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Ashkarran AA, Hosseini A, Loloee R, Perry G, Lee KB, Lund M, Ejtehadi MR, Mahmoudi M. Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides. J Colloid Interface Sci 2022; 606:2038-2050. [PMID: 34749450 DOI: 10.1016/j.jcis.2021.09.185] [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: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation demonstrated a wider energy bandgap of the CT peptide, as compared to the TT peptide, which causes a reduction in its electron tunneling current. Our findings also revealed the critical role of phosphorylation in altering the charge transport characteristics of short peptides; more specifically, we found that the presence of phosphate groups can reduce the energy band gap in tau peptides and alter their electrical properties. Our results suggest that conformational and phosphorylation of short peptides (e.g., tau) can significantly change their charge transport characteristics and energy levels.
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Affiliation(s)
- Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA.
| | - Atiyeh Hosseini
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.
| | | | - Morteza Mahmoudi
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA
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2
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Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J Comput Biol 2020; 27:796-814. [DOI: 10.1089/cmb.2019.0193] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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3
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Araújo THA, Barreto FK, Menezes ADL, Lima CPSD, Oliveira RSD, Lemos PDS, Galvão-Castro B, Kashima S, Farre L, Bittencourt AL, Carvalho EMD, Santos LA, Rego FFDA, Mota-Miranda ACA, Nunes MRT, Alcântara LCJ. Complete genome sequence of human T-cell lymphotropic type 1 from patients with different clinical profiles, including infective dermatitis. INFECTION GENETICS AND EVOLUTION 2019; 79:104166. [PMID: 31883457 DOI: 10.1016/j.meegid.2019.104166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
The HTLV-1 is the first human retrovirus and is associated with several clinical syndromes, however, the pathogenesis of these clinical manifestations is still not fully understood. Furthermore, there are few complete genomes publicly available, about 0.12 complete genomes per 10,000 infected individuals and the databases have a major deficiency of sequences information. This study generated and characterized 31 HTLV-1 complete genomes sequences derived from individuals with Tropical Spastic Paraparesis/HTLV-1-Associated Myelopathy (TSP/HAM), Adult T-cell leukemia/lymphoma (ATL), infective dermatitis associated to HTLV-1 (IDH) and asymptomatic patients. These sequences are associated to clinical and epidemiological information about the patients. The sequencing data generated on Ion Torrent PGM platform were assembled and mapped against the reference HTLV-1 genome. These sequences were genotyped as Cosmopolitan subtype, Transcontinental subgroup. We identified the variants in the coding regions of the genome of the different clinical profiles, however, no statistical relation was detected. This study contributed to increase of HTLV-1 complete genomes in the world. Furthermore, to better investigate the contribution of HTLV-1 mutations for the disease outcome it is necessary to evaluate the interaction of the viral genome and characteristics of the human host.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lourdes Farre
- Fundação Oswaldo Cruz, Brazil; Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | | | | | - Luciane Amorim Santos
- Fundação Oswaldo Cruz, Brazil; Escola Bahiana de Medicina e Saúde Pública Salvador, Brazil
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4
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Yu S, Zhang Y, Wu Y, Yang H, Chen Y, Yang Y, Zhang Z. Subcellular localization of mutated β-catenins with different incidences of cis-peptide bonds at the Xaa246-P247 site in HepG2 cells. FASEB J 2019; 33:6574-6583. [PMID: 30807699 PMCID: PMC6497428 DOI: 10.1096/fj.201801937rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mutations may ultimately change the local conformation of proteins; however, little attention has been paid to alterations in protein function caused by the incidence of cis-peptide bonds (ICPB) in mammalian cells. In this study, a statistical approach, coimmunoprecipitation, and immunofluorescence staining have been used to confirm that S246→Y and S246→W missense mutations, which help increase the ICPB in Xaa246-P247 (Xaa is any amino acid) in human β-catenin, can reduce the interactions between β-catenin and adenomatous polyposis coli (APC) and between β-catenin and Ca2+-dependent cell adhesion molecule family in epithelial tissue (E-cadherin), eventually leading to increased nuclear migration of β-catenin in the HepG2 cell line (an immortalized cell line consisting of human liver carcinoma cells). Conversely, S246→L and S246→M missense mutations, which reduce the ICPB in Xaa246-P247 in human β-catenin, can enhance interactions between β-catenin and APC and between β-catenin and E-cadherin, leading to decreased nuclear migration of β-catenin. These results not only indicate that a change in the ICPB may be an important cause of functional protein changes but also provide a new basis for the study of genetic disease prediction, gene diagnosis, individualized treatment, and protein modification at the gene level for clinicians and other professionals.—Yu, S., Zhang, Y., Wu, Y., Yang, H., Chen, Y., Yang, Y., Zhang, Z. Subcellular localization of mutated β-catenins with different incidences of cis-peptide bonds at the Xaa246-P247 site in HepG2 cells.
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Affiliation(s)
- Shuhui Yu
- School of Life Sciences, Chongqing University, Chongqing, China.,Information Institute of Southwest University, Southwest University, Chongqing, China
| | - Yali Zhang
- School of Life Science, Southwest University, Chongqing, China.,Department of Hematology, First Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Yuyun Wu
- School of Life Science, Southwest University, Chongqing, China
| | - Hongying Yang
- School of Life Science, Southwest University, Chongqing, China
| | - Yang Chen
- School of Life Science, Southwest University, Chongqing, China
| | - Yingbin Yang
- School of Life Science, Southwest University, Chongqing, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
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5
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Singh J, Hanson J, Heffernan R, Paliwal K, Yang Y, Zhou Y. Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. J Chem Inf Model 2018; 58:2033-2042. [PMID: 30118602 DOI: 10.1021/acs.jcim.8b00442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It has been long established that cis conformations of amino acid residues play many biologically important roles despite their rare occurrence in protein structure. Because of this rarity, few methods have been developed for predicting cis isomers from protein sequences, most of which are based on outdated datasets and lack the means for independent testing. In this work, using a database of >10000 high-resolution protein structures, we update the statistics of cis isomers and develop a sequence-based prediction technique using an ensemble of residual convolutional and long short-term memory bidirectional recurrent neural networks that allow learning from the whole protein sequence. We show that ensembling eight neural network models yields maximum Matthews correlation coefficient values of approximately 0.35 for cis-Pro isomers and 0.1 for cis-nonPro residues. The method should be useful for prioritizing functionally important residues in cis isomers for experimental validations and improving the sampling of rare protein conformations for ab initio protein structure prediction.
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Affiliation(s)
- Jaswinder Singh
- Signal Processing Laboratory , Griffith University , Brisbane , QLD 4122 , Australia
| | - Jack Hanson
- Signal Processing Laboratory , Griffith University , Brisbane , QLD 4122 , Australia
| | - Rhys Heffernan
- Signal Processing Laboratory , Griffith University , Brisbane , QLD 4122 , Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory , Griffith University , Brisbane , QLD 4122 , Australia
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology , Griffith University , Southport , QLD 4222 , Australia.,School of Data and Computer Science , Sun Yat-Sen University , Guangzhou , Guangdong 510006 , China
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology , Griffith University , Southport , QLD 4222 , Australia
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6
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Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform 2018; 19:482-494. [PMID: 28040746 PMCID: PMC5952956 DOI: 10.1093/bib/bbw129] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88-90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction.
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Affiliation(s)
- Yuedong Yang
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
| | - Jianzhao Gao
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Rhys Heffernan
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Jack Hanson
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Yaoqi Zhou
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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7
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Singh MK, Manoj N. Structural role of a conserved active sitecisproline in theThermotoga maritimaacetyl esterase from the carbohydrate esterase family 7. Proteins 2017; 85:694-708. [DOI: 10.1002/prot.25249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/17/2016] [Accepted: 01/04/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Mrityunjay K. Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 Tamil Nadu India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 Tamil Nadu India
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8
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Pybus LP, James DC, Dean G, Slidel T, Hardman C, Smith A, Daramola O, Field R. Predicting the expression of recombinant monoclonal antibodies in Chinese hamster ovary cells based on sequence features of the CDR3 domain. Biotechnol Prog 2013; 30:188-97. [DOI: 10.1002/btpr.1839] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/27/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Leon P. Pybus
- ChELSI Institute; Dept. of Chemical and Biological Engineering; University of Sheffield; Mappin Street, Sheffield S1 3JD U.K
| | - David C. James
- ChELSI Institute; Dept. of Chemical and Biological Engineering; University of Sheffield; Mappin Street, Sheffield S1 3JD U.K
| | - Greg Dean
- MedImmune Ltd.; Granta Park Cambridge CB21 6GH U.K
| | - Tim Slidel
- MedImmune Ltd.; Granta Park Cambridge CB21 6GH U.K
| | | | - Andrew Smith
- MedImmune Ltd.; Granta Park Cambridge CB21 6GH U.K
| | | | - Ray Field
- MedImmune Ltd.; Granta Park Cambridge CB21 6GH U.K
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9
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Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
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Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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10
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Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P, Basu G. Direct Evidence for CH···π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs. J Am Chem Soc 2012; 134:4661-9. [DOI: 10.1021/ja209334v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Himal K. Ganguly
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Barun Majumder
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sarbani Chattopadhyay
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Gautam Basu
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
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11
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Bernstein RM, Sterner KN, Wildman DE. Adrenal androgen production in catarrhine primates and the evolution of adrenarche. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 147:389-400. [PMID: 22271526 DOI: 10.1002/ajpa.22001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Accepted: 11/22/2011] [Indexed: 01/29/2023]
Abstract
Adrenarche is a developmental event involving differentiation of the adrenal gland and production of adrenal androgens, and has been hypothesized to play a role in the extension of the preadolescent phase of human ontogeny. It remains unclear whether any nonhuman primate species shows a similar suite of endocrine, biochemical, and morphological changes as are encompassed by human adrenarche. Here, we report serum concentrations of the adrenal androgens dehydroepiandrosterone (DHEA) and dehydroepiandrosterone sulfate (DHEAS) measured in 698 cross-sectional and mixed longitudinal serum samples from catarrhine primates ranging from 0.6 to 47 years of age. DHEAS in Pan is most similar to that of humans in both age-related pattern and absolute levels, and a transient early increase appears to be present in Gorilla. DHEA levels are highest in Cercocebus, Cercopithecus, and Macaca. We also tested for evidence of adaptive evolution in six genes that code for proteins involved in DHEA/S synthesis. Our genetic analyses demonstrate the protein-coding regions of these genes are highly conserved among sampled primates. We describe a tandem gene duplication event probably mediated by a retrotransposon that resulted in two 3-β-hydroxysteroid dehydrogenase/Delta 5-Delta 4 genes (HSD3B1 and HSD3B2) with tissue specific functions in catarrhines. In humans, HSD3B2 is expressed primarily in the adrenals, ovary, and testis, while HSD3B1 is expressed in the placenta. Taken together, our findings suggest that while adrenarche has been suggested to be unique to hominoids, the evolutionary roots for this developmental stage are more ancient.
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Affiliation(s)
- Robin M Bernstein
- Department of Anthropology, Center for the Advanced Study of Hominid Paleobiology, George Washington University, Washington, DC 20052, USA.
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12
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Exarchos KP, Exarchos TP, Rigas G, Papaloukas C, Fotiadis DI. Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment. BMC Bioinformatics 2011; 12:142. [PMID: 21569261 PMCID: PMC3097163 DOI: 10.1186/1471-2105-12-142] [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: 09/17/2010] [Accepted: 05/10/2011] [Indexed: 12/02/2022] Open
Abstract
Background In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro). Results In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the cis-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with cis-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between cis-nonPro and trans-nonPro formations. Conclusions In terms of functional implications, we observe a significant association of cis-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.
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Affiliation(s)
- Konstantinos P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Dept, of Materials Science and Engineering, University of Ioannina, GR 45110, Ioannina, Greece
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13
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Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins. Top Curr Chem (Cham) 2011; 328:35-67. [DOI: 10.1007/128_2011_151] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Kamlekar RK, Gao Y, Kenoth R, Molotkovsky JG, Prendergast FG, Malinina L, Patel DJ, Wessels WS, Venyaminov SY, Brown RE. Human GLTP: Three distinct functions for the three tryptophans in a novel peripheral amphitropic fold. Biophys J 2010; 99:2626-35. [PMID: 20959104 PMCID: PMC2955354 DOI: 10.1016/j.bpj.2010.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 07/27/2010] [Accepted: 08/10/2010] [Indexed: 01/17/2023] Open
Abstract
Human glycolipid transfer protein (GLTP) serves as the GLTP-fold prototype, a novel, to our knowledge, peripheral amphitropic fold and structurally unique lipid binding motif that defines the GLTP superfamily. Despite conservation of all three intrinsic Trps in vertebrate GLTPs, the Trp functional role(s) remains unclear. Herein, the issue is addressed using circular dichroism and fluorescence spectroscopy along with an atypical Trp point mutation strategy. Far-ultraviolet and near-ultraviolet circular dichroism spectroscopic analyses showed that W96F-W142Y-GLTP and W96Y-GLTP retain their native conformation and stability, whereas W85Y-W96F-GLTP is slightly altered, in agreement with relative glycolipid transfer activities of >90%, ∼85%, and ∼45%, respectively. In silico three-dimensional modeling and acrylamide quenching of Trp fluorescence supported a nativelike folding conformation. With the Trp⁹⁶-less mutants, changes in emission intensity, wavelength maximum, lifetime, and time-resolved anisotropy decay induced by phosphoglyceride membranes lacking or containing glycolipid and by excitation at different wavelengths along the absorption-spectrum red edge indicated differing functions for W142 and W85. The data suggest that W142 acts as a shallow-penetration anchor during docking with membrane interfaces, whereas the buried W85 indole helps maintain proper folding and possibly regulates membrane-induced transitioning to a glycolipid-acquiring conformation. The findings illustrate remarkable versatility for Trp, providing three distinct intramolecular functions in the novel amphitropic GLTP fold.
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Affiliation(s)
| | - Yongguang Gao
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Roopa Kenoth
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Julian G. Molotkovsky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Lucy Malinina
- Structural Biology, Centro de Investigación Cooperativa BioGUNE, Derio, Spain
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
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