1
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Firdos, Mittal A. Secretory Conservation in Insulin Producing Cells: Is There a System-Level Law of Mass Action in Biology? ACS OMEGA 2023; 8:37573-37583. [PMID: 37954232 PMCID: PMC10635588 DOI: 10.1021/acsomega.3c06058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023]
Abstract
Altered secretion of insulin from pancreatic β-cells can manifest into disorders. For example, a lack of endogenously produced and/or secreted insulin results in Type 1 diabetes (and other associated subtypes). Pancreatic β-cells are the endocrine secretory cells that promote insulin secretion in response to glucose stimulation. Secretion in response to extracellular triggers is an interplay among various signaling pathways, transcription factors, and molecular mechanisms. The Mouse Insulinoma 6 (MIN6) cell line serves as a model system for gaining mechanistic insights into pancreatic β-cell functions. It is obvious that higher glucose consumption and increased insulin secretion are correlated. However, it has been reported that intracellular ATP levels remain ∼ constant beyond the extracellular glucose (EG) concentration of 10 mM. Therefore, any cause-effect relationship between glucose consumption (GC) and enhanced insulin secretion (eIS) remains unclear. We also found that total cellular protein, as well as total protein content in the culture "supernatant," remains constant regardless of varying EG concentrations. This indicated that eIS may be at the cost of (a) intracellular synthesis of other proteins and (b) secretion of other secretory proteins, or both (a) and (b), somehow coupled with GC by cells. To gain insights into the above, we carried out a transcriptome study of MIN6 cells exposed to hypoglycemic (HoG = 2.8 mM EG) and hyperglycemic (HyG = 25 mM EG) conditions. Expression of transcripts was analyzed in terms of Fragments Per Kilobase of transcript per Million mapped reads and Transcripts Per Million (FPKM and TPM) as well as values obtained by normalizing w.r.t. "∑(FPKM)" and "∑(TPM)." We report that HyG extracellular conditions lead to an ∼2-fold increase in insulin secretion compared to HoG measured by the enzyme-linked immunosorbent assay (ELISA) and transcripts of secreted proteins as well as their isoforms decreased in HyG conditions compared to HoG. Our results show for the first time that eIS in HyG conditions is at the cost of reduced transcription of other secreted proteins and is coupled with higher GC. The higher GC at increased extracellular glucose also indicates a yet undiscovered role of glucose molecules enhancing insulin secretion, since ATP levels resulting from glucose metabolism have been reported to be constant above an EG concentration of 10 mM. While extrapolation of our results to clinical implications is ambitious at best, this work reports novel cellular level aspects that seem relevant in some clinical observations pertaining to Type 1 diabetes. In addition, the conservatory nature of cellular secretions in insulin-secreting cells, discovered here, may be a general feature in cell biology.
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Affiliation(s)
- Firdos
- Kusuma
School of Biological Sciences, Indian Institute
of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi 110016, India
| | - Aditya Mittal
- Kusuma
School of Biological Sciences, Indian Institute
of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi 110016, India
- Supercomputing
Facility for Bioinformatics and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi 110016, India
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2
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Singh H, Pragya P, Mittal A, Haridas V. Pseudopeptosomes: non-lipidated vesicular assemblies from bispidine-appended pseudopeptides. Org Biomol Chem 2023; 21:3557-3566. [PMID: 36883655 DOI: 10.1039/d3ob00201b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
We report a novel molecular topology-based approach for creating reproducible vesicular assemblies in different solvent environments (including aqueous) using specifically designed pseudopeptides. Deviating from the classical "polar head group and hydrophobic tail" model of amphiphiles, we showed (reversible) self-assembly of synthesized pseudopeptides into vesicles. Naming these new type/class of vesicles "pseudopetosomes", we characterized them by high-resolution microscopy (scanning electron, transmission electron, atomic force, epifluorescence and confocal) along with dynamic light scattering. While accounting for hydropathy index of the constituent amino acids (side chains) of pseudopeptides, we probed molecular interactions, resulting in assembly of pseudopeptosomes by spectroscopy (fourier-transform infrared and fluorescence). Molecular characterization by X-ray crystallography and circular dichroism revealed "tryptophan (Trp)-Zip" arrangements and/or hydrogen-bonded one-dimensional assembly depending on specific pseudopeptides and solvent environments. Our data indicated that pseudopeptosomes are formed in solutions by self-assembly of bispidine pseudopeptides (of Trp, leucine and alanine amino-acid constituents) into sheets that transform into vesicular structures. Thus, we showed that assembly of pseudopeptosomes utilizes the full spectrum of all four weak interactions essential in biological systems. Our findings have direct implications in chemical and synthetic biology, but may also provide a new avenue of investigations on origins of life via pseudopeptosome-like assemblies. We also showed that these designer peptides can act as carriers for cellular transport.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Pragya Pragya
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Aditya Mittal
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. .,Supercomputing Facility for Bioinformatics, and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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3
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Mittal A, Chauhan A. Aspects of Biological Replication and Evolution Independent of the Central Dogma: Insights from Protein-Free Vesicular Transformations and Protein-Mediated Membrane Remodeling. J Membr Biol 2022; 255:185-209. [PMID: 35333977 PMCID: PMC8951669 DOI: 10.1007/s00232-022-00230-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/06/2022] [Indexed: 11/21/2022]
Abstract
Biological membrane remodeling is central to living systems. In spite of serving as “containers” of whole-living systems and functioning as dynamic compartments within living systems, biological membranes still find a “blue collar” treatment compared to the “white collar” nucleic acids and proteins in biology. This may be attributable to the fact that scientific literature on biological membrane remodeling is only 50 years old compared to ~ 150 years of literature on proteins and a little less than 100 years on nucleic acids. However, recently, evidence for symbiotic origins of eukaryotic cells from data only on biological membranes was reported. This, coupled with appreciation of reproducible amphiphilic self-assemblies in aqueous environments (mimicking replication), has already initiated discussions on origins of life beyond nucleic acids and proteins. This work presents a comprehensive compilation and meta-analyses of data on self-assembly and vesicular transformations in biological membranes—starting from model membranes to establishment of Influenza Hemagglutinin-mediated membrane fusion as a prototypical remodeling system to a thorough comparison between enveloped mammalian viruses and cellular vesicles. We show that viral membrane fusion proteins, in addition to obeying “stoichiometry-driven protein folding”, have tighter compositional constraints on their amino acid occurrences than general-structured proteins, regardless of type/class. From the perspective of vesicular assemblies and biological membrane remodeling (with and without proteins) we find that cellular vesicles are quite different from viruses. Finally, we propose that in addition to pre-existing thermodynamic frameworks, kinetic considerations in de novo formation of metastable membrane structures with available “third-party” constituents (including proteins) were not only crucial for origins of life but also continue to offer morphological replication and/or functional mechanisms in modern life forms, independent of the central dogma.
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Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India. .,Supercomputing Facility for Bioinformatics and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Akanksha Chauhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
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4
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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5
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Bhat R, Kaushik R, Singh A, DasGupta D, Jayaraj A, Soni A, Shandilya A, Shekhar V, Shekhar S, Jayaram B. A comprehensive automated computer-aided discovery pipeline from genomes to hit molecules. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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6
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Mittal A, Changani AM, Taparia S. Unique and exclusive peptide signatures directly identify intrinsically disordered proteins from sequences without structural information. J Biomol Struct Dyn 2020; 39:2885-2893. [PMID: 32295482 DOI: 10.1080/07391102.2020.1756410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Intrinsically disordered proteins are now widely accepted to play crucial roles in biological functions. Identification of signatures of intrinsic disorder is one of the key steps towards building a proper repertoire for their occurrence in proteomes. In this work, systematic computational synthesis of a library of all possible (3368400) dipeptides, tripeptides, tetrapeptides and pentapeptides using the natural 20 amino acids allowed us to identify 36 unique tetrapeptides present exclusively in intrinsically disordered proteins and absent in the complete primary sequence space of naturally occurring structured proteins. Further, out of more than 530000 known naturally occurring primary sequences without any structural information, 1349 sequences contain the above identified unique signatures of intrinsic disorder. These sequences, having cellular functions varying from housekeeping to metabolic to transport, more than double the number of the currently known intrinsically disordered proteins. On similar lines, we report that 26577 pentapeptide signatures exclusive to intrinsically disordered proteins, and absent in naturally occurring structured proteins, identify ∼50% of more than half-a-million curated protein sequences without structural information to be intrinsically disordered. The results reported are a major leap forward in exploring functional manifestations of intrinsically disordered proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | | | - Sakshi Taparia
- Department of Mathematics (Bachelors Program in Mathematics & Computing), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
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7
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Mittal A, Changani AM, Taparia S, Goel D, Parihar A, Singh I. Structural disorder originates beyond narrow stoichiometric margins of amino acids in naturally occurring folded proteins. J Biomol Struct Dyn 2020; 39:2364-2375. [PMID: 32238088 DOI: 10.1080/07391102.2020.1751299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Rigorous analyses of Euclidean distances between non-peptide bonded residues in structures of several thousand naturally occurring folded proteins yielded a surprising "margin of life" for percentage occurrence of individual amino acids in naturally occurring folded proteins. On one hand, the concept of "margin of life", referring to lower than expected variances in average stoichiometric occurrences of individual amino acids in folded proteins, remains unchallenged since its discovery a decade ago. On the other hand, within this past decade there has been a strong emergence of a gradual paradigm shift in biology, from sequence-structure-function in proteins to sequence-disorder-function, fuelled by discoveries on functional implications of intrinsically disordered proteins (primary sequences that do not form stable structures). Thus the applicability of "margin of life" to peptide-bonded residues in all known natural proteins, adopting stable structures vis-à-vis intrinsically disordered needs to be explored. Therefore in this work, we analyze compositions of the complete naturally occurring primary sequence space (over 560000 sequences) after dividing it into mutually exclusive subsets of structured and intrinsically disordered proteins along with a subset without any structural information. While finding that occurrence of different peptides (up to pentapeptides) is a direct consequence of the relative occurrences of their constituting residues in folded proteins, we report that structural disorder in natural proteins originates beyond the narrow stoichiometric margins of amino acids found in structured proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | | | - Sakshi Taparia
- Department of Mathematics (Bachelors program in Mathematics & Computing), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Deepanshu Goel
- Department of Biochemical Engineering and Biotechnology (Bachelors program), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Animesh Parihar
- Department of Biochemical Engineering and Biotechnology (Bachelors program), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | - Ishan Singh
- Department of Computer Science & Engineering (Bachelors program Computer Science), Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
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8
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Pollack JD, Gerard D, Makhatadze GI, Pearl DK. Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence. J Biomol Struct Dyn 2019; 38:3700-3719. [DOI: 10.1080/07391102.2019.1679666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- J. Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, USA
| | - George I. Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Dennis K. Pearl
- Department of Statistics, Penn State University, University Park, Pennsylvania, USA
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9
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Mittal A, Changani AM, Taparia S. What limits the primary sequence space of natural proteins? J Biomol Struct Dyn 2019; 38:4579-4583. [DOI: 10.1080/07391102.2019.1682051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
| | | | - Sakshi Taparia
- Department of Mathematics, Bachelors Program in Mathematics & Computing, Indian Institute of Technology Delhi (IIT Delhi), New Delhi, India
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10
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Tian K, Zhao X, Zhang Y, Yau S. Comparing protein structures and inferring functions with a novel three-dimensional Yau-Hausdorff method. J Biomol Struct Dyn 2018; 37:4151-4160. [PMID: 30518311 DOI: 10.1080/07391102.2018.1540359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Structures and functions of proteins play various essential roles in biological processes. The functions of newly discovered proteins can be predicted by comparing their structures with that of known-functional proteins. Many approaches have been proposed for measuring the protein structure similarity, such as the template-modeling (TM)-score method, GRaphlet (GR)-Align method as well as the commonly used root-mean-square deviation (RMSD) measures. However, the alignment comparisons between the similarity of protein structure cost much time on large dataset, and the accuracy still have room to improve. In this study, we introduce a new three-dimensional (3D) Yau-Hausdorff distance between any two 3D objects. The (3D) Yau-Hausdorff distance can be used in particular to measure the similarity/dissimilarity of two proteins of any size and does not need aligning and superimposing two structures. We apply structural similarity to study function similarity and perform phylogenetic analysis on several datasets. The results show that (3D) Yau-Hausdorff distance could serve as a more precise and effective method to discover biological relationships between proteins than other methods on structure comparison. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kun Tian
- Department of Mathematical Sciences, Tsinghua University , Beijing , P.R. China
| | - Xin Zhao
- Department of Mathematical Sciences, Tsinghua University , Beijing , P.R. China
| | - Yuning Zhang
- School of Life Sciences, Tsinghua University , Beijing , P.R. China
| | - Stephen Yau
- Department of Mathematical Sciences, Tsinghua University , Beijing , P.R. China
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11
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Mukherjee S, Nithin C, Divakaruni Y, Bahadur RP. Dissecting water binding sites at protein–protein interfaces: a lesson from the atomic structures in the Protein Data Bank. J Biomol Struct Dyn 2018; 37:1204-1219. [DOI: 10.1080/07391102.2018.1453379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sunandan Mukherjee
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Yasaswi Divakaruni
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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12
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Mallika V, Sivakumar KC, Aiswarya G, Soniya EV. In silico approaches illustrate the evolutionary pattern and protein-small molecule interactions of quinolone synthase from Aegle marmelos Correa. J Biomol Struct Dyn 2018; 37:195-209. [PMID: 29308712 DOI: 10.1080/07391102.2017.1422991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a Rutacean-specific plant type III polyketide synthase that synthesizes quinolone, acridone, and benzalacetone with therapeutic potential. Simple architecture and broad substrate affinity of AmQNS make it as one of the target enzymes to produce novel structural scaffolds. Another unique feature of AmQNS despite its high similarity to acridone forming type III polyketide synthase from Citrus microcarpa is the variation in the product formation. Hence, to explore the characteristic features of AmQNS, an in-depth sequence and structure-based bioinformatics analyses were performed. Our studies indicated that AmQNS and its nearest homologs have evolved by a series of gene duplication events and strong purifying selection pressure constrains them in the evolutionary process. Additionally, some amino acid alterations were identified in the functionally important region(s), which can contribute to the functional divergence of the enzyme. Prediction of favorable amino acid substitutions will be advantageous in the metabolic engineering of AmQNS for the production of novel compounds. Furthermore, comparative modeling and docking studies were utilized to investigate the structural behavior and small molecule interaction pattern of AmQNS. The observations and results reported here are crucial for advancing our understanding of AmQNS's phylogenetic position, selection pressure, evolvability, interaction pattern and thus providing the foundation for further studies on the structural and reaction mechanism.
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Affiliation(s)
- V Mallika
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - K C Sivakumar
- b Bioinformatics Facility , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - G Aiswarya
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - E V Soniya
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
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Saidijam M, Azizpour S, Patching SG. Amino acid composition analysis of human secondary transport proteins and implications for reliable membrane topology prediction. J Biomol Struct Dyn 2016; 35:929-949. [PMID: 27159787 DOI: 10.1080/07391102.2016.1167622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Secondary transporters in humans are a large group of proteins that transport a wide range of ions, metals, organic and inorganic solutes involved in energy transduction, control of membrane potential and osmotic balance, metabolic processes and in the absorption or efflux of drugs and xenobiotics. They are also emerging as important targets for development of new drugs and as target sites for drug delivery to specific organs or tissues. We have performed amino acid composition (AAC) and phylogenetic analyses and membrane topology predictions for 336 human secondary transport proteins and used the results to confirm protein classification and to look for trends and correlations with structural domains and specific substrates and/or function. Some proteins showed statistically high contents of individual amino acids or of groups of amino acids with similar physicochemical properties. One recurring trend was a correlation between high contents of charged and/or polar residues with misleading results in predictions of membrane topology, which was especially prevalent in Mitochondrial Carrier family proteins. We demonstrate how charged or polar residues located in the middle of transmembrane helices can interfere with their identification by membrane topology tools resulting in missed helices in the prediction. Comparison of AAC in the human proteins with that in 235 secondary transport proteins from Escherichia coli revealed similar overall trends along with differences in average contents for some individual amino acids and groups of similar amino acids that are presumed to result from a greater number of functions and complexity in the higher organism.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK
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Singh S, Mittal A. Transmembrane Domain Lengths Serve as Signatures of Organismal Complexity and Viral Transport Mechanisms. Sci Rep 2016; 6:22352. [PMID: 26925972 PMCID: PMC4772119 DOI: 10.1038/srep22352] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/12/2016] [Indexed: 12/24/2022] Open
Abstract
It is known that membrane proteins are important in various secretory pathways, with
a possible role of their transmembrane domains (TMDs) as sorting determinant
factors. One key aspect of TMDs associated with various
“checkposts” (i.e. organelles) of intracellular trafficking
is their length. To explore possible linkages in organisms with varying
“complexity” and differences in TMD lengths of membrane
proteins associated with different organelles (such as Endoplasmic Reticulum, Golgi,
Endosomes, Nucleus, Plasma Membrane), we analyzed ~70000 membrane
protein sequences in over 300 genomes of fungi, plants, non-mammalian vertebrates
and mammals. We report that as we move from simpler to complex organisms, variation
in organellar TMD lengths decreases, especially compared to their respective plasma
membranes, with increasing organismal complexity. This suggests an evolutionary
pressure in modulating length of TMDs of membrane proteins with increasing
complexity of communication between sub-cellular compartments. We also report
functional applications of our findings by discovering remarkable distinctions in
TMD lengths of membrane proteins associated with different intracellular transport
pathways. Finally, we show that TMD lengths extracted from viral proteins can serve
as somewhat weak indicators of viral replication sites in plant cells but very
strong indicators of different entry pathways employed by animal viruses.
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Affiliation(s)
- Snigdha Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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15
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Onofrio A, Parisi G, Punzi G, Todisco S, Di Noia MA, Bossis F, Turi A, De Grassi A, Pierri CL. Distance-dependent hydrophobic-hydrophobic contacts in protein folding simulations. Phys Chem Chem Phys 2015; 16:18907-17. [PMID: 25083519 DOI: 10.1039/c4cp01131g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Successful prediction of protein folding from an amino acid sequence is a challenge in computational biology. In order to reveal the geometric constraints that drive protein folding, highlight those constraints kept or missed by distinct lattices and for establishing which class of intra- and inter-secondary structure element interactions is the most relevant for the correct folding of proteins, we have calculated inter-alpha carbon distances in a set of 42 crystal structures consisting of mainly helix, sheet or mixed conformations. The inter-alpha carbon distances were also calculated in several lattice "hydrophobic-polar" models built from the same protein set. We found that helix structures are more prone to form "hydrophobic-hydrophobic" contacts than beta-sheet structures. At a distance lower than or equal to 3.8 Å (very short-range interactions), "hydrophobic-hydrophobic" contacts are almost absent in the native structures, while they are frequent in all the analyzed lattice models. At distances in-between 3.8 and 9.5 Å (short-/medium-range interactions), the best performing lattice for reproducing mainly helix structures is the body-centered-cubic lattice. If protein structures contain sheet portions, lattice performances get worse, with few exceptions observed for double-tetrahedral and body-centered-cubic lattices. Finally, we can observe that ab initio protein folding algorithms, i.e. those based on the employment of lattices and Monte Carlo simulated annealings, can be improved simply and effectively by preventing the generation of "hydrophobic-hydrophobic" contacts shorter than 3.8 Å, by monitoring the "hydrophobic-hydrophobic/polar-polar" contact ratio in short-/medium distance ranges and by using preferentially a body-centered-cubic lattice.
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Affiliation(s)
- Angelo Onofrio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125, Bari, Italy.
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Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Petrov VV, Ibragimov RI. [Effect of point substitutions of Asp-714 and Asp-720 residues on the structure and function of the H+ -ATPase of the yeast plasma membrane]. APPL BIOCHEM MICRO+ 2015; 50:508-16. [PMID: 25707108 DOI: 10.1134/s000368381405007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Membrane-spanning M5 and M6 segments, which play a role in the formation of cation transport sites in H(+)-, Ca2(+)-, K(+)-, Na(+)-, and other P2-ATPases, are connected by a short extracytoplasmic loop. In the yeast plasma membrane H(+)-ATPase, which belongs to a family of P2-ATPases, the loop is connected to M5 and M6 through the Asp-714 and Asp-720 residues. In this work, the effect of point amino, acidreplacements of Asp-714 and Asp-720 by Ala, Val, Asn, and Glu residues on the function of the enzyme was studied. The Asp714Asn point mutant possessed activities similar to those of the wild-type enzyme, whereas the replacement of Asp-714 by other amino acid residues disrupted biogenesis and led to a loss of activity. All mutants with substitution of Asp-720 were expressed and possessed relatively high activity. The D720V mutant displayed significantly reduced expression levels, activity, H+ transport, and ATP hydrolyzing activity. Thus, substitutions of Asp-714, except for the D714N mutant, led to significant defects in biogenesis and/or function of the enzyme. The results indicate the important role for the Asp-714 residue in biogenesis, structure stability, and enzyme function.
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Petrov VV. Role of loop L5-6 connecting transmembrane segments M5 and M6 in biogenesis and functioning of yeast Pma1 H+-ATPase. BIOCHEMISTRY (MOSCOW) 2015; 80:31-44. [PMID: 25754037 DOI: 10.1134/s0006297915010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The L5-6 loop is a short extracytoplasmic stretch (714-DNSLDID) connecting transmembrane segments M5 and M6 and forming along with segments M4 and M8 the core through which cations are transported by H+-, Ca2+-, K+,Na+-, H+,K+-, and other P2-ATPases. To study structure-function relationships within this loop of the yeast plasma membrane Pma1 H+-ATPase, alanine- and cysteine-scanning mutagenesis has been employed. Ala and Cys substitutions for the most conserved residue (Leu717) led to complete block in biogenesis preventing the enzyme from reaching secretory vesicles. The Ala replacement at Asp714 led to five-fold decrease in the mutant expression and loss of its activity, while the Cys substitution blocked biogenesis completely. Replacements of other residues did not lead to loss of enzymatic activity. Additional replacements were made for Asp714 and Asp720 (Asp®Asn/Glu). Of the substitutions made at Asp714, only D714N partially restored the mutant enzyme biogenesis and functioning. However, all mutant enzymes with substituted Asp720 were active. The expressed mutants (34-95% of the wild-type level) showed activity high enough (35-108%) to be analyzed in detail. One of the mutants (I719A) had three-fold reduced coupling ratio between ATP hydrolysis and H+ transport; however, the I719C mutation was rather indistinguishable from the wild-type enzyme. Thus, substitutions at two of the seven positions seriously affected biogenesis and/or functioning of the enzyme. Taken together, these results suggest that the M5-M6 loop residues play an important role in protein stability and function, and they are probably responsible for proper arrangement of transmembrane segments M5 and M6 and other domains of the enzyme. This might also be important for the regulation of the enzyme.
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Affiliation(s)
- V V Petrov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Bansal S, Mittal A. A statistical anomaly indicates symbiotic origins of eukaryotic membranes. Mol Biol Cell 2015; 26:1238-48. [PMID: 25631820 PMCID: PMC4454172 DOI: 10.1091/mbc.e14-06-1078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We report a remarkable statistical paradox from a compositional analysis of membrane lipids of archaea, eubacteria, and eukaryotes. The presence of Simpson's paradox in the analysis of lipids common to plasma membranes of all domains provides the first evidence based on the compositional analysis of lipidomics data for the symbiotic origins of eukaryotic cells. Compositional analyses of nucleic acids and proteins have shed light on possible origins of living cells. In this work, rigorous compositional analyses of ∼5000 plasma membrane lipid constituents of 273 species in the three life domains (archaea, eubacteria, and eukaryotes) revealed a remarkable statistical paradox, indicating symbiotic origins of eukaryotic cells involving eubacteria. For lipids common to plasma membranes of the three domains, the number of carbon atoms in eubacteria was found to be similar to that in eukaryotes. However, mutually exclusive subsets of same data show exactly the opposite—the number of carbon atoms in lipids of eukaryotes was higher than in eubacteria. This statistical paradox, called Simpson's paradox, was absent for lipids in archaea and for lipids not common to plasma membranes of the three domains. This indicates the presence of interaction(s) and/or association(s) in lipids forming plasma membranes of eubacteria and eukaryotes but not for those in archaea. Further inspection of membrane lipid structures affecting physicochemical properties of plasma membranes provides the first evidence (to our knowledge) on the symbiotic origins of eukaryotic cells based on the “third front” (i.e., lipids) in addition to the growing compositional data from nucleic acids and proteins.
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Affiliation(s)
- Suneyna Bansal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Mishra A, Rana PS, Mittal A, Jayaram B. D2N: Distance to the native. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1798-807. [DOI: 10.1016/j.bbapap.2014.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/03/2014] [Accepted: 07/15/2014] [Indexed: 12/26/2022]
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Ekambaram R, Kannaiyan A, Marimuthu V, Swaminathan VC, Renganathan S, Perumal AG. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins. Bioinformation 2014; 10:138-43. [PMID: 24748753 PMCID: PMC3974240 DOI: 10.6026/97320630010138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 11/28/2022] Open
Abstract
Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.
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Affiliation(s)
- Rajasekaran Ekambaram
- Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore –641114, Tamil Nadu, India
| | - Akila Kannaiyan
- Department of Bioinformatics, Bishop Heber College, Trichy-620017, Tamil Nadu, India
| | - Vijayasarathy Marimuthu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | | | - Senthil Renganathan
- Department of Bioinformatics, Marudhu Pandiyar College, Vallam, Thanjavur – 613403, Tamil Nadu, India
| | - Ananda Gopu Perumal
- BioInformatics Research Centre, School of Computer Engineering, Nanyang Technological University, Block NS4-04-33, Singapore - 639798 Singapore
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Petrov VV. Point mutations in the extracytosolic loop between transmembrane segments M5 and M6 of the yeast Pma1 H+-ATPase: alanine-scanning mutagenesis. J Biomol Struct Dyn 2013; 33:70-84. [PMID: 24256122 DOI: 10.1080/07391102.2013.849619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane-spanning segments M4, M5, M6, and M8 of the H(+)-, Ca(2+)-, and K(+), Na(+)-ATPases, which belong to the P2-type pumps are the core through which cations are transported. M5 and M6 loop is a short extracytoplasmic stretch of the seven amino acid residues (714-DNSLDID) connecting two of these segments, M5 and M6, where residues involved in the formation of the proton-binding site(s) are located. In the present study, we have used alanine-scanning mutagenesis to explore the structural and functional relationships within this loop of the yeast plasma membrane Pma1 H(+)-ATPase. Of the 7 Ala mutants made, substitution for the most conserved residue (Leu-717) has led to a severe misfolding and complete block in biogenesis of the mutant enzyme. The replacement of Asp-714 has also caused misfolding leading to significant decrease in the expression of the mutant and loss of activity. The remaining mutants were expressed in secretory vesicles at 21-119% of the wild-type level and were active enough to be analyzed in detail. One of these mutants (I719A) showed five- to threefold decrease in both expression and ATP hydrolyzing and H(+) pumping activities and also threefold reduction in the coupling ratio between ATP hydrolysis and H(+) transport. Thus, Ala substitutions at three positions of the seven seriously affected biogenesis, folding, stability and/or functioning of the enzyme. Taken together, these results lead to suggestion that M5 and M6 loop play an important role in the protein stability and function and is responsible for proper arrangement of transmembrane segments M5 and M6 and probably other domains of the enzyme. Results for additional conserved substitutions (Asn and Glu) at Asp-714 and Asp-720 confirmed this suggestion.
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Affiliation(s)
- Valery V Petrov
- a Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences , pr. Nauki 5, Pushchino 142290 , Russia
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Dhingra P, Jayaram B. A homology/ab initio hybrid algorithm for sampling near-native protein conformations. J Comput Chem 2013; 34:1925-36. [PMID: 23728619 DOI: 10.1002/jcc.23339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/09/2013] [Accepted: 04/21/2013] [Indexed: 12/19/2022]
Abstract
One of the major challenges for protein tertiary structure prediction strategies is the quality of conformational sampling algorithms, which can effectively and readily search the protein fold space to generate near-native conformations. In an effort to advance the field by making the best use of available homology as well as fold recognition approaches along with ab initio folding methods, we have developed Bhageerath-H Strgen, a homology/ab initio hybrid algorithm for protein conformational sampling. The methodology is tested on the benchmark CASP9 dataset of 116 targets. In 93% of the cases, a structure with TM-score ≥ 0.5 is generated in the pool of decoys. Further, the performance of Bhageerath-H Strgen was seen to be efficient in comparison with different decoy generation methods. The algorithm is web enabled as Bhageerath-H Strgen web tool which is made freely accessible for protein decoy generation (http://www.scfbio-iitd.res.in/software/Bhageerath-HStrgen1.jsp).
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Affiliation(s)
- Priyanka Dhingra
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
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Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1520-31. [PMID: 23665455 DOI: 10.1016/j.bbapap.2013.04.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 12/15/2022]
Abstract
Specification of the three dimensional structure of a protein from its amino acid sequence, also called a "Grand Challenge" problem, has eluded a solution for over six decades. A modestly successful strategy has evolved over the last couple of decades based on development of scoring functions (e.g. mimicking free energy) that can capture native or native-like structures from an ensemble of decoys generated as plausible candidates for the native structure. A scoring function must be fast enough in discriminating the native from unfolded/misfolded structures, and requires validation on a large data set(s) to generate sufficient confidence in the score. Here we develop a scoring function called pcSM that detects true native structure in the top 5 with 93% accuracy from an ensemble of candidate structures. If we eliminate the native from ensemble of decoys then pcSM is able to capture near native structure (RMSD<=5Ǻ) in top 10 with 86% accuracy. The parameters considered in pcSM are a C-alpha Euclidean metric, secondary structural propensity, surface areas and an intramolecular energy function. pcSM has been tested on 415 systems consisting 142,698 decoys (public and CASP-largest reported hitherto in literature). The average rank for the native is 2.38, a significant improvement over that existing in literature. In-silico protein structure prediction requires robust scoring technique(s). Therefore, pcSM is easily amenable to integration into a successful protein structure prediction strategy. The tool is freely available at http://www.scfbio-iitd.res.in/software/pcsm.jsp.
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Mittal A, Acharya C. Protein folding: is it simply surface to volume minimization? J Biomol Struct Dyn 2013; 31:953-5. [PMID: 23297677 DOI: 10.1080/07391102.2012.748526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 10016, India.
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Soni A, Pandey KM, Ray P, Jayaram B. Genomes to hits in silico - a country path today, a highway tomorrow: a case study of chikungunya. Curr Pharm Des 2013; 19:4687-700. [PMID: 23260020 PMCID: PMC3831887 DOI: 10.2174/13816128113199990379] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/17/2012] [Indexed: 12/11/2022]
Abstract
These are exciting times for bioinformaticians, computational biologists and drug designers with the genome and proteome sequences and related structural databases growing at an accelerated pace. The post-genomic era has triggered high expectations for a rapid and successful treatment of diseases. However, in this biological information rich and functional knowledge poor scenario, the challenges are indeed grand, no less than the assembly of the genome of the whole organism. These include functional annotation of genes, identification of druggable targets, prediction of three-dimensional structures of protein targets from their amino acid sequences, arriving at lead compounds for these targets followed by a transition from bench to bedside. We propose here a "Genome to Hits In Silico" strategy (called Dhanvantari) and illustrate it on Chikungunya virus (CHIKV). "Genome to hits" is a novel pathway incorporating a series of steps such as gene prediction, protein tertiary structure determination, active site identification, hit molecule generation, docking and scoring of hits to arrive at lead compounds. The current state of the art for each of the steps in the pathway is high-lighted and the feasibility of creating an automated genome to hits assembly line is discussed.
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Affiliation(s)
- Anjali Soni
- Department of Chemistry, Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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Wu JW, Liu HL. In silico investigation of the disease-associated retinoschisin C110Y and C219G mutants. J Biomol Struct Dyn 2012; 29:937-59. [PMID: 22292953 DOI: 10.1080/07391102.2012.10507420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The juvenile X-linked retinoschisis (XLRS) is a retinal disease caused by mutations in the secretory protein, retinoschisin (RS1). Majority of the disease is resulted from single point mutations on the RS1 discoidin domain with cysteine mutations being related to some of the more severe cases of XLRS. Previous studies have indicated that two mutations (C110Y and C219G), which involve cysteines that form intramolecular disulfide bonds in the native discoidin domain, resulted in different oligomerization states of the proteins and did not correlate with the degree of protein stability as calculated by the change in folding free energy. Through homology modeling, bioinformatics predictions, molecular dynamics (MD) and docking simulations, we attempt to investigate the effects of these two mutations on the structure of the RS1 discoidin domain in relevance to the discrepancy found between structural stability and aggregation propensity. Based on our findings, this discrepancy can be explained by the ability of C110Y mutant to establish suitable modules for initiating amorphous aggregation and to expand the aggregating mass through predominantly hydrophobic interactions. The low capability of C219G mutant to oligomerize, on the other hand, may be due to its greater structural instability and lesser hydrophobic tendency, two properties that may be unsupportive of aggregation. The results, altogether, indicate that aggregation propensity in the RS1 C110Y mutant is dependent upon the formation of suitable aggregating substrates for propagation of aggregation and not directly related to or determined by overall structural instability. As for the wildtype protein, the binding specificity of the spikes for biological function and the formation of octameric structure are contributed by important loop interactions, as well as evolved structural and sequence-based properties that prevent aggregation.
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Affiliation(s)
- Josephine W Wu
- Institute of Biotechnology, National Taipei University of Technology, Taipei 10608, Taiwan
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Bansal M, Jayaram B, Mittal A. Nucleic acids in disease and disorder: Understanding the language of life emerging from the ‘ABC’ of DNA. J Biosci 2012; 37:375-8. [DOI: 10.1007/s12038-012-9226-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mittal A. Self-Generated and Reproducible Dynamics in “Gene Years” Represent Life. J Biomol Struct Dyn 2012; 29:609-11. [DOI: 10.1080/073911012010525002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules. COMPUTATIONAL MODELING OF BIOLOGICAL SYSTEMS 2012. [DOI: 10.1007/978-1-4614-2146-7_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Moughon SE, Samudrala R. LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics 2011; 12:368. [PMID: 21920038 PMCID: PMC3184297 DOI: 10.1186/1471-2105-12-368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 09/15/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Successful protein structure prediction requires accurate low-resolution scoring functions so that protein main chain conformations that are close to the native can be identified. Once that is accomplished, a more detailed and time-consuming treatment to produce all-atom models can be undertaken. The earliest low-resolution scoring used simple distance-based "contact potentials," but more recently, the relative orientations of interacting amino acids have been taken into account to improve performance. RESULTS We developed a new knowledge-based scoring function, LoCo, that locates the interaction partners of each individual residue within a local coordinate system based only on the position of its main chain N, Cα and C atoms. LoCo was trained on a large set of experimentally determined structures and optimized using standard sets of modeled structures, or "decoys." No structure used to train or optimize the function was included among those used to test it. When tested against 29 other published main chain functions on a group of 77 commonly used decoy sets, our function outperformed all others in Cα RMSD rank of the best-scoring decoy, with statistically significant p-values < 0.05 for 26 out of the 29 other functions considered. LoCo is fast, requiring on average less than 6 microseconds per residue for interaction and scoring on commonly-used computer hardware. CONCLUSIONS Our function demonstrates an unmatched combination of accuracy, speed, and simplicity and shows excellent promise for protein structure prediction. Broader applications may include protein-protein interactions and protein design.
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Affiliation(s)
- Stewart E Moughon
- Department of Microbiology, University of Washington, Box 357735, Seattle, Washington 98195-7242, USA.
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Mittal A, Jayaram B. The Newest View on Protein Folding: Stoichiometric and Spatial Unity in Structural and Functional Diversity. J Biomol Struct Dyn 2011. [DOI: 10.1080/073911011010524984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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