1
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Parker E, Haberichter SL, Lollar P. Subunit Flexibility of Multimeric von Willebrand Factor/Factor VIII Complexes. ACS OMEGA 2022; 7:31183-31196. [PMID: 36092565 PMCID: PMC9453814 DOI: 10.1021/acsomega.2c03389] [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: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Von Willebrand factor (VWF) is a plasma glycoprotein that participates in platelet adhesion and aggregation and serves as a carrier for blood coagulation factor VIII (fVIII). Plasma VWF consists of a population of multimers that range in molecular weight from ∼ 0.55 MDa to greater than 10 MDa. The VWF multimer consists of a variable number of concatenated disulfide-linked ∼275 kDa subunits. We fractionated plasma-derived human VWF/fVIII complexes by size-exclusion chromatography at a pH of 7.4 and subjected them to analysis by sodium dodecyl sulfate agarose gel electrophoresis, sedimentation velocity analytical ultracentrifugation (SV AUC), dynamic light scattering (DLS), and multi-angle light scattering (MALS). Weight-average molecular weights, M w, were independently measured by MALS and by application of the Svedberg equation to SV AUC and DLS measurements. Estimates of the Mark-Houwink-Kuhn-Sakurada exponents , αs, and αD describing the functional relationship between the z-average radius of gyration, , weight-average sedimentation coefficient, s w, z-average diffusion coefficient, D z , and M w were consistent with a random coil conformation of the VWF multimer. Ratios of to the z-average hydrodynamic radius, , estimated by DLS, were calculated across an M w range from 2 to 5 MDa. When compared to values calculated for a semi-flexible, wormlike chain, these ratios were consistent with a contour length over 1000-fold greater than the persistence length. These results indicate a high degree of flexibility between domains of the VWF subunit.
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Affiliation(s)
- Ernest
T. Parker
- Aflac
Cancer and Blood Disorders Center, Children’s Healthcare of
Atlanta; Department of Pediatrics, Emory
University, Atlanta Georgia 30322, United States
| | - Sandra L. Haberichter
- Diagnostic
Laboratories and Blood Research Institute, Versiti, Milwaukee, Wisconsin 53201-2178, United States
- Pediatric
Hematology/Oncology, Medical College of
Wisconsin, Milwaukee, Wisconsin 53226, United States
- Children’s
Research Institute, Children’s Hospital
of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Pete Lollar
- Aflac
Cancer and Blood Disorders Center, Children’s Healthcare of
Atlanta; Department of Pediatrics, Emory
University, Atlanta Georgia 30322, United States
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2
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The neuropeptide galanin adopts an irregular secondary structure. Biochem Biophys Res Commun 2022; 626:121-128. [PMID: 35994823 DOI: 10.1016/j.bbrc.2022.08.032] [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: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022]
Abstract
Human galanin is a 30-residue neuropeptide targeted for development of analgesics, antidepressants, and anticonvulsants. While previous work from our group and others has already produced significant insights into galanin's N-terminal region, no extant structures of galanin in databases include its full-length sequence and the function of its C-terminus remains ambiguous. We report the NMR solution structure of full-length human galanin C-terminal amide, determined from 2D 1H-1H COSY, TOCSY, and ROESY NMR data. Galanin adopts an irregular helical structure across its N-terminus, likely the average of several coiling states. We present the NMR structure of a peptide encompassing the C-terminus of galanin as a stand-alone fragment. The C-terminus of full-length galanin appears to indirectly assist the intramolecular association of hydrophobic sidechains within its N-terminus, remotely rigidifying their position when compared to previously studied N-terminal galanin fragments. By contrast, there is flexibility in the C-terminus of galanin, characterized by two i to i + 2 hydrogen-bonded turns within an otherwise dynamic backbone. The C-terminal portion of the peptide renders it soluble, and plays a hitherto undescribed biophysical role in pre-organizing the galanin receptor binding epitope. We speculate that hydrophilic microdomains of signaling peptides, hormones, and perhaps intrinsically disordered proteins may also function similarly.
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3
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Target-binding behavior of IDPs via pre-structured motifs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:187-247. [PMID: 34656329 DOI: 10.1016/bs.pmbts.2021.07.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pre-Structured Motifs (PreSMos) are transient secondary structures observed in many intrinsically disordered proteins (IDPs) and serve as protein target-binding hot spots. The prefix "pre" highlights that PreSMos exist a priori in the target-unbound state of IDPs as the active pockets of globular proteins pre-exist before target binding. Therefore, a PreSMo is an "active site" of an IDP; it is not a spatial pocket, but rather a secondary structural motif. The classical and perhaps the most effective approach to understand the function of a protein has been to determine and investigate its structure. Ironically or by definition IDPs do not possess structure (here structure refers to tertiary structure only). Are IDPs then entirely structureless? The PreSMos provide us with an atomic-resolution answer to this question. For target binding, IDPs do not rely on the spatial pockets afforded by tertiary or higher structures. Instead, they utilize the PreSMos possessing particular conformations that highly presage the target-bound conformations. PreSMos are recognized or captured by targets via conformational selection (CS) before their conformations eventually become stabilized via structural induction into more ordered bound structures. Using PreSMos, a number of, if not all, IDPs can bind targets following a sequential pathway of CS followed by an induced fit (IF). This chapter presents several important PreSMos implicated in cancers, neurodegenerative diseases, and other diseases along with discussions on their conformational details that mediate target binding, a structural rationale for unstructured proteins.
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4
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Duan J, Lupyan D, Wang L. Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations. Biophys J 2020; 119:115-127. [PMID: 32533939 DOI: 10.1016/j.bpj.2020.05.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 01/17/2023] Open
Abstract
Accurately predicting the protein thermostability changes upon single point mutations in silico is a challenge that has implications for understanding diseases as well as industrial applications of protein engineering. Free energy perturbation (FEP) has been applied to predict the effect of single point mutations on protein stability for over 40 years and emerged as a potentially reliable prediction method with reasonable throughput. However, applications of FEP in protein stability calculations in industrial settings have been hindered by a number of limitations, including the inability to model mutations to and from prolines in which the bonded topology of the backbone is modified and the complexity in modeling charge-changing mutations. In this study, we have extended the FEP+ protocol to enable the accurate modeling of the effects on protein stability from proline mutations and from charge-changing mutations. We also evaluated the influence of the unfolded model in the stability calculations using increasingly longer peptides with native sequence and conformations. With the abovementioned improvements, the accuracy of FEP predictions of protein stability over a data set of 87 mutations on five different proteins has drastically improved compared with previous studies, with a mean unsigned error of 0.86 kcal/mol and root mean square error of 1.11 kcal/mol, comparable with the accuracy of previously published state-of-the-art small-molecule relative binding affinity calculations, which have been shown to be capable of driving discovery projects.
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5
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Passalia FJ, Carvalho E, Heinemann MB, Vieira ML, Nascimento ALTO. The Leptospira interrogans LIC10774 is a multifunctional surface protein that binds calcium and interacts with host components. Microbiol Res 2020; 235:126470. [PMID: 32247916 DOI: 10.1016/j.micres.2020.126470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 02/06/2023]
Abstract
Leptospirosis is a global re-emerging zoonosis, caused by pathogenic bacteria of the genus Leptospira. Humans are infected mainly through contact with contaminated water or soil. The understanding of the molecular mechanisms of leptospirosis through the characterization of unknown outer membrane proteins may contribute to the development of new treatments, diagnostic methods and vaccines. We have identified using bioinformatics analysis a protein that is encoded by the gene LIC10774, predicted to be localized at the leptospiral outer membrane and exhibit beta-roll folding. Surface exposure was confirmed by flow cytometry, ELISA and immunofluorescence-based confocal microscopy. Through circular dichroism spectroscopy and hydrophobic dye binding we have shown that rLIC10774 binds calcium ions, which imposes changes to secondary and tertiary structures. The recombinant protein was capable of binding to several host extracellular matrix and serum components. Therefore, we describe LIC10774 as a calcium-binding protein exposed in the outer surface of pathogenic leptospires with possible multifunctional roles in adhesion to host tissues, evasion of the immune system and participation in dissemination processes during leptospirosis. In addition, we hypothesize that the calcium binding is important for temperature-dependent functional roles during leptospirosis.
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Affiliation(s)
- Felipe José Passalia
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, 05503-900, São Paulo, Brazil; Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900, São Paulo, Brazil
| | - Eneas Carvalho
- Laboratório de Bacteriologia, Instituto Butantan, 05503-900, São Paulo, Brazil
| | - Marcos Bryan Heinemann
- Laboratório de Zoonoses Bacterianas, Faculdade de Medicina Veterinária e Zootecnia, Universidade de Sao Paulo, Brazil
| | - Mônica Larucci Vieira
- Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil.
| | - Ana Lucia T O Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, 05503-900, São Paulo, Brazil; Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900, São Paulo, Brazil.
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6
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Anuar NFSK, Wahab RA, Huyop F, Halim KBA, Hamid AAA. In silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability. J Biomol Struct Dyn 2019; 38:4493-4507. [DOI: 10.1080/07391102.2019.1683074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Nurul Fatin Syamimi Khairul Anuar
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Fahrul Huyop
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota Kuantan, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota Kuantan, Malaysia
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7
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Kim DH, Han KH. PreSMo Target-Binding Signatures in Intrinsically Disordered Proteins. Mol Cells 2018; 41:889-899. [PMID: 30352491 PMCID: PMC6199570 DOI: 10.14348/molcells.2018.0192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions. The discovery of IDPs has destroyed the classical structure-function paradigm in protein science, 3-D structure = function, because IDPs even without well-folded 3-D structures are still capable of performing important biological functions and furthermore are associated with fatal diseases such as cancers, neurodegenerative diseases and viral pandemics. Pre-structured motifs (PreSMos) refer to transient local secondary structural elements present in the target-unbound state of IDPs. During the last two decades PreSMos have been steadily acknowledged as the critical determinants for target binding in dozens of IDPs. To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution. Here we present a brief developmental history of PreSMos and describe their common characteristics. We also provide a list of newly discovered PreSMos along with their functional relevance.
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Affiliation(s)
- Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
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8
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Titus J, Ghimire H, Viennois E, Merlin D, Perera AGU. Protein secondary structure analysis of dried blood serum using infrared spectroscopy to identify markers for colitis screening. JOURNAL OF BIOPHOTONICS 2018; 11:10.1002/jbio.201700057. [PMID: 28742273 PMCID: PMC6587188 DOI: 10.1002/jbio.201700057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/20/2017] [Accepted: 07/23/2017] [Indexed: 05/07/2023]
Abstract
There remains a great need for diagnosis of inflammatory bowel disease, for which the current technique, colonoscopy, is costly and also has risks for complications. Attenuated total reflectance Fourier transform infrared spectroscopy is a new screening technique to evaluate colitis. Using second derivative spectral deconvolution of the absorbance spectra, a full set of spectral markers were identified based on statistical analysis. Using this method, Amide I group frequencies, (specifically, α-helix to β-sheet ratio of the protein secondary structure) were identified in addition to the previously reported glucose and mannose signatures in sera of chronic and acute mice models of colitis. We also used the same technique to demonstrate that these spectral markers (α-helix/β-sheet ratio, glucose and mannose) are recovering to basal levels upon anti-TNFα therapy. Hence, this technique will be able to identify changes in the sera due to diseases.
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Affiliation(s)
- Jitto Titus
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia
| | - Hemendra Ghimire
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia
| | - Emilie Viennois
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Didier Merlin
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
- Atlanta Veterans Affairs Medical Center, Decatur, Georgia
| | - A. G. Unil Perera
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
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9
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Sousa F, Sarmento B, Neves-Petersen MT. Biophysical study of bevacizumab structure and bioactivity under thermal and pH-stresses. Eur J Pharm Sci 2017; 105:127-136. [DOI: 10.1016/j.ejps.2017.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
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10
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Abstract
Monoclonal antibodies have deserved a remarkable interest for more than 40 years as a vital tool for the treatment of various diseases. Still, there is a raising interest to develop advanced monoclonal antibody delivery systems able to tailor pharmacokinetics. Bevacizumab is a humanized immunoglobulin IgG1 used in antiangiogenic therapies due to its capacity to inhibit the interaction between vascular endothelial growth factor and its receptor. However, bevacizumab-based antiangiogenic therapy is not always effective due to poor treatment compliance associated to multiples administrations and drug resistance. In this work, we show a promising strategy of encapsulating bevacizumab to protect and deliver it, in a controlled manner, increasing the time between administrations and formulation shelf-life. Nanoencapsulation of bevacizumab represents a significant advance for selective antiangiogenic therapies since extracellular, cell surface and intracellular targets can be reached. The present study shows that bevacizumab-loaded poly (lactic-co-glycolic acid) (PLGA) nanoparticles does not impair its native-like structure after encapsulation and fully retain the bioactivity, making this nanosystem a new paradigm for the improvement of angiogenic therapy.
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11
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Gao Y, Zhang C, Zhang JZH, Mei Y. Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. J Chem Inf Model 2017; 57:267-274. [PMID: 28095698 DOI: 10.1021/acs.jcim.6b00589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2D force fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.
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Affiliation(s)
- Ya Gao
- College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China
| | - Chaomin Zhang
- College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China
| | - John Z H Zhang
- College of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China
| | - Ye Mei
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China.,State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China
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12
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Haimov B, Srebnik S. A closer look into the α-helix basin. Sci Rep 2016; 6:38341. [PMID: 27917894 PMCID: PMC5137006 DOI: 10.1038/srep38341] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/08/2016] [Indexed: 11/24/2022] Open
Abstract
α-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ). In this way, valuable information on the helical structure becomes directly available. Analysis of α-helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the α-helix backbone can be harmonically approximated on the (ρ, ϑ) space, which is not applicable to the (φ, ψ) space due to the diagonal distribution of the conformations. The observed trends of helical conformations obtained from the PDB are captured by four conceptual simulations that theoretically examine the effects of residue bulkiness, external electric field, and externally applied mechanical forces. Flory’s isolated pair hypothesis is shown to be partially correct for α-helical conformations.
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Affiliation(s)
- Boris Haimov
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Simcha Srebnik
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 32000, Israel.,Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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13
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Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series. Biophys J 2016; 110:348-361. [PMID: 26789758 DOI: 10.1016/j.bpj.2015.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/04/2015] [Accepted: 12/08/2015] [Indexed: 01/21/2023] Open
Abstract
Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure. The use of these random-coil data sets rests on the perception that the reference chemical shifts arise from states where there is little or no conformational bias. However, there is growing evidence that the conformational composition of natively and nonnatively unfolded proteins fail to approach anything that can be construed as random coil. Here, we use molecular dynamics simulations of an alanine-based host-guest peptide series (AAXAA) as a model of unfolded and denatured states to examine the intrinsic propensities of the amino acids. We produced ensembles that are in good agreement with the experimental NMR chemical shifts and confirm that the sampling of the 20 natural amino acids in this peptide series is be far from random. Preferences toward certain regions of conformational space were both present and dependent upon the environment when compared under conditions typically used to denature proteins, i.e., thermal and chemical denaturation. Moreover, the simulations allowed us to examine the conformational makeup of the underlying ensembles giving rise to the ensemble-averaged chemical shifts. We present these data as an intrinsic backbone propensity library that forms part of our Structural Library of Intrinsic Residue Propensities to inform model building, to aid in interpretation of experiment, and for structure prediction of natively and nonnatively unfolded states.
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14
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Chi H, Wang X, Li J, Ren H, Huang F. Chaperonin-enhanced Escherichia coli cell-free expression of functional CXCR4. J Biotechnol 2016; 231:193-200. [PMID: 27316829 DOI: 10.1016/j.jbiotec.2016.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/23/2016] [Accepted: 06/13/2016] [Indexed: 11/15/2022]
Abstract
G protein-coupled receptors (GPCRs) are important therapeutic targets for a broad spectrum of diseases and disorders. Obtaining milligram quantities of functional receptors through the development of robust production methods are highly demanded to probe GPCR structure and functions. In this study, we analyzed synergies of the bacterial chaperonin GroEL-GroES and cell-free expression for the production of functionally folded C-X-C chemokine GPCR type 4 (CXCR4). The yield of soluble CXCR4 in the presence of detergent Brij-35 reached ∼1.1mg/ml. The chaperonin complex added was found to significantly enhance the productive folding of newly synthesized CXCR4, by increasing both the rate (∼30-fold) and the yield (∼1.3-fold) of folding over its spontaneous behavior. Meanwhile, the structural stability of CXCR4 was also improved with supplied GroEL-GroES, as was the soluble expression of biologically active CXCR4 with a ∼1.4-fold increase. The improved stability together with the higher ligand binding affinity suggests more efficient folding. The essential chaperonin GroEL was shown to be partially effective on its own, but for maximum efficiency both GroEL and its co-chaperonin GroES were necessary. The method reported here should prove generally useful for cell-free production of large amounts of natively folded GPCRs, and even other classes of membrane proteins.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China; College of Science, China University of Petroleum (East China), Qingdao 266580, PR China.
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, Qingdao 266580, PR China.
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15
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Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
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Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
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16
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Uversky VN. Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis. Biopolymers 2016; 99:870-87. [PMID: 23754493 PMCID: PMC7161862 DOI: 10.1002/bip.22298] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal‐like structure in a functional protein. The two only places for conformational ensembles of under‐folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under‐folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms–functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under‐folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under‐folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under‐folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under‐folded proteins, the different categories of under‐foldedness are differently encoded in protein amino acid sequences. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 870–887, 2013.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
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17
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Chi H, Wang X, Li J, Ren H, Huang F. Folding of newly translated membrane protein CCR5 is assisted by the chaperonin GroEL-GroES. Sci Rep 2015; 5:17037. [PMID: 26585937 PMCID: PMC4653635 DOI: 10.1038/srep17037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/23/2015] [Indexed: 01/20/2023] Open
Abstract
The in vitro folding of newly translated human CC chemokine receptor type 5
(CCR5), which belongs to the physiologically important family of G protein-coupled
receptors (GPCRs), has been studied in a cell-free system supplemented with the
surfactant Brij-35. The freshly synthesized CCR5 can spontaneously fold into its
biologically active state but only slowly and inefficiently. However, on addition of
the GroEL-GroES molecular chaperone system, the folding of the nascent CCR5 was
significantly enhanced, as was the structural stability and functional expression of
the soluble form of CCR5. The chaperonin GroEL was partially effective on its own,
but for maximum efficiency both the GroEL and its GroES lid were necessary. These
results are direct evidence for chaperone-assisted membrane protein folding and
therefore demonstrate that GroEL-GroES may be implicated in the folding of membrane
proteins.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
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18
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Zerze GH, Best RB, Mittal J. Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations. J Phys Chem B 2015; 119:14622-30. [PMID: 26498157 DOI: 10.1021/acs.jpcb.5b08619] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Robert B Best
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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19
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Kim DH, Lee C, Cho YJ, Lee SH, Cha EJ, Lim JE, Sabo TM, Griesinger C, Lee D, Han KH. A pre-structured helix in the intrinsically disordered 4EBP1. MOLECULAR BIOSYSTEMS 2014; 11:366-9. [PMID: 25431930 DOI: 10.1039/c4mb00532e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The eIF4E-binding protein 1 (4EBP1) has long been known to be completely unstructured without any secondary structures, which contributed significantly to the proposal of the induced fit mechanism for target binding of intrinsically disordered proteins. We show here that 4EBP1 is not completely unstructured, but contains a pre-structured helix.
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Affiliation(s)
- Do-Hyoung Kim
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Korea.
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20
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Tastan O, Dutta A, Booth P, Klein-Seetharaman J. Retinal proteins as model systems for membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:656-63. [PMID: 24333783 DOI: 10.1016/j.bbabio.2013.11.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/19/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Abstract
Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks.
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Affiliation(s)
- Oznur Tastan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Arpana Dutta
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, USA
| | - Paula Booth
- School of Biochemistry, University of Bristol, UK
| | - Judith Klein-Seetharaman
- Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, UK.
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21
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Sullivan DC, Lim C. Configurational Entropy of Proteins: Covariance Matrix versus Cumulative Distribution Calculations. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Holt C, Carver JA, Ecroyd H, Thorn DC. Invited review: Caseins and the casein micelle: their biological functions, structures, and behavior in foods. J Dairy Sci 2013; 96:6127-46. [PMID: 23958008 DOI: 10.3168/jds.2013-6831] [Citation(s) in RCA: 286] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/09/2013] [Indexed: 12/27/2022]
Abstract
A typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosphorylation and the same type of flexible, unfolded conformation as caseins. The ability to suppress amyloid fibril formation by forming an alternative amorphous aggregate is also not unique to caseins and underlies the action of molecular chaperones such as the small heat-shock proteins. The open structure of the protein matrix of casein micelles is fragile and easily perturbed by changes in its environment. Perturbations can cause the polypeptide chains to segregate into regions of greater and lesser density. As a result, the reliable determination of the native structure of casein micelles continues to be extremely challenging. The biological functions of caseins, such as their chaperone activity, are determined by their composition and flexible conformation and by how the casein polypeptide chains interact with each other. These same properties determine how caseins behave in the manufacture of many dairy products and how they can be used as functional ingredients in other foods.
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Affiliation(s)
- C Holt
- Institute of Molecular, Cell and Systems Biology, School of Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
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23
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Elam WA, Schrank TP, Campagnolo AJ, Hilser VJ. Temperature and urea have opposing impacts on polyproline II conformational bias. Biochemistry 2013; 52:949-58. [PMID: 23350874 DOI: 10.1021/bi301435p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The native states of globular proteins have been accessed in atomic detail by X-ray crystallography and nuclear magnetic resonance spectroscopy, yet characterization of denatured proteins beyond global metrics has proven to be elusive. Denatured proteins have been observed to exhibit global geometric properties of a random coil polymer. However, this does not preclude the existence of nonrandom, local conformational bias that may be significant for protein folding and function. Indeed, circular dichroism (CD) spectroscopy and other methods have suggested that the denatured state contains considerable local bias to the polyproline II (PII) conformation. Here, we develop predictive models to determine the extent that temperature and the chemical denaturant urea modulate PII propensity. In agreement with our predictive model, PII propensity is observed experimentally to decrease with an increase in temperature. Conversely, urea appears to promote the PII conformation as determined by CD and isothermal titration calorimetry. Importantly, the calorimetric data are in quantitative agreement with a model that predicts the stability of the PII helix relative to other denatured state conformations based upon solvent accessible surface area and experimentally measured Gibbs transfer free energies. The ability of urea to promote the PII conformation can be attributed to the favorable interaction of urea with the peptide backbone. Thus, perturbing denatured states by temperature or cosolutes has subtle, yet opposing, impacts on local PII conformational biases. These results have implications for protein folding as well as for the function of signaling proteins that bind proline-rich targets in globular or intrinsically disordered proteins.
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Affiliation(s)
- W Austin Elam
- T. C. Jenkins Department of Biophysics and Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
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24
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Ghavami A, van der Giessen E, Onck PR. Coarse-Grained Potentials for Local Interactions in Unfolded Proteins. J Chem Theory Comput 2012; 9:432-40. [DOI: 10.1021/ct300684j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ali Ghavami
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Erik van der Giessen
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick R. Onck
- Micromechanics of Materials, Zernike
Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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25
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Tompa P, Rose GD. The Levinthal paradox of the interactome. Protein Sci 2011; 20:2074-9. [PMID: 21987416 DOI: 10.1002/pro.747] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 02/06/2023]
Abstract
The central biological question of the 21st century is: how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components? Here, we estimate the combinatorics of self-assembling the protein constituents of a yeast cell, a number so vast that the functional interactome could only have emerged by iterative hierarchic assembly of its component sub-assemblies. A protein can undergo both reversible denaturation and hierarchic self-assembly spontaneously, but a functioning interactome must expend energy to achieve viability. Consequently, it is implausible that a completely "denatured" cell could be reversibly renatured spontaneously, like a protein. Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions and evolving responses to the origin of life on the prebiotic earth. We surmise that this non-deterministic temporal continuum could not be reconstructed de novo under present conditions.
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Affiliation(s)
- Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium.
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26
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Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints. Proc Natl Acad Sci U S A 2010; 108:109-13. [PMID: 21148101 DOI: 10.1073/pnas.1014674107] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A protein backbone has two degrees of conformational freedom per residue, described by its ϕ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate 3/4 of ϕ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of ϕ,ψ-space for a blocked peptide; for conformers within this region, an amide hydrogen is solvent-inaccessible, depriving it of a hydrogen-bonding partner. Yet, this "forbidden" region is well populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners for these otherwise unsatisfied polar groups. Consequently, conformational space expands under folding conditions, a paradigm-shifting realization that prompts an experimentally verifiable conjecture about likely folding pathways.
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27
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Abstract
Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins. In this review, we provide a survey of computational studies of protein disorder with an emphasis on the interdisciplinary nature of these studies. The application of simulation techniques to the study of disordered states is described in the context of experimental and bioinformatics approaches. Experimental data can be incorporated into simulations, and simulations can provide predictions for experiment. In this way, simulations have been integrated into the existing methodologies for the study of disordered state ensembles. We provide recent examples of simulations of disordered states from the literature and our own work. Throughout the review, we emphasize important predictions and biophysical understanding made possible through the use of simulations. This review is intended as both an overview and a guide for structural biologists and theoretical biophysicists seeking accurate, atomic-level descriptions of disordered state ensembles.
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Affiliation(s)
- Sarah Rauscher
- Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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28
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Dutta A, Tirupula KC, Alexiev U, Klein-Seetharaman J. Characterization of membrane protein non-native states. 1. Extent of unfolding and aggregation of rhodopsin in the presence of chemical denaturants. Biochemistry 2010; 49:6317-28. [PMID: 20575534 DOI: 10.1021/bi100338e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Little is known about the general folding mechanisms of helical membrane proteins. Unfolded, i.e., non-native states, in particular, have not yet been characterized in detail. Here, we establish conditions under which denatured states of the mammalian membrane protein rhodopsin, a prototypic G protein coupled receptor with primary function in vision, can be studied. We investigated the effects of the chemical denaturants sodium dodecyl sulfate (SDS), urea, guanidine hydrochloride (GuHCl), and trifluoroacetic acid (TFA) on rhodopsin's secondary structure and propensity for aggregation. Ellipticity at 222 nm decreases in the presence of maximum concentrations of denaturants in the order TFA > GuHCl > urea > SDS + urea > SDS. Interpretation of these changes in ellipticity in terms of helix loss is challenged because the addition of some denaturants leads to aggregation. Through a combination of SDS-PAGE, dependence of ellipticity on protein concentration, and 1D (1)H NMR we show that aggregates form in the presence of GuHCl, TFA, and urea but not in any concentration of SDS, added over a range of 0.05%-30%. Mixed denaturant conditions consisting of 3% SDS and 8 M urea, added in this order, also did not result in aggregation. We conclude that SDS is able to prevent the exposure of large hydrophobic regions present in membrane proteins which otherwise leads to aggregation. Thus, 30% SDS and 3% SDS + 8 M urea are the denaturing conditions of choice to study maximally unfolded rhodopsin without aggregation.
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Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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29
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Makarov DE. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes. J Chem Phys 2010; 132:035104. [DOI: 10.1063/1.3284509] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Krishnan VV, Lau EY, Yamada J, Denning DP, Patel SS, Colvin ME, Rexach MF. Intramolecular cohesion of coils mediated by phenylalanine--glycine motifs in the natively unfolded domain of a nucleoporin. PLoS Comput Biol 2008; 4:e1000145. [PMID: 18688269 PMCID: PMC2475668 DOI: 10.1371/journal.pcbi.1000145] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 06/26/2008] [Indexed: 01/23/2023] Open
Abstract
The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine–glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin–cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion. The nuclear pore complex is a molecular filter that gates macromolecular exchange between the cytoplasm and the nucleoplasm of cells. It contains a size-selective diffusion barrier at its center composed of proteins named FG nucleoporins. These nucleoporins feature large, structurally disordered domains that are highly decorated with phenylalanine–glycine (FG) sequence motifs. The dynamic structure of these disordered FG domains excludes them from classical structural biology analyses such as X-ray crystallography; thus, new approaches are needed to characterize their shape. Here computational and biophysical approaches were used to elucidate the ensemble of structures adopted by the FG domain of a nucleoporin. The analyses showed that the FG motifs function as intramolecular cohesion elements that compact the shape of the FG domain, forcing it to adopt loosely knit globular configurations that are constantly reconfiguring. Within the nuclear pore complex, dozens of these nucleoporin FG domains may stack as loosely knit globules forming a porous sieve that gates molecular diffusion by size exclusion.
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Affiliation(s)
- V. V. Krishnan
- Department of Applied Science, University of California Davis, Davis, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry, California State University Fresno, Fresno, California, United States of America
| | - Edmond Y. Lau
- Chemistry, Materials, Earth and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Justin Yamada
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Daniel P. Denning
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Samir S. Patel
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael E. Colvin
- Center for Computational Biology, School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Michael F. Rexach
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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31
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Keskin O, Gursoy A, Ma B, Nussinov R. Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem Rev 2008; 108:1225-44. [DOI: 10.1021/cr040409x] [Citation(s) in RCA: 476] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Flexibility of the cytoplasmic domain of the phototaxis transducer II from Natronomonas pharaonis. JOURNAL OF BIOPHYSICS (HINDAWI PUBLISHING CORPORATION : ONLINE) 2008; 2008:267912. [PMID: 20107574 PMCID: PMC2809331 DOI: 10.1155/2008/267912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 07/21/2008] [Indexed: 11/17/2022]
Abstract
Chemo- and phototaxis systems in bacteria and archaea serve as models for more complex signal transduction mechanisms in higher eukaryotes. Previous studies of the cytoplasmic fragment of the phototaxis transducer (pHtrII-cyt) from the halophilic archaeon Natronomonas pharaonis showed that it takes the shape of a monomeric or dimeric rod under low or high salt conditions, respectively. CD spectra revealed only approximately 24% helical structure, even in 4 M KCl, leaving it an open question how the rod-like shape is achieved. Here, we conducted CD, FTIR, and NMR spectroscopic studies under different conditions to address this question. We provide evidence that pHtrII-cyt is highly dynamic with strong helical propensity, which allows it to change from monomeric to dimeric helical coiled-coil states without undergoing dramatic shape changes. A statistical analysis of predicted disorder for homologous sequences suggests that structural flexibility is evolutionarily conserved within the methyl-accepting chemotaxis protein family.
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33
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Naseem F, Khan RH. Transition of a compact intermediate state of pea lectin under the influence of different molecular weight polyethylene glycols. Protein J 2007; 26:415-21. [PMID: 17516155 DOI: 10.1007/s10930-007-9081-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The compact intermediate of the pea lectin found to exist at pH 2.4 was treated with low (PEG-400), medium (PEG-4000) and high (PEG-20,000) molecular weight PEGs. The changes occurring in the secondary structure of the protein were monitored by CD spectropolarimetry in the far-UV range, intrinsic fluorescence was used as a probe to observe the changes in the tertiary structure which is reflected by the changes in the tryptophan environment, further ANS binding studies were made to know the extent of exposure of the hydrophobic patches which is again indicative of the overall changes occurring in the tertiary structure of the protein. It was found that the three PEGs altered the secondary as well as tertiary structure of the pH 2.4 intermediate leading to the formation of three different intermediates. The intermediates were found to have non-native secondary structure as well as non-native tertiary structure. The intermediate formed by the action of PEG-400 was due to the induction of secondary and tertiary structure while the intermediates formed under the influence of PEG-4000 and PEG-20,000 were due to loss in secondary structure and rearrangement in tertiary structure. Also the ANS binding studies showed the absence of any MG or MG-like structures formed in the folding /unfolding pathway induced by PEGs.
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Affiliation(s)
- Farah Naseem
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
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34
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Geething NC, Spudich JA. Identification of a minimal myosin Va binding site within an intrinsically unstructured domain of melanophilin. J Biol Chem 2007; 282:21518-28. [PMID: 17513864 DOI: 10.1074/jbc.m701932200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myosin V is a molecular motor that transports a variety of cellular cargo, including organelles, vesicles, and messenger RNA. The proper peripheral distribution of melanosomes, a dense pigment-containing organelle, is dependent on actin and the activity of myosin Va. The recruitment of myosin Va to the melanosome and proper transport of the melanosome requires melanophilin, which directly binds to myosin Va and is tethered to the melanosome membrane via Rab27a. Here we use highly purified proteins to demonstrate that the globular tail domain of myosin Va binds directly to an intrinsically unstructured domain of melanophilin. The myosin Va binding domain of melanophilin lacks stable secondary structure, and (1)H NMR measurements indicate that the protein is unfolded. This domain is extremely sensitive to mild proteolysis and has a hydrodynamic radius that is consistent with a random coil-like polypeptide. We show that myosin Va binding does not induce the global folding of melanophilin. Truncations of melanophilin were utilized to define a short peptide sequence (26 residues) within melanophilin that is critical for myosin Va binding. We demonstrate that a peptide corresponding to these residues binds directly to the globular tail domain with the same affinity as melanophilin. We discuss the possible implications of protein intrinsic disorder in recruitment and maintenance of myosin Va on melanosome membranes.
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Affiliation(s)
- Nathan C Geething
- Department of Biochemistry, Stanford University, Stanford, California 94041, USA
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35
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Shi Z, Chen K, Liu Z, Sosnick TR, Kallenbach NR. PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV. Proteins 2007; 63:312-21. [PMID: 16362932 DOI: 10.1002/prot.20788] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A great deal of attention has been paid lately to the structures in unfolded proteins due to the recent discovery of many biologically functional but natively unfolded proteins and the far-reaching implications of order in unfolded states for protein folding. Recently, studies on oligo-Ala, oligo-Lys, oligo-Asp, and oligo-Glu, as well as oligo-Pro, have indicated that the left-handed polyproline II (PII) is the major local structure in these short peptides. Here, we show by NMR and CD studies that ubiquitin fragments, model unfolded peptides composed of nonrepeating amino acids, and four alanine-rich peptides containing QQQ, SSS, FFF, and VVV sequences are all present in aqueous solution predominantly in the extended PII or beta conformation. The results from this and related studies indicate that PII might be a major backbone conformation in unfolded proteins. The presence of defined local backbone structure in unfolded proteins is inconsistent with predictions from random coil models.
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, New York, NY 10003, USA
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36
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Skrabana R, Sevcik J, Novak M. Intrinsically Disordered Proteins in the Neurodegenerative Processes: Formation of Tau Protein Paired Helical Filaments and Their Analysis. Cell Mol Neurobiol 2006; 26:1085-97. [PMID: 16779670 DOI: 10.1007/s10571-006-9083-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 05/01/2006] [Indexed: 01/24/2023]
Abstract
1. Several intrinsically disordered proteins (IDPs) play principal role in the neurodegenerative processes of various types. Among them, alpha-synuclein is involved in Parkinson's disease, prion protein in transmissible spongiform encephalopathies, and tau protein in Alzheimer's disease (AD) and related tauopathies. Neuronal damage in AD is accompanied by the presence of tau protein fibrils composed of paired helical filaments (PHF). 2. Tau protein represents a typical IDP. IDPs do not exhibit any stable secondary structure in the free form, but they are able to fold after binding to targets and contain regions with large propensity to adopt a defined type of secondary structure. Binding-folding event at tau protein leading to PHF generation is believed to happen in the course of tauopathies. 3. Detailed molecular topology of PHF formation is unknown. There are evidences about the cross-beta structure in PHF core; however the precise arrangement of the tau polypeptide chain is unclear. In this review we summarize current attempts at in vitro PHF reconstruction and the development of methods for PHF structure determination. The emphasis is put on the monoclonal antibodies used as structural molecular probes for research on the role of IDPs in pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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37
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Vermeulen W, Van Troys M, Bourry D, Dewitte D, Rossenu S, Goethals M, Borremans FAM, Vandekerckhove J, Martins JC, Ampe C. Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold. J Mol Biol 2006; 359:1277-92. [PMID: 16697408 DOI: 10.1016/j.jmb.2006.04.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2006] [Revised: 04/16/2006] [Accepted: 04/20/2006] [Indexed: 11/22/2022]
Abstract
The HeadPiece (HP) domain, present in several F-actin-binding multi-domain proteins, features a well-conserved, solvent-exposed PXWK motif in its C-terminal subdomain. The latter is an autonomously folding subunit comprised of three alpha-helices organised around a hydrophobic core, with the sequence motif preceding the last helix. We report the contributions of each conserved residue in the PXWK motif to human villin HP function and structure, as well as the structural implications of the naturally occurring Pro to Ala mutation in dematin HP. NMR shift perturbation mapping reveals that substitution of each residue by Ala induces only minor, local perturbations in the full villin HP structure. CD spectroscopic thermal analysis, however, shows that the Pro and Trp residues in the PXWK motif afford stabilising interactions. This indicates that, in addition to the residues in the hydrophobic core, the Trp-Pro stacking within the motif contributes to HP stability. This is reinforced by our data on isolated C-terminal HP subdomains where the Pro is also essential for structure formation, since the villin, but not the dematin, C-terminal subdomain is structured. Proper folding can be induced in the dematin C-terminal subdomain by exchanging the Ala for Pro. Conversely, the reverse substitution in the villin C-terminal subdomain leads to loss of structure. Thus, we demonstrate a crucial role for this proline residue in structural stability and folding potential of HP (sub)domains consistent with Pro-Trp stacking as a more general determinant of protein stability.
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Affiliation(s)
- Wim Vermeulen
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Faculty of Sciences, Ghent University, Belgium
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38
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, 100 Washington Place, New York, New York 10003-5180, USA
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39
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Gursoy A, Keskin O, Turkay M, Erman B. Relationships between unfolded configurations of proteins and dynamics of folding to the native state. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/polb.21018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Scolnik Y, Portnaya I, Cogan U, Tal S, Haimovitz R, Fridkin M, Elitzur AC, Deamer DW, Shinitzky M. Subtle differences in structural transitions between poly-l- and poly-d-amino acids of equal length in water. Phys Chem Chem Phys 2006; 8:333-9. [PMID: 16482275 DOI: 10.1039/b513974k] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mirror-image asymmetric molecules, i.e., chiral isomers or enantiomers, are classically considered as chemically identical. Recent studies, however, have indicated that parity violation by the nuclear weak force induces a tiny energy difference between chiral isomers. Upon combination with a massive amplification process, expansion of this difference to a detectable macroscopic level may be achieved. Yet, experimental tests of this possibility, where one enantiomer is compared to the other in solution, are hampered by the possible presence of undetectable impurities. In this study we have overcome this problem by comparing structural and dynamic features of synthetic D- and L-polyglutamic acid and polylysine molecules each of 24 identical residues. In these water-soluble polypeptides helix formation is an intramolecular autocatalytic process amplified by each turn, which is actually unaffected by low level of putative impurities in the solvent. The helix and random coil configurations and their transition were determined in this study by circular dichroism (CD) and isothermal titration calorimetry (ITC) in water and deuterium oxide. Distinct differences in structure and transition energies between the enantiomeric polypeptides were detected by both CD and ITC when dissolved in water. Intriguingly, these differences were by and large abolished in deuterium oxide. Our findings suggest that deviation from physical invariance between the D- and L-polyamino acids is induced in part by different hydration in water which is eliminated in deuterium oxide. Based on the recent findings by Tikhonov and Volkov (V. I. Tikhonov and A. A. Volkov, Science 2002, 296, 2363) we suggest that ortho-H(2)O, which constitutes 75% of bulk H(2)O, has a preferential affinity to L-enantiomers. Differential hydration of enantiomers may have played a role in the selection of L-amino acids by early forms of life.
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Affiliation(s)
- Yosef Scolnik
- Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Shi Z, Chen K, Liu Z, Ng A, Bracken WC, Kallenbach NR. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales. Proc Natl Acad Sci U S A 2005; 102:17964-8. [PMID: 16330763 PMCID: PMC1312395 DOI: 10.1073/pnas.0507124102] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is growing appreciation of the functional relevance of unfolded proteins in biology. However, unfolded states of proteins have proven inaccessible to the usual techniques for high-resolution structural and energetic characterization. Unfolded states are still generally conceived of as statistical coils, based on the pioneering work of Flory [(1969) Statistical Mechanics of Chain Molecules (Wiley, New York)] and Tanford [(1968) Adv. Protein Chem. 23, 121-282]. Recently, several lines of independent evidence have raised doubts about the random coil model and offer support for alternative views. Here, we show that polyproline II conformation is dominant in a host-guest peptide model AcGGXGGNH(2) (X not equal glycine), in equilibrium predominantly with beta-structure. This result is inconsistent with a random coil model and the general view that these peptides are unstructured. By calculating a set of apparent DeltaG values from the measured coupling constants of the backbone amides, we can construct a polyproline II scale that correlates negatively with beta-sheet scales.
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42
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Wieczorek R, Dannenberg JJ. The Energetic and Structural Effects of Single Amino Acid Substitutions upon Capped α-Helical Peptides Containing 17 Amino Acid Residues. An ONIOM DFT/AM1 Study. J Am Chem Soc 2005; 127:17216-23. [PMID: 16332068 DOI: 10.1021/ja052689j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluate the effect of the amino acid mutations of glycine, leucine, valine, phenylalanine, serine, and proline for the 10th alanine in the capped peptide, acetly(Ala)(17)NH(2), upon the energies of the alpha-helices and beta-strands using ONIOM DFT/AM1 molecular orbital calculations. The relative stabilities of the alpha-helix (to the beta-strand) derive from the differences between the effects upon not only the helix but the strand as well. Thus, Ala --> Pro significantly destabilizes both but destabilizes the alpha-helix more, while Ala --> Gly stabilizes both but stabilizes the beta-strand more. The theoretical results are discussed in the context of the known experimental reports. We suggest that the solvation of the unfolded state drives the helix/coil equilibrium in solution.
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Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA
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43
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Receveur-Bréchot V, Bourhis JM, Uversky VN, Canard B, Longhi S. Assessing protein disorder and induced folding. Proteins 2005; 62:24-45. [PMID: 16287116 DOI: 10.1002/prot.20750] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins (IDPs) defy the structure-function paradigm as they fulfill essential biological functions while lacking well-defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the use of multiples techniques.
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Affiliation(s)
- Véronique Receveur-Bréchot
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Universités Aix-Marseille I et II, Campus de Luminy, Marseille Cedex 09, France
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44
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Gong H, Fleming PJ, Rose GD. Building native protein conformation from highly approximate backbone torsion angles. Proc Natl Acad Sci U S A 2005; 102:16227-32. [PMID: 16251268 PMCID: PMC1283474 DOI: 10.1073/pnas.0508415102] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Indexed: 11/18/2022] Open
Abstract
Reconstructing a protein in three dimensions from its backbone torsion angles is an ongoing challenge because minor inaccuracies in these angles produce major errors in the structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm, the longer the arm, the larger the displacement. Even accurate knowledge of the backbone torsions and Psi is insufficient, owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, also lead to major errors in the structure. Against this background, we conducted a computational experiment to assess whether protein conformation can be determined from highly approximate backbone torsion angles, the kind of information that is now obtained readily from NMR. Specifically, backbone torsion angles were taken from proteins of known structure and mapped into 60 degrees x 60 degrees grid squares, called mesostates. Side-chain atoms beyond the beta -carbon were discarded. A mesostate representation of the protein backbone was then used to extract likely candidates from a fragment library of mesostate pentamers, followed by Monte Carlo-based fragment-assembly simulations to identify stable conformations compatible with the given mesostate sequence. Only three simple energy terms were used to gauge stability: molecular compaction, soft-sphere repulsion, and hydrogen bonding. For the six representative proteins described here, stable conformers can be partitioned into a remarkably small number of topologically distinct clusters. Among these, the native topology is found with high frequency and can be identified as the cluster with the most favorable energy.
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Affiliation(s)
- Haipeng Gong
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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45
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Chen K, Liu Z, Zhou C, Shi Z, Kallenbach NR. Neighbor effect on PPII conformation in alanine peptides. J Am Chem Soc 2005; 127:10146-7. [PMID: 16028907 DOI: 10.1021/ja052094o] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyproline II (PPII) conformation is dominant in short alanine oligomers. The noncooperativity of PPII structure in alanine peptides indicates that PPII in water is locally determined and that alanine neighbors are consistent with Flory's isolated pair hypothesis. However, neighbor effects from beta-branched or bulky aromatic residues tend to increase the Phi angle of the nearest neighbor as observed in coil library data. Here we demonstrate directly the neighbor effect using short alanine model peptides GGAAAGG, GGLnALnGG (Ln is norleucine), GGIAAGG, and GGIAIGG. The far-UV CD spectra, NMR 3JalphaN coupling constant, and H-D hydrogen exchange measurements reveal that Ile reduces the PPII content of the probe Ala side chain relative to Ala or norLeu. The free energy differences are consistent with predictions from electrostatic solvation free energy (ESF) calculations. The results indicate that prediction of PPII propensities or scales requires including the neighbor effect.
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Affiliation(s)
- Kang Chen
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
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46
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Fitzkee NC, Rose GD. Sterics and solvation winnow accessible conformational space for unfolded proteins. J Mol Biol 2005; 353:873-87. [PMID: 16185713 DOI: 10.1016/j.jmb.2005.08.062] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 08/19/2005] [Accepted: 08/26/2005] [Indexed: 10/25/2022]
Abstract
The magnitude of protein conformational space is over-estimated by the traditional random-coil model, in which local steric restrictions arise exclusively from interactions between adjacent chain neighbors. Using a five-state model, we assessed the extent to which steric hindrance and hydrogen bond satisfaction, energetically significant factors, impose additional conformational restrictions on polypeptide chains, beyond adjacent residues. Steric hindrance is repulsive: the distance of closest approach between any two atoms cannot be less than the sum of their van der Waals radii. Hydrogen bond satisfaction is attractive: polar backbone atoms must form hydrogen bonds, either intramolecularly or to solvent water. To gauge the impact of these two factors on the magnitude of conformational space, we systematically enumerated and classified the disfavored conformations that restrict short polyalanyl backbone chains. Applying such restrictions to longer chains, we derived a scaling law to estimate conformational restriction as a function of chain length. Disfavored conformations predicted by the model were tested against experimentally determined structures in the coil library, a non-helix, non-strand subset of the PDB. These disfavored conformations are usually absent from the coil library, and exceptions can be uniformly rationalized.
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Affiliation(s)
- Nicholas C Fitzkee
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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47
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Fitzkee NC, Fleming PJ, Gong H, Panasik N, Street TO, Rose GD. Are proteins made from a limited parts list? Trends Biochem Sci 2005; 30:73-80. [PMID: 15691652 DOI: 10.1016/j.tibs.2004.12.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture?
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Affiliation(s)
- Nicholas C Fitzkee
- Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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48
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Sullivan DC, Kuntz ID. Distributions in protein conformation space: implications for structure prediction and entropy. Biophys J 2004; 87:113-20. [PMID: 15240450 PMCID: PMC1304334 DOI: 10.1529/biophysj.104.041723] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 03/23/2004] [Indexed: 11/18/2022] Open
Abstract
By considering how polymer structures are distributed in conformation space, we show that it is possible to quantify the difficulty of structural prediction and to provide a measure of progress for prediction calculations. The critical issue is the probability that a conformation is found within a specified distance of another conformer. We address this question by constructing a cumulative distribution function (CDF) for the average probability from observations about its limiting behavior at small displacements and numerical simulations of polyalanine chains. We can use the CDF to estimate the likelihood that a structure prediction is better than random chance. For example, the chance of randomly predicting the native backbone structure of a 150-amino-acid protein to low resolution, say within 6 A, is 10(-14). A high-resolution structural prediction, say to 2 A, is immensely more difficult (10(-57)). With additional assumptions, the CDF yields the conformational entropy of protein folding from native-state coordinate variance. Or, using values of the conformational entropy change on folding, we can estimate the native state's conformational span. For example, for a 150-mer protein, equilibrium alpha-carbon displacements in the native ensemble would be 0.3-0.5 A based on T Delta S of 1.42 kcal/(mol residue).
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Affiliation(s)
- David C Sullivan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143-2240, USA
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49
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Keskin O, Yuret D, Gursoy A, Turkay M, Erman B. Relationships between amino acid sequence and backbone torsion angle preferences. Proteins 2004; 55:992-8. [PMID: 15146495 DOI: 10.1002/prot.20100] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of phipsi pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge-based pairwise dependent phipsi energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all-atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native-state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context-dependent phipsi correlations into the chain that would affect the choice of native-state torsional angles.
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Affiliation(s)
- O Keskin
- College of Engineering and Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
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50
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Mayor U, Grossmann JG, Foster NW, Freund SMV, Fersht AR. The denatured state of Engrailed Homeodomain under denaturing and native conditions. J Mol Biol 2003; 333:977-91. [PMID: 14583194 DOI: 10.1016/j.jmb.2003.08.062] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein folding starts from the elusive form of the denatured state that is present under conditions that favour the native state. We have studied the denatured state of Engrailed Homeodomain (En-HD) under mildly and strongly denaturing conditions at the level of individual residues by NMR and more globally by conventional spectroscopy and solution X-ray scattering. We have compared these states with a destabilized mutant, L16A, which is predominantly denatured under conditions where the wild-type is native. This engineered denatured state, which could be directly studied under native conditions, was in genuine equilibrium with the native state, which could be observably populated by changing the conditions or introducing a stabilizing mutation. The denatured state had extensive native secondary structure and was significantly compact and globular. But, the side-chains and backbone were highly mobile. Non-cooperative melting of the residual structure on the denatured state of En-HD was observed, both at the residue and the molecular level, with increasingly denaturing conditions. The absence of a co-operative transition could result from the denatured state ensemble progressing through a series of intermediates or from a more general slide (second-order transition) from the compact form under native conditions to the more extended at highly denaturing conditions. In either case, the starting point for folding under native conditions is highly structured and already poised to adopt the native structure.
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Affiliation(s)
- Ugo Mayor
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK
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