N-terminal domain in the full-length yPGK displays a strong unfolding intermediate 13% of the time, whereas the truncated domain (yPGKNT) transitions through the intermediate 81% of the time. This effect indicates that the mechanical properties of yPGK cannot be simply deduced from the mechanical properties of its constituents. We also find that Escherichia coli PGK is significantly less mechanically stable as compared to yPGK, contrary to bulk unfolding measurements. Our results support the growing body of observations that the folding behavior of multidomain proteins is difficult to predict based solely on the studies of isolated domains.
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Affiliation(s)
- Qing Li
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Piotr E Marszalek
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
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20
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Verma R, Pandit SB. Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions. PLoS One 2019; 14:e0220336. [PMID: 31374091 PMCID: PMC6677297 DOI: 10.1371/journal.pone.0220336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Intra-chain domain interactions are known to play a significant role in the function and stability of multidomain proteins. These interactions are mediated through a physical interaction at domain-domain interfaces (DDIs). With a motivation to understand evolution of interfaces, we have investigated similarities among DDIs. Even though interfaces of protein-protein interactions (PPIs) have been previously studied by structurally aligning interfaces, similar analyses have not yet been performed on DDIs of either multidomain proteins or PPIs. For studying the structural landscape of DDIs, we have used iAlign to structurally align intra-chain domain interfaces of domains. The interface alignment of spatially constrained domains (due to inter-domain linkers) showed that ~88% of these could identify a structural matching interface having similar C-alpha geometry and contact pattern despite that aligned domain pairs are not structurally related. Moreover, the mean interface similarity score (IS-score) is 0.307, which is higher compared to the average random IS-score (0.207) suggesting domain interfaces are not random. The structural space of DDIs is highly connected as ~84% of all possible directed edges among interfaces are found to have at most path length of 8 when 0.26 is IS-score threshold. At this threshold, ~83% of interfaces form the largest strongly connected component. Thus, suggesting that structural space of intra-chain domain interfaces is degenerate and highly connected, as has been found in PPI interfaces. Interestingly, searching for structural neighbors of inter-chain interfaces among intra-chain interfaces showed that ~86% could find a statistically significant match to intra-chain interface with a mean IS-score of 0.311. This implies that domain interfaces are degenerate whether formed within a protein or between proteins. The interface degeneracy is most likely due to limited possible ways of packing secondary structures. In principle, interface similarities can be exploited to accurately model domain interfaces in structure prediction of multidomain proteins.
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Affiliation(s)
- Rivi Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shashi Bhushan Pandit
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
- * E-mail:
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21
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Dequeker C, Laine E, Carbone A. Decrypting protein surfaces by combining evolution, geometry, and molecular docking. Proteins 2019; 87:952-965. [PMID: 31199528 PMCID: PMC6852240 DOI: 10.1002/prot.25757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Accepted: 06/07/2019] [Indexed: 01/30/2023]
Abstract
The growing body of experimental and computational data describing how proteins interact with each other has emphasized the multiplicity of protein interactions and the complexity underlying protein surface usage and deformability. In this work, we propose new concepts and methods toward deciphering such complexity. We introduce the notion of interacting region to account for the multiple usage of a protein's surface residues by several partners and for the variability of protein interfaces coming from molecular flexibility. We predict interacting patches by crossing evolutionary, physicochemical and geometrical properties of the protein surface with information coming from complete cross-docking (CC-D) simulations. We show that our predictions match well interacting regions and that the different sources of information are complementary. We further propose an indicator of whether a protein has a few or many partners. Our prediction strategies are implemented in the dynJET2 algorithm and assessed on a new dataset of 262 protein on which we performed CC-D. The code and the data are available at: http://www.lcqb.upmc.fr/dynJET2/.
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Affiliation(s)
- Chloé Dequeker
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France.,Institut Universitaire de France (IUF), Paris, France
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22
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Models for Antibody Behavior in Hydrophobic Interaction Chromatography and in Self-Association. J Pharm Sci 2019; 108:1434-1441. [DOI: 10.1016/j.xphs.2018.11.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/01/2018] [Accepted: 11/19/2018] [Indexed: 11/15/2022]
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23
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Pradhan S, Das P, Mattaparthi VSK. Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics Approach. ACS OMEGA 2018; 3:15442-15454. [PMID: 31458200 PMCID: PMC6643373 DOI: 10.1021/acsomega.8b01793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/01/2018] [Indexed: 05/23/2023]
Abstract
The scaffold nature of Xeroderma pigmentosum complementation group A (XPA) protein makes it an important member of nucleotide excision repair (NER) that removes bulky DNA lesions with the help of various protein-protein interactions (PPI) and DNA-protein interactions. However, many structural insights of XPA's interaction and the binding patterns with other NER proteins are yet to be understood. Here, we have studied one such crucial PPI of XPA with another NER protein, Xeroderma pigmentosum complementation group A (XPE), by using the previously identified binding site of XPA (residues 185-226) in the Assisted Model Building With Energy Refinement force-field-mediated dynamic system. We studied the relationship between XPA185-226-XPE complex using three different docked models. The major residues observed in all of the models that were responsible for the PPI of this complex were Arg20, Arg47, Asp51, and Leu57 from XPE and the residues Leu191, Gln192, Val193, Trp194, Glu198, Glu202, Glu205, Arg207, Glu209, Gln216, and Phe219 from XPE185-226. During the simulation study, the orientation of XPA was also noted to be changed by almost 180° in models 1 and 3, which remain unchanged in model 2, indicating that XPA interacts with XPE with its N-terminal end facing downward and C-terminal end facing upward. The same was concurrent with the binding of DNA-binding domain region of XPA (aa98-239) with XPE. The N-terminal of XPE was stretched for accommodating XPA. Using the per-residue energy decomposition analysis for the interface residues of all models, the binding affinity between these proteins were found to be dependent on R20, R47, and L57 of XPE and the residues L191, V193, W194, E198, E202, E205, R207, and F219 of XPA. The net binding free energy of the XPA185-226-XPE protein complex was found to be -48.3718 kcal mol-1 for model 1, -49.09 kcal mol-1 for model 2, and -56.51 kcal mol-1 for model 3.
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24
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Pradhan S, Sarma H, Mattaparthi VSK. Investigation of the probable homo-dimer model of the Xeroderma pigmentosum complementation group A (XPA) protein to represent the DNA-binding core. J Biomol Struct Dyn 2018; 37:3322-3336. [PMID: 30205752 DOI: 10.1080/07391102.2018.1517051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Xeroderma pigmentosum complementation group A (XPA) protein functions as a primary damage verifier and as a scaffold protein in nucleotide excision repair (NER) in all higher organisms. New evidence of XPA's existence as a dimer and the redefinition of its DNA-binding domain (DBD) raises new questions regarding the stability and functional position of XPA in NER. Here, we have investigated XPA's dimeric status with respect to its previously defined DBD (XPA98-219) as well as with its redefined DBD (XPA98-239). We studied the stability of XPA98-210 and XPA98-239 homo-dimer systems using all-atom molecular dynamics simulation, and we have also characterized the protein-protein interactions (PPI) of these two homo-dimeric forms of XPA. After conducting the root mean square deviation (RMSD) analyses, it was observed that the XPA98-239 homo-dimer has better stability than XPA98-210. It was also found that XPA98-239 has a larger number of hydrogen bonds, salt bridges, and hydrophobic interactions than the XPA98-210 homo-dimer. We further found that Lys, Glu, Gln, Asn, and Arg residues shared the major contribution toward the intermolecular interactions in XPA homo-dimers. The binding free energy (BFE) analysis, which used the molecular mechanics Poisson-Boltzmann method (MM-PBSA) and the generalized Born and surface area continuum solvation model (GBSA) for both XPA homo-dimers, also substantiated the positive result in favor of the stability of the XPA98-239 homo-dimer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sushmita Pradhan
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Himakshi Sarma
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Venkata Satish Kumar Mattaparthi
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
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25
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A model for hydrophobic protrusions on peripheral membrane proteins. PLoS Comput Biol 2018; 14:e1006325. [PMID: 30048443 PMCID: PMC6080788 DOI: 10.1371/journal.pcbi.1006325] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 08/07/2018] [Accepted: 06/24/2018] [Indexed: 11/19/2022] Open
Abstract
With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein surfaces. The purpose of this contribution is to identify simple but essential components for membrane binding, through structural criteria that distinguish exposed hydrophobes at membrane binding sites from those that are frequently found on any protein surface. We formulate the concepts of protruding hydrophobes and co-insertability and have analysed more than 300 families of proteins that are classified as peripheral membrane binders. We find that this structural motif strongly discriminates the surfaces of membrane-binding and non-binding proteins. Our model constitutes a novel formulation of a structural pattern for membrane recognition and emphasizes the importance of subtle structural properties of hydrophobic membrane binding sites. Peripheral membrane proteins bind cellular membranes transiently, and are otherwise soluble proteins. As the interaction between proteins and membranes happens at cellular interfaces they are naturally involved in important interfacial processes such as recognition, signaling and trafficking. Commonly their binding sites are also soluble, and their binding mechanisms poorly understood. This complicates the elaboration of conceptual and quantitative models for peripheral membrane binding and makes binding site prediction difficult. It is therefore of great interest to discover traits that are common between these binding sites and that distinguishes them from other protein surfaces. In this work we identify simple and general structural features that facilitate membrane recognition by soluble proteins. We show that these motifs are highly over-represented on peripheral membrane proteins.
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26
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Vishwanath S, de Brevern AG, Srinivasan N. Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. PLoS Comput Biol 2018; 14:e1006008. [PMID: 29432415 PMCID: PMC5825166 DOI: 10.1371/journal.pcbi.1006008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/23/2018] [Accepted: 01/29/2018] [Indexed: 02/01/2023] Open
Abstract
The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties. High prevalence of multi-domain proteins in proteomes has been attributed to higher stability and functional and folding advantages of the multi-domain proteins. Influence of tethering of domains on the overall properties of proteins has been well studied but its influence on the properties of the constituent domains is largely unaddressed. Here, we investigate the influence of tethering of domains in multi-domain proteins on the structural, dynamics and energetics properties of the constituent domains and its implications on the functions of proteins. To this end, comparative analyses were carried out for identical protein domains crystallized in tethered and untethered forms. Also, comparative analyses of single-domain proteins and their homologous multi-domain proteins were performed. The analyses suggest that tethering influences the structural, dynamic and energetic properties of constituent protein domains. Our observations hint at regulation of protein domains by tethered domains in multi-domain systems, which may manifest at the differential function observed between single-domain and homologous multi-domain proteins.
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Grants
- IISc-DBT partnership programme
- DST, India (Mathematical Biology Initiative & J.C. Bose National Fellowship, FIST program)
- UGC, India – Centre for Advanced Studies
- Ministry of Human Resource Development
- Ministry of Research (France), University of Paris Diderot, Sorbonne Paris Cité
- National Institute for Blood Transfusion (INTS, France), Institute for Health and Medical Research (INSERM, France), Laboratory of Excellence GR-Ex
- The labex GR-Ex is funded by the program Investissements d’avenir of the French National Research Agency,
- Indo-French Centre for the Promotion of Advanced Research/CEFIPRA for a collaborative grant
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Affiliation(s)
- Sneha Vishwanath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G. de Brevern
- INSERM, U 1134, DSIMB, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR_S 1134, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- Laboratoire d' Excellence GR-Ex, Paris, France
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27
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Arif SM, Patil AG, Varshney U, Vijayan M. Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:349-364. [PMID: 28375146 DOI: 10.1107/s2059798317002534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/14/2017] [Indexed: 01/12/2023]
Abstract
Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate. The role of domain 2 appears to be limited to speeding up the reaction. Crystal structures of the apoenzyme and those of ligand-bound enzyme prepared in the presence of 8-oxo-GTP or 8-oxo-dGTP and different concentrations of magnesium were determined. In all of the structures except one, the molecules arrange themselves in a head-to-tail fashion in which domain 1 is brought into contact with domain 2 (trans domain 2) of a neighbouring molecule. The binding site for NTP (site A) is almost exclusively made up of residues from domain 1, while those for NDP (site B) and NMP (site C) are at the interface between domain 1 and trans domain 2 in an unusual instance of intermolecular interactions leading to binding sites. Protein-ligand interactions at site A lead to a proposal for the mechanism of hydrolysis of NTP to NDP and phosphate. A small modification in site A in the crystal which does not exhibit the head-to-tail arrangement appears to facilitate the production of NMP and pyrophosphate from NTP. The two arrangements could be in dynamic equilibrium in the cellular milieu.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A G Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Medvedev KE, Kolchanov NA, Afonnikov DA. High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations. J Biomol Struct Dyn 2017; 36:68-82. [DOI: 10.1080/07391102.2016.1268070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill E. Medvedev
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolay A. Kolchanov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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29
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Shih O, Yeh YQ, Liao KF, Sung TC, Chiang YW, Jeng US. Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution. Phys Chem Chem Phys 2017; 19:7947-7954. [DOI: 10.1039/c6cp08820a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear oligomerization of ditopic BAX-dimers into tri-dimer helical units then into a rod-like structure, as revealed using integrated ESR/SAXS/MD analyses.
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Affiliation(s)
- Orion Shih
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Tai-Ching Sung
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
- Department of Chemical Engineering
- National Tsing Hua University
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30
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Spudich JA, Aksel T, Bartholomew SR, Nag S, Kawana M, Yu EC, Sarkar SS, Sung J, Sommese RF, Sutton S, Cho C, Adhikari AS, Taylor R, Liu C, Trivedi D, Ruppel KM. Effects of hypertrophic and dilated cardiomyopathy mutations on power output by human β-cardiac myosin. ACTA ACUST UNITED AC 2016; 219:161-7. [PMID: 26792326 DOI: 10.1242/jeb.125930] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypertrophic cardiomyopathy is the most frequently occurring inherited cardiovascular disease, with a prevalence of more than one in 500 individuals worldwide. Genetically acquired dilated cardiomyopathy is a related disease that is less prevalent. Both are caused by mutations in the genes encoding the fundamental force-generating protein machinery of the cardiac muscle sarcomere, including human β-cardiac myosin, the motor protein that powers ventricular contraction. Despite numerous studies, most performed with non-human or non-cardiac myosin, there is no clear consensus about the mechanism of action of these mutations on the function of human β-cardiac myosin. We are using a recombinantly expressed human β-cardiac myosin motor domain along with conventional and new methodologies to characterize the forces and velocities of the mutant myosins compared with wild type. Our studies are extending beyond myosin interactions with pure actin filaments to include the interaction of myosin with regulated actin filaments containing tropomyosin and troponin, the roles of regulatory light chain phosphorylation on the functions of the system, and the possible roles of myosin binding protein-C and titin, important regulatory components of both cardiac and skeletal muscles.
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Affiliation(s)
- James A Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tural Aksel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sadie R Bartholomew
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Suman Nag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Masataka Kawana
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elizabeth Choe Yu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Saswata S Sarkar
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jongmin Sung
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruth F Sommese
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Sutton
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carol Cho
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arjun S Adhikari
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rebecca Taylor
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Liu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Darshan Trivedi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathleen M Ruppel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA Department of Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA 94305, USA
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31
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Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces. PLoS One 2015; 10:e0140965. [PMID: 26517868 PMCID: PMC4627654 DOI: 10.1371/journal.pone.0140965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 10/03/2015] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions (PPIs) play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP) complexes, and 161 protein-ligand (PL) complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophys J 2015. [PMID: 26213149 DOI: 10.1016/j.bpj.2015.06.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank; however, available protein complexes cover less than 10% of the human proteome. Although it is theoretically possible to infer interactions in human proteins based on structures of homologous protein complexes, it is still unclear to what extent protein interactions and binding sites are conserved, and whether protein complexes from remotely related species can be used to infer interactions and binding sites. We considered biological units of protein complexes and clustered protein-protein binding sites into similarity groups based on their structure and sequence, which allowed us to identify unique binding sites. We showed that the growth rate of the number of unique binding sites in the Protein Data Bank was much slower than the growth rate of the number of structural complexes. Next, we investigated the evolutionary roots of unique binding sites and identified the major phyletic branches with the largest expansion in the number of novel binding sites. We found that many binding sites could be traced to the universal common ancestor of all cellular organisms, whereas relatively few binding sites emerged at the major evolutionary branching points. We analyzed the physicochemical properties of unique binding sites and found that the most ancient sites were the largest in size, involved many salt bridges, and were the most compact and least planar. In contrast, binding sites that appeared more recently in the evolution of eukaryotes were characterized by a larger fraction of polar and aromatic residues, and were less compact and more planar, possibly due to their more transient nature and roles in signaling processes.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Alexey K Shaytan
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Benjamin A Shoemaker
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Anna R Panchenko
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland.
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34
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López-Pelegrín M, Ksiazek M, Karim AY, Guevara T, Arolas JL, Potempa J, Gomis-Rüth FX. A novel mechanism of latency in matrix metalloproteinases. J Biol Chem 2015; 290:4728-4740. [PMID: 25555916 DOI: 10.1074/jbc.m114.605956] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Abdulkarim Y Karim
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Tibisay Guevara
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Joan L Arolas
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and; the Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
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Sudha G, Nussinov R, Srinivasan N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:141-50. [PMID: 25077409 DOI: 10.1016/j.pbiomolbio.2014.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/13/2014] [Indexed: 12/20/2022]
Abstract
Rich data bearing on the structural and evolutionary principles of protein-protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial 'driver' mutations in oncogenesis. They also provide the foundation toward the design of protein-protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein-protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein-protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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36
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Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:187-93. [PMID: 24931138 DOI: 10.1016/j.pbiomolbio.2014.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 05/17/2014] [Indexed: 11/16/2022]
Abstract
Protein interactions have evolved into highly precise and regulated networks adding an immense layer of complexity to cellular systems. The most accurate atomistic description of protein binding sites can be obtained directly from structures of protein complexes. The availability of structurally characterized protein interfaces significantly improves our understanding of interactomes, and the progress in structural characterization of protein-protein interactions (PPIs) can be measured by calculating the structural coverage of protein domain families. We analyze the coverage of protein domain families (defined according to CDD and Pfam databases) by structures, structural protein-protein complexes and unique protein binding sites. Structural PPI coverage of currently available protein families is about 30% without any signs of saturation in coverage growth dynamics. Given the current growth rates of domain databases and structural PPI deposition, complete domain coverage with PPIs is not expected in the near future. As a result of this study we identify families without any protein-protein interaction evidence (listed on a supporting website http://www.ncbi.nlm.nih.gov/Structure/ibis/coverage/) and propose them as potential targets for structural studies with a focus on protein interactions.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Benjamin A Shoemaker
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Dachuan Zhang
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Alexey Sarychev
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Anna R Panchenko
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States.
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37
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Finn RD, Miller BL, Clements J, Bateman A. iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res 2013; 42:D364-73. [PMID: 24297255 PMCID: PMC3965099 DOI: 10.1093/nar/gkt1210] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain–domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain–domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain–domain and 15 500 domain–ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.
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Affiliation(s)
- Robert D Finn
- HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn VA 20147 USA and European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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38
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Warwicker J, Charonis S, Curtis RA. Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design. Mol Pharm 2013; 11:294-303. [PMID: 24283752 PMCID: PMC3885198 DOI: 10.1021/mp4004749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prediction and engineering of protein solubility is an important but imprecise area. While some features are routinely used, such as the avoidance of extensive non-polar surface area, scope remains for benchmarking of sequence and structural features with experimental data. We study properties in the context of experimental solubilities, protein gene expression levels, and families of abundant proteins (serum albumin and myoglobin) and their less abundant paralogues. A common feature that emerges for proteins with elevated solubility and at higher expression and abundance levels is an increased ratio of lysine content to arginine content. We suggest that the same properties of arginine that give rise to its recorded propensity for specific interaction surfaces also lead to favorable interactions at nonspecific contacts, and thus lysine is favored for proteins at relatively high concentration. A survey of protein therapeutics shows that a significant subset possesses a relatively low lysine to arginine ratio, and therefore may not be favored for high protein concentration. We conclude that modulation of lysine and arginine content could prove a useful and relatively simple addition to the toolkit available for engineering protein solubility in biotechnological applications.
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Affiliation(s)
- Jim Warwicker
- Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, U.K
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39
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Mosca R, Céol A, Aloy P. Interactome3D: adding structural details to protein networks. Nat Methods 2013; 10:47-53. [DOI: 10.1038/nmeth.2289] [Citation(s) in RCA: 339] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/30/2012] [Indexed: 01/13/2023]
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40
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Zawaira A, Shibayama Y. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2012; 13:185-200. [PMID: 22956349 DOI: 10.1007/s10969-012-9141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/08/2012] [Indexed: 06/01/2023]
Abstract
The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.
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Affiliation(s)
- Alexander Zawaira
- Gene Expression and Biophysics Group, Synthetic Biology, ERA, CSIR Biosciences, Brummeria, Pretoria, South Africa.
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41
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Lafontaine CA, Grainger S, Hess BL, Béland M, Lohnes D. Cdx1 interacts physically with a subset of Hox proteins. Biochemistry 2012; 51:9698-705. [PMID: 23121490 DOI: 10.1021/bi301241q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cdx and Hox gene families encode homeodomain-containing transcription factors involved in anterior-posterior vertebral patterning. Although Cdx proteins are direct transcriptional regulators of Hox gene expression, both Hox and Cdx proteins are known to interact with other homeodomain transcription factors, leading us to speculate that Cdx and Hox proteins may also interact physically. In testing this, we found that that Cdx1 is indeed capable of associating with a subset of Hox proteins. This interaction is localized to the homeodomain region of both classes of proteins, is reliant on specific arginine residues in helix I of the Hox homeodomain, and is further modulated by N-terminal Hox sequences. More promiscuous interactions were seen with Hox proteins expressed in vivo, suggestive of bridging factors or post-translational modifications. Finally, we demonstrate that this interaction modulates Cdx-Hox transcriptional activity on a Hox-responsive element. This study is the first example of Cdx-Hox protein interactions and suggests that such complexes may modulate Hox and/or Cdx function.
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Affiliation(s)
- Christine A Lafontaine
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada
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42
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Pang B, Kuang X, Zhao N, Korkin D, Shyu CR. PBSword: a web server for searching similar protein-protein binding sites. Nucleic Acids Res 2012; 40:W428-34. [PMID: 22689645 PMCID: PMC3394332 DOI: 10.1093/nar/gks527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
PBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein–protein binding sites from a large-scale database. The basic idea of PBSword is that each protein binding site is first represented by a high-dimensional vector of ‘visual words’, which characterizes both the global and local shape features of the binding site. It then uses a scalable indexing technique to search for those binding sites whose visual words representations are similar to that of the query binding site. Our system is able to return ranked results of binding sites in short time from a database of 194 322 domain–domain binding sites. PBSword supports query by protein ID and by new structures uploaded by users. PBSword is a useful tool to investigate functional connections among proteins based on the local structures of binding site and has potential applications to protein–protein docking and drug discovery. The system is hosted at http://pbs.rnet.missouri.edu.
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Affiliation(s)
- Bin Pang
- Informatics Institute and Department of Computer Science, University of Missouri, Columbia, MO, USA
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Imtaiyaz Hassan M, Shajee B, Waheed A, Ahmad F, Sly WS. Structure, function and applications of carbonic anhydrase isozymes. Bioorg Med Chem 2012; 21:1570-82. [PMID: 22607884 DOI: 10.1016/j.bmc.2012.04.044] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/02/2012] [Accepted: 04/21/2012] [Indexed: 01/16/2023]
Abstract
The carbonic anhydrases enzymes (CAs, EC 4.2.1.1) are zinc containing metalloproteins, which efficiently catalyse the reversible conversion of carbon dioxide to bicarbonate and release proton. These enzymes are essentially important for biological system and play several important physiological and patho-physiological functions. There are 16 different alpha-carbonic anhydrase isoforms studied, differing widely in their cellular localization and biophysical properties. The catalytic domains of all CAs possess a conserved tertiary structure fold, with predominately β-strands. We performed an extensive analysis of all 16 mammalian CAs for its structure and function in order to establish a structure-function relationship. CAs have been a potential therapeutic target for many diseases. Sulfonamides are considered as a strong and specific inhibitor of CA, and are being used as diuretics, anti-glaucoma, anti-epileptic, anti-ulcer agents. Currently CA inhibitors are widely used as a drug for the treatment of neurological disorders, anti-glaucoma drugs, anti-cancer, or anti-obesity agents. Here we tried to emphasize how CAs can be used for drug discovery, design and screening. Furthermore, we discussed the role of CA in carbon capture, carbon sensor and metabolon. We hope this review provide many useful information on structure, function, mechanism, and applications of CAs in various discipline.
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Affiliation(s)
- Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Shameer K, Sowdhamini R. Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. J Clin Bioinforma 2012; 2:8. [PMID: 22472218 PMCID: PMC3508620 DOI: 10.1186/2043-9113-2-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/03/2012] [Indexed: 11/20/2022] Open
Abstract
Background 3D domain swapping is a novel structural phenomenon observed in diverse set of protein structures in oligomeric conformations. A distinct structural feature, where structural segments in a protein dimer or higher oligomer were shared between two or more chains of a protein structure, characterizes 3D domain swapping. 3D domain swapping was observed as a key mediator of numerous functional mechanisms and play pathogenic role in various diseases including conformational diseases like amyloidosis, Alzheimer's disease, Parkinson's disease and prion diseases. We report the first study with a focus on identifying functional classes, pathways and diseases mediated by 3D domain swapping in the human proteome. Methods We used a panel of four enrichment tools with two different ontologies and two annotations database to derive biological and clinical relevant information associated with 3D domain swapping. Protein domain enrichment analysis followed by Gene Ontology (GO) term enrichment analysis revealed the functional repertoire of proteins involved in swapping. Pathway analysis using KEGG annotations revealed diverse pathway associations of human proteins involved in 3D domain swapping. Disease Ontology was used to find statistically significant associations with proteins in swapped conformation and various disease categories (P-value < 0.05). Results We report meta-analysis results of a literature-curated dataset of human gene products involved in 3D domain swapping and discuss new insights about the functional repertoire, pathway associations and disease implications of proteins involved in 3D domain swapping. Conclusions Our integrated bioinformatics pipeline comprising of four different enrichment tools, two ontologies and two annotations revealed new insights into the functional and disease correlations with 3D domain swapping. GO term enrichment were used to infer terms associated with three different GO categories. Protein domain enrichment was used to identify conserved domains enriched in swapped proteins. Pathway enrichment analysis using KEGG annotations revealed that proteins with swapped conformations are present in all six classes of KEGG BRITE hierarchy and significantly enriched KEGG pathways were observed in five classes. Five major classes of disease were found to be associated with 3D domain swapping using functional disease ontology based enrichment analysis. Five classes of human diseases: cancer, diseases of the respiratory or pulmonary system, degenerative diseases of the central nervous system, vascular disease and encephalitis were found to be significant. In conclusion, our study shows that bioinformatics based analytical approaches using curated data can enhance the understanding of functional and disease implications of 3D domain swapping.
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Affiliation(s)
- Khader Shameer
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, India.
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Parbhoo N, Stoychev SH, Fanucchi S, Achilonu I, Adamson RJ, Fernandes M, Gildenhuys S, Dirr HW. A Conserved Interdomain Interaction Is a Determinant of Folding Cooperativity in the GST Fold. Biochemistry 2011; 50:7067-75. [DOI: 10.1021/bi2006509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nishal Parbhoo
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Stoyan H. Stoychev
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Sylvia Fanucchi
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Ikechukwu Achilonu
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Roslin J. Adamson
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Manuel Fernandes
- School of
Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Samantha Gildenhuys
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Heini W. Dirr
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
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Xue LC, Dobbs D, Honavar V. HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics 2011; 12:244. [PMID: 21682895 PMCID: PMC3213298 DOI: 10.1186/1471-2105-12-244] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/17/2011] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. RESULTS We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence.Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used to predict the interface residues of a query protein with a specific target protein.Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC) of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of both the query and the target can be reliably identified. The HomPPI web server is available at http://homppi.cs.iastate.edu/. CONCLUSIONS Sequence homology-based methods offer a class of computationally efficient and reliable approaches for predicting the protein-protein interface residues that participate in either obligate or transient interactions. For query proteins involved in transient interactions, the reliability of interface residue prediction can be improved by exploiting knowledge of putative interaction partners.
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Affiliation(s)
- Li C Xue
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA.
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Zandarashvili L, Li DW, Wang T, Brüschweiler R, Iwahara J. Signature of mobile hydrogen bonding of lysine side chains from long-range 15N-13C scalar J-couplings and computation. J Am Chem Soc 2011; 133:9192-5. [PMID: 21591797 DOI: 10.1021/ja202219n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid side chains involved in hydrogen bonds and electrostatic interactions are crucial for protein function. However, detailed investigations of such side chains in solution are rare. Here, through the combination of long-range (15)N-(13)C scalar J-coupling measurements and an atomic-detail molecular dynamics (MD) simulation, direct insight into the structural dynamic behavior of lysine side chains in human ubiquitin has been gained. On the basis of (1)H/(13)C/(15)N heteronuclear correlation experiments selective for lysine NH(3)(+) groups, we analyzed two different types of long-range (15)N-(13)C J-coupling constants: one between intraresidue (15)Nζ and (13)Cγ nuclei ((3)J(NζCγ)) and the other between (15)Nζ and carbonyl (13)C' nuclei across a hydrogen bond ((h3)J(NζC')). The experimental (3)J(NζCγ) data confirm the highly mobile nature of the χ(4) torsion angles of lysine side chains seen in the MD simulation. The NH(3)(+) groups of Lys29 and Lys33 exhibit measurable (h3)J(NζC') couplings arising from hydrogen bonds with backbone carbonyl groups of Glu16 and Thr14, respectively. When interpreted together with the (3)J(NζCγ)-coupling constants and NMR-relaxation-derived S(2) order parameters of the NH(3)(+) groups, they strongly suggest that hydrogen bonds involving NH(3)(+) groups are of a transient and highly dynamic nature, in remarkably good agreement with the MD simulation results.
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Affiliation(s)
- Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
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Role of the interface between the FMN and FAD domains in the control of redox potential and electronic transfer of NADPH-cytochrome P450 reductase. Biochem J 2011; 435:197-206. [PMID: 21265736 DOI: 10.1042/bj20101984] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CPR (NADPH-cytochrome P450 reductase) is a multidomain protein containing two flavin-containing domains joined by a connecting domain thought to control the necessary movements of the catalytic domains during electronic cycles. We present a detailed biochemical analysis of two chimaeric CPRs composed of the association of human or yeast FMN with the alternative connecting/FAD domains. Despite the assembly of domains having a relatively large evolutionary distance between them, our data support the idea that the integrity of the catalytic cycle is conserved in our chimaeric enzymes, whereas the recognition, interactions and positioning of both catalytic domains are probably modified. The main consequences of the chimaerogenesis are a decrease in the internal electron-transfer rate between both flavins correlated with changes in the geometry of chimaeric CPRs in solution. Results of the present study highlight the role of the linker and connecting domain in the recognition at the interfaces between the catalytic domains and the impact of interdomain interactions on the redox potentials of the flavins, the internal electron-transfer efficiency and the global conformation and dynamic equilibrium of the CPRs.
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Chuang GY, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D, Vajda S, Beamer LJ. Domain motion and interdomain hot spots in a multidomain enzyme. Protein Sci 2011; 19:1662-72. [PMID: 20589904 DOI: 10.1002/pro.446] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this article is to analyze conformational changes by comparing 10 different structures of Pseudomonas aeruginosa phosphomannomutase/phosphoglucomutase (PMM/PGM), a four-domain enzyme in which both substrate binding and catalysis require substantial movement of the C-terminal domain. We focus on changes in interdomain and active site crevices using a method called computational solvent mapping rather than superimposing the structures. The method places molecular probes (i.e., small organic molecules containing various functional groups) around the protein to find hot spots. One of the most important hot spots is in the active site, consistent with the ability of the enzyme to bind both glucose and mannose phosphosugar substrates. The protein has eight additional hot spots at domain-domain interfaces and hinge regions. The locations and nature of six of these hot spots vary between the open, half-open, and closed conformers of the enzyme, in good agreement with the ligand-induced conformational changes. In the closed structures the number of probe clusters at the hinge region significantly depends on the position of the phosphorylated oxygen in the substrate (e.g., glucose 1-phosphate versus glucose 6-phosphate), but the protein remains almost unchanged in terms of the overall RMSD, indicating that computational solvent mapping is a more sensitive approach to detect changes in binding sites and interdomain crevices. Focusing on multidomain proteins we show that the subresolution conformational differences revealed by the mapping are in fact significant, and present a general statistical method of analysis to determine the significance of rigid body domain movements in X-ray structures.
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Affiliation(s)
- Gwo-Yu Chuang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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50
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Zander U, Faust A, Klink BU, de Sanctis D, Panjikar S, Quentmeier A, Bardischewsky F, Friedrich CG, Scheidig AJ. Structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase SoxCD. J Biol Chem 2010; 286:8349-8360. [PMID: 21147779 DOI: 10.1074/jbc.m110.193631] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six-electron oxidation reaction within the Sox cycle. SoxCD is an α(2)β(2) heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D(1) and D(2). SoxCD(1) misses the heme-2 domain D(2) and is catalytically as active as SoxCD. The crystal structure of SoxCD(1) was solved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys-110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD(1) substrate funnel toward the molybdopterin is narrow and partially shielded by side-chain residues of SoxD(1). For access of the sulfane-sulfur of SoxY-Cys-110 persulfide we propose that (i) the blockage by SoxD-Arg-98 is opened via interaction with the C terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine-bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom that is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Because SoxYZ, SoxXA, and SoxB are already structurally characterized, with SoxCD(1) the structures of all key enzymes of the Sox cycle are known with atomic resolution.
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Affiliation(s)
- Ulrich Zander
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany,; the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany
| | - Annette Faust
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Björn U Klink
- the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany
| | - Daniele de Sanctis
- the Structural Biology Group, European Synchrotron Radiation Facility Grenoble, 6 Rue Jules Horowitz, B.P. 220, 38043 Grenoble Cedex 9, France, and
| | - Santosh Panjikar
- the EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Armin Quentmeier
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Frank Bardischewsky
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Cornelius G Friedrich
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany,.
| | - Axel J Scheidig
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany,; the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany,.
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