1
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Cieplak AS. Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation. Front Neurosci 2019; 13:488. [PMID: 31156372 PMCID: PMC6530265 DOI: 10.3389/fnins.2019.00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar "strand" propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FP i ; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FP i plots show that the "strand" propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
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2
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Scheerer D, Chi H, McElheny D, Keiderling TA, Hauser K. Isotopically Site-Selected Dynamics of a Three-Stranded β-Sheet Peptide Detected with Temperature-Jump Infrared-Spectroscopy. J Phys Chem B 2018; 122:10445-10454. [PMID: 30372071 DOI: 10.1021/acs.jpcb.8b08336] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared detected temperature-jump (T-jump) spectroscopy and site-specific isotopic labeling were applied to study a model three-stranded β-sheet peptide with the goal of individually probing the dynamics of strand and turn structural elements. This peptide had two DPro-Gly (pG) turn sequences to stabilize the two component hairpins, which were labeled with 13C═O on each of the Gly residues to resolve them spectroscopically. Labeling the second turn on the amide preceding the DPro (Xxx-DPro amide) provided an alternate turn label as a control. Placing 13C═O labels on specific in-strand residues gave shifted modes that overlap the Xxx-DPro amide I' modes. Their impact could be separated from the turn dynamics by a novel difference transient analysis approach. Fourier-transform infrared spectra were modeled with density functional theory-computations which showed the local, isotope-selected vibrations were effectively uncoupled from the other amide I modes. Our T-jump dynamics results, combined with nuclear magnetic resonance structures and equilibrium spectral measurements, showed the first turn to be most stable and best formed with the slowest dynamics, whereas the second turn and first strand (N-terminus) had similar dynamics, and the third strand (C-terminus) had the fastest dynamics and was the least structured. The relative dynamics of the strands, Xxx-DPro amides, and 13C-labeled Gly residues on the turns also qualitatively corresponded to molecular dynamics (MD) simulations of turn and strand fluctuations. MD trajectories indicated the turns to be bistable, with the first turn being Type I' and the second turn flipping from I' to II'. The differences in relaxation times for each turn and the separate strands revealed that the folding process of this turn-stabilized β-sheet structure proceeds in a multistep process.
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Affiliation(s)
- David Scheerer
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany
| | - Heng Chi
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States.,Jiangsu Food and Pharmaceutical Science College , 223003 Huai'an , China
| | - Dan McElheny
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States
| | - Timothy A Keiderling
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States
| | - Karin Hauser
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany
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3
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Linares Mendez IJ, Pleizier JS, Wang HB, Wisner JA. 1
H NMR-based method for the determination of complexation equilibrium parameters and chemical shifts in a hydrogen-bonded system with dynamic composition. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Iamnica J. Linares Mendez
- Department of Chemistry; Western University; London ON Canada
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Chemical and Environmental Engineering; Jianghan University; Wuhan Hubei China
| | | | - Hong-Bo Wang
- Department of Chemistry; Western University; London ON Canada
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Chemical and Environmental Engineering; Jianghan University; Wuhan Hubei China
| | - James A. Wisner
- Department of Chemistry; Western University; London ON Canada
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Chemical and Environmental Engineering; Jianghan University; Wuhan Hubei China
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4
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Scheerer D, Chi H, McElheny D, Samer A, Keiderling TA, Hauser K. Role of Aromatic Cross-Links in Structure and Dynamics of Model Three-Stranded β-Sheet Peptides. J Phys Chem A 2018; 122:543-553. [DOI: 10.1021/acs.jpca.7b10190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Scheerer
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Heng Chi
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
- Jiangsu Food and Pharmaceutical Science College, Huai’an, China
| | - Dan McElheny
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Ayesha Samer
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Timothy A. Keiderling
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Karin Hauser
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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5
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Diana D, Di Salvo C, Celentano V, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. Conformational stabilization of a β-hairpin through a triazole–tryptophan interaction. Org Biomol Chem 2018; 16:787-795. [DOI: 10.1039/c7ob02815f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triazole and indole rings stabilize a β-hairpin conformation through an aromatic–aromatic interaction.
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Affiliation(s)
| | | | | | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini
- CNR
- Napoli
- Italy
| | | | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali
- Biologiche e Farmaceutiche
- Università della Campania “L. Vanvitelli”
- Caserta
- Italy
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6
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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7
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Rajeshwar T R, Krishnan M. Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters. J Phys Chem B 2017; 121:5174-5186. [PMID: 28452484 DOI: 10.1021/acs.jpcb.7b01402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (Oaxis2) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, Oaxis2, conformational entropy (Sconf), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with Oaxis2 ∼ 0) to highly restricted (with Oaxis2 ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.
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Affiliation(s)
- Rajitha Rajeshwar T
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
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8
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Kumar A, Ranbhor R, Patel K, Ramakrishnan V, Durani S. Automated protein design: Landmarks and operational principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 125:24-35. [PMID: 27979438 DOI: 10.1016/j.pbiomolbio.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022]
Abstract
Protein design has an eventful history spanning over three decades, with handful of success stories reported, and numerous failures not reported. Design practices have benefited tremendously from improvements in computer hardware and advances in scientific algorithms. Though protein folding problem still remains unsolved, the possibility of having multiple sequence solutions for a single fold makes protein design a more tractable problem than protein folding. One of the most significant advancement in this area is the implementation of automated design algorithms on pre-defined templates or completely new folds, optimized through deterministic and heuristic search algorithms. This progress report provides a succinct presentation of important landmarks in automated design attempts, followed by brief account of operational principles in automated design methods.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, ON, M5S3H6, Canada.
| | | | | | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India.
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology, Bombay, 400076, India
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9
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Anderson JM, Jurban B, Huggins KNL, Shcherbakov AA, Shu I, Kier B, Andersen NH. Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability. Biochemistry 2016; 55:5537-5553. [DOI: 10.1021/acs.biochem.6b00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jordan M. Anderson
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Kelly N. L. Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | | | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brandon Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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10
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Celentano V, Diana D, Di Salvo C, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. 1,2,3-Triazole Bridge as Conformational Constrain in β-Hairpin Peptides: Analysis of Hydrogen-Bonded Positions. Chemistry 2016; 22:5534-7. [DOI: 10.1002/chem.201600154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Indexed: 12/22/2022]
Affiliation(s)
- V. Celentano
- Istituto di Biostrutture e Bioimmagini CNR; Via Mezzocannone 16 80134 Napoli (Italy)
| | - D. Diana
- Istituto di Biostrutture e Bioimmagini CNR; Via Mezzocannone 16 80134 Napoli (Italy)
| | - C. Di Salvo
- Istituto di Biostrutture e Bioimmagini CNR; Via Mezzocannone 16 80134 Napoli (Italy)
- National University of Ireland; Galway (Ireland)
| | - L. De Rosa
- Istituto di Biostrutture e Bioimmagini CNR; Via Mezzocannone 16 80134 Napoli (Italy)
| | - A. Romanelli
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Via Mezzocannone 16 80134 Napoli (Italy)
| | - R. Fattorusso
- Dipartimento di Scienze Ambientali, Biologiche e Farmaceutiche; Seconda Università di Napoli; Via Vivaldi 46 81100 Caserta, Napoli (Italy)
| | - L. D. D'Andrea
- Istituto di Biostrutture e Bioimmagini CNR; Via Mezzocannone 16 80134 Napoli (Italy)
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11
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Zhao Y, Truhlar DG. Density Functionals for Noncovalent Interaction Energies of Biological Importance. J Chem Theory Comput 2015; 3:289-300. [PMID: 26627172 DOI: 10.1021/ct6002719] [Citation(s) in RCA: 466] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty density functionals and one wavefunction method are assessed against a recently published database of accurate noncovalent interaction energies of biological importance. The comparison shows that two newly developed density functional theory (DFT) methods, PWB6K and M05-2X, give the best performance for this benchmark database of 22 noncovalent complexes, including both hydrogen-bonding and dispersion-dominated complexes. In contrast, the more popular B3LYP and PBEh functionals fail to describe the interactions in the dispersion-dominated complexes. The local spin density approximation and BHandH functionals give good performance for dispersion-dominated interactions at the expense of a large error for hydrogen bonding. PWB6K and M05-2X constitute a new generation of DFT methods based on simultaneously optimized exchange and correlation functionals that include kinetic energy density in both the exchange and correlation functional, and the present study confirms that they have greatly improved performance for noncovalent interactions as compared to previous DFT methods. We interpret this as being due to an improved treatment of medium-range correlation effects by the exchange-correlation functional. We recommend the PWB6K and M05-2X methods for investigating large biological systems and soft materials.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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12
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Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Catalán J. On dimers and complexes of tetracene and the Kasha's molecular excitonic model. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Javier Catalán
- Departamento de Quimica Fisica Aplicada; Universidad Autónoma de Madrid; 28049 Madrid Spain
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14
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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15
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Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Chang-Sheng Wang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
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16
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Diez-García F, Pantoja-Uceda D, Jiménez MÁ, Chakrabartty A, Laurents DV. Structure of a simplified β-hairpin and its ATP complex. Arch Biochem Biophys 2013; 537:62-71. [PMID: 23811197 DOI: 10.1016/j.abb.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/13/2013] [Accepted: 06/16/2013] [Indexed: 11/29/2022]
Abstract
The capacity of three designed duodecamer peptides with the low diversity sequence: H1ϕ2I3K4I5D6G7K8ϕ9I10K11H12 where ϕ is His, Phe or Trp, to adopt a β-hairpin conformation was studied using NMR spectroscopy. Whereas KIAβH, the variant with His at positions two and nine, is disordered, KIAβF, the peptide with Phe at these positions, adopts a small population of β-hairpin. A high population of β-hairpin structure was detected for KIAβW, the variant with Trp. Utilizing NMR data, the structure of KIAβW was solved and it reveals a β-hairpin stabilized by hydrophobic interactions between Ile residues on one face and Trp-Trp and cation-π interactions on the opposite face. Upon adding ATP, these peptides show chemical shift changes indicative of ATP binding. The binding of ATP to KIAβW shows a KD ≈ 20 μM at pH 5, 5 °C and has a 1:1 stoichiometry. The KIAβW-ATP complex was determined using NMR spectroscopy and reveals the adenine ring sandwiched between the two Trp indole rings and that ATP binding induces important conformational changes in His1, Trp2, Lys4, Trp9 and Lys11 in the β-hairpin. The implications of these results for the hypothetic presence of β-hairpins and amyloids alongside RNAs on the prebiotic Earth are discussed.
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17
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Kim SH, Parquette JR. A model for the controlled assembly of semiconductor peptides. NANOSCALE 2012; 4:6940-6947. [PMID: 23034819 DOI: 10.1039/c2nr32140h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The self-assembly of small molecules provides a potentially powerful method to create functional nanomaterials for many applications ranging from optoelectronics to oncology. However, the design of well-defined nanostructures via molecular assembly is a highly empirical process, which severely hampers efforts to create functional nanostructures using this method. In this review, we describe a simple strategy to control the assembly of functionalized peptides by balancing attractive hydrophobic effects that drive assembly with opposing electrostatic repulsions. Extended π-π contacts are created in the nanostructures when assembly is driven by π-stacking interactions among chromophores that are appended to the peptide. The formation of insoluble β-sheet aggregates are mitigated by incorporating charged side-chains capable of attenuating the assembly process. Although the application of this approach to the assembly of organic semiconductors is described, we expect this strategy to be effective for many other functional organic materials.
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Affiliation(s)
- Se Hye Kim
- Department of Chemistry, The Ohio State University, 100 W. 18th Ave, Columbus, Ohio 43210, USA
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18
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Yin H. Constrained peptides as miniature protein structures. ISRN BIOCHEMISTRY 2012; 2012:692190. [PMID: 25969758 PMCID: PMC4392992 DOI: 10.5402/2012/692190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022]
Abstract
This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, 596 University of Colorado at Boulder, Boulder, CO 80309-0596, USA
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19
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Jiang P, Hansmann UHE. Modeling Structural Flexibility of Proteins with Go-Models. J Chem Theory Comput 2012; 8:2127-2133. [PMID: 24039551 DOI: 10.1021/ct3000469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based models are an efficient tool for folding studies of proteins since by construction their energy landscape is only minimal frustrated. However, their intrinsic drawback is a lack of structural flexibility as usually only one target structure is employed to construct the potentials. Hence, a Go-model may not capture differences in mutation-induced protein dynamics, if - as in the case of the disease-related A629P mutant of the Menkes protein ATP7A - the structural differences between mutant and wild type are small. In this work, we introduced three implementations of Go-models that take into account the flexibility of proteins in the NMR ensemble. Comparing the wild type and the mutant A629P of the 75-residue large 6th domain Menkes protein, we find that these new Go-potentials lead to broader distributions than Go-models relying on a single member of the NMR-ensemble. This allows us to detect the transient unfolding of a loosely formed β1β4-sheet in the mutant protein. Our results are consistent with previous simulations using physical force field and an explicit solvent, and suggests a mechanism by which these mutations cause Menkes disease. In addition, the improved Go-models suggest differences in the folding pathway between wild type and mutant, an observation that was not accessible to simulations of this 75-residue protein with a physical all-atom force field and explicit solvent.
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Affiliation(s)
- Ping Jiang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-5251, USA
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20
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Notash B, Safari N, Khavasi HR. Anion-controlled structural motif in one-dimensional coordination networks via cooperative weak noncovalent interactions. CrystEngComm 2012. [DOI: 10.1039/c2ce25554e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Celentano V, Diana D, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. β-Hairpin stabilization through an interstrand triazole bridge. Chem Commun (Camb) 2011; 48:762-4. [PMID: 22134485 DOI: 10.1039/c1cc16017f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
β-Hairpin peptides were conformationally stabilized through a 1,4 disubstituted 1,2,3-triazole interstrand linkage. A NMR conformational analysis revealed that the β-hairpin content depends on the number and position of substituent methylene units of the 1,2,3-triazole ring. These results will allow the design of metabolically stable peptidomimetic analogs of bioactive β-hairpin peptides.
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Affiliation(s)
- Veronica Celentano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
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22
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Kong F, King J. Contributions of aromatic pairs to the folding and stability of long-lived human γD-crystallin. Protein Sci 2011; 20:513-28. [PMID: 21432932 DOI: 10.1002/pro.583] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human γD-crystallin (HγD-Crys) is a highly stable protein that remains folded in the eye lens for the majority of an individual's lifetime. HγD-Crys exhibits two homologous crystallin domains, each containing two Greek key motifs with eight β-strands. Six aromatic pairs (four Tyr/Tyr, one Tyr/Phe and one Phe/Phe) are present in the β-hairpin sequences of the Greek keys. Ultraviolet damage to the aromatic residues in lens crystallins may contribute to the genesis of cataract. Mutant proteins with these aromatic residues substituted with alanines were constructed and expressed in E. coli. All mutant proteins except F115A and F117A had lower thermal stability than the WT protein. In equilibrium experiments in guanidine hydrochloride (GuHCl), all mutant proteins had lower thermodynamic stability than the WT protein. N-terminal domain (N-td) substitutions shifted the N-td transition to lower GuHCl concentration, but the C-terminal domain (C-td) transition remained unaffected. C-td substitutions led to a more cooperative unfolding/refolding process, with both the N-td and C-td transitions shifted to lower GuHCl concentration. The aromatic pairs conserved for each Greek key motif (Greek key pairs) had larger contributions to both thermal stability and thermodynamic stability than the other pairs. Aromatic-aromatic interaction was estimated as 1.5-2.0 kcal/mol. In kinetic experiments, N-td substitutions accelerated the early phase of unfolding, while C-td substitutions accelerated the late phase, suggesting independent domain unfolding. Only substitutions of the second Greek key pair of each crystallin domain slowed refolding. The second Greek keys may provide nucleation sites during the folding of the double-Greek-key crystallin domains.
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Affiliation(s)
- Fanrong Kong
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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Biswal HS, Gloaguen E, Mons M, Bhattacharyya S, Shirhatti PR, Wategaonkar S. Structure of the Indole−Benzene Dimer Revisited. J Phys Chem A 2011; 115:9485-92. [DOI: 10.1021/jp1119684] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Himansu S. Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
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24
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Stewart AL, Park JH, Waters ML. Redesign of a WW domain peptide for selective recognition of single-stranded DNA. Biochemistry 2011; 50:2575-84. [PMID: 21332166 DOI: 10.1021/bi101116a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A β-sheet miniprotein based on the FBP11 WW1 domain sequence has been redesigned for the molecular recognition of ssDNA. A previous report showed that a β-hairpin peptide dimer, (WKWK)(2), binds ssDNA with low micromolar affinity but with little selectivity over duplex DNA. This report extends those studies to a three-stranded β-sheet miniprotein designed to mimic the OB-fold. The new peptide binds ssDNA with low micromolar affinity and shows about 10-fold selectivity for ssDNA over duplex DNA. The redesigned peptide no longer binds its native ligand, the polyproline helix, confirming that the peptide has been redesigned for the function of binding ssDNA. Structural studies provide evidence that this peptide consists of a well-structured β-hairpin made of strands 2 and 3 with a less structured first strand that provides affinity for ssDNA but does not improve the stability of the full peptide. These studies provide insight into protein-DNA interactions as well as a novel example of protein redesign.
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Affiliation(s)
- Amanda L Stewart
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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25
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Zhang C. Shape and size effects in π-π interactions: Face-to-face dimers. J Comput Chem 2010; 32:152-60. [DOI: 10.1002/jcc.21612] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Foster ME, Sohlberg K. A New Empirical Correction to the AM1 Method for Macromolecular Complexes. J Chem Theory Comput 2010; 6:2153-66. [DOI: 10.1021/ct100177u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Michael E. Foster
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Karl Sohlberg
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
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27
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Hamley IW, Nutt DR, Brown GD, Miravet JF, Escuder B, Rodríguez-Llansola F. Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation. J Phys Chem B 2010; 114:940-51. [PMID: 20039666 DOI: 10.1021/jp906107p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide Abeta16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations. The solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures were used to simulate circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally (in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.
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Affiliation(s)
- I W Hamley
- Department of Chemistry, University of Reading, Reading RG6 6AD, UK
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28
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Shao H, Nguyen T, Romano NC, Modarelli DA, Parquette JR. Self-Assembly of 1-D n-Type Nanostructures Based on Naphthalene Diimide-Appended Dipeptides. J Am Chem Soc 2009; 131:16374-6. [DOI: 10.1021/ja906377q] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Shao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Tuan Nguyen
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Natalie C. Romano
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - David A. Modarelli
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
| | - Jon R. Parquette
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, and Department of Chemistry and The Center for Laser and Optical Spectroscopy, Knight Chemical Laboratory, The University of Akron, Akron, Ohio 44325-3601
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29
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Mirassou Y, Santiveri CM, Pérez de Vega MJ, González-Muñiz R, Jiménez MA. Disulfide Bonds versus Trp⋅⋅⋅Trp Pairs in Irregular β-Hairpins: NMR Structure of Vammin Loop 3-Derived Peptides as a Case Study. Chembiochem 2009; 10:902-10. [DOI: 10.1002/cbic.200800834] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Jager M, Deechongkit S, Koepf EK, Nguyen H, Gao J, Powers ET, Gruebele M, Kelly JW. Understanding the mechanism of beta-sheet folding from a chemical and biological perspective. Biopolymers 2009; 90:751-8. [PMID: 18844292 DOI: 10.1002/bip.21101] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Perturbing the structure of the Pin1 WW domain, a 34-residue protein comprised of three beta-strands and two intervening loops has provided significant insight into the structural and energetic basis of beta-sheet folding. We will review our current perspective on how structure acquisition is influenced by the sequence, which determines local conformational propensities and mediates the hydrophobic effect, hydrogen bonding, and analogous intramolecular interactions. We have utilized both traditional site-directed mutagenesis and backbone mutagenesis approaches to alter the primary structure of this beta-sheet protein. Traditional site-directed mutagenesis experiments are excellent for altering side-chain structure, whereas amide-to-ester backbone mutagenesis experiments modify backbone-backbone hydrogen bonding capacity. The transition state structure associated with the folding of the Pin1 WW domain features a partially H-bonded, near-native reverse turn secondary structure in loop 1 that has little influence on thermodynamic stability. The thermodynamic stability of the Pin1 WW domain is largely determined by the formation of a small hydrophobic core and by the formation of desolvated backbone-backbone H-bonds enveloped by this hydrophobic core. Loop 1 engineering to the consensus five-residue beta-bulge-turn found in most WW domains or a four-residue beta-turn found in most beta-hairpins accelerates folding substantially relative to the six-residue turn found in the wild type Pin1 WW domain. Furthermore, the more efficient five- and four-residue reverse turns now contribute to the stability of the three-stranded beta-sheet. These insights have allowed the design of Pin1 WW domains that fold at rates that approach the theoretical speed limit of folding.
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Affiliation(s)
- Marcus Jager
- Department of Chemistry, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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31
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Xu Y, Bunagan MR, Tang J, Gai F. Probing the Kinetic Cooperativity of β-Sheet Folding Perpendicular to the Strand Direction. Biochemistry 2008; 47:2064-70. [DOI: 10.1021/bi702195c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yao Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michelle R. Bunagan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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32
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Santiveri C, León E, Rico M, Jiménez M. Context-Dependence of the Contribution of Disulfide Bonds to β-Hairpin Stability. Chemistry 2008; 14:488-99. [DOI: 10.1002/chem.200700845] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Emerging trends in molecular recognition: Utility of weak aromatic interactions. Bioorg Med Chem 2008; 16:126-43. [DOI: 10.1016/j.bmc.2007.09.023] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 09/03/2007] [Accepted: 09/12/2007] [Indexed: 11/21/2022]
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34
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Araki M, Tamura A. Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state. Proteins 2007; 66:860-8. [PMID: 17177204 DOI: 10.1002/prot.21263] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Intrinsic rules of determining the tertiary structure of a protein have been unknown partly because physicochemical factors that contribute to stabilization of a protein structure cannot be represented as a linear combination of local interactions. To clarify the rules on the nonlinear term caused by nonlocal interaction in a protein, we tried to transform a peptide that has a fully helical structure (Target Peptide or TP) into a peptide that has a beta-hairpin structure (Designed Peptide or DP) by adding seven residues to the C terminus of TP. According to analyses of nuclear magnetic resonance measurements, while the beta-hairpin structure is stabilized in some DPs, it is evident that the helical structure observed in TP is also persistent and even extended throughout the length of the molecule. As a result, we have produced a peptide molecule that contains both the alpha-helix and beta-hairpin conformation at an almost equally populated level. The helical structures contained in these DPs were more stable than the helix in TP, suggesting that stabilizing one conformation does not result in destabilizing the other conformation. These DPs can thus be regarded as an isolated peptide version of the chameleon sequence, which has the capability of changing the secondary structure depending on the context of the surrounding environment in a protein structure. The fact that the transformation of one secondary structure caused stabilization of both the original and the induced structure would shed light on the mechanism of protein folding.
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Affiliation(s)
- Mitsugu Araki
- Graduate School of Science and Technology, Kobe University, Nada, Kobe 657-8501, Japan
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35
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Shao H, Lockman JW, Parquette JR. Coupled Conformational Equilibria in β-Sheet Peptide−Dendron Conjugates. J Am Chem Soc 2007; 129:1884-5. [PMID: 17256863 DOI: 10.1021/ja068154n] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Shao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue Columbus, Ohio 43210, USA
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36
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Metselaar GA, Adams PJHM, Nolte RJM, Cornelissen JJLM, Rowan AE. Polyisocyanides Derived from Tripeptides of Alanine. Chemistry 2007; 13:950-60. [PMID: 17048287 DOI: 10.1002/chem.200600928] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Helical polymers of isocyanotripeptides derived from alanine have been synthesized and their architectures studied in detail. The helical conformation of the polyisocyanotripeptides is stabilized by internal hydrogen-bonding arrays between the tripeptide side chains. The possibility of extending the well-defined hydrogen-bonded array, from dipeptide to tripeptide side chains, depends strongly on the stereochemistry of the constituent alanine amino acids, as has been shown by circular dichroism and IR studies. In polymers containing a weaker hydrogen-bonding array adjacent to the polymer backbone, due to steric interactions between the alanine methyl groups, a stronger second hydrogen-bonding array was present between the peptide bonds furthest away from the main chain, which is probably a result of stretching/compression of the helical-polymer conformation.
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Affiliation(s)
- Gerald A Metselaar
- Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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37
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Hudson FM, Andersen NH. Measuring cooperativity in the formation of a three-stranded beta sheet (double hairpin). Biopolymers 2006; 83:424-33. [PMID: 16850496 DOI: 10.1002/bip.20575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently validated chemical shift measures of hairpin structuring have been applied to a series of turn mutants of the Schenck-Gellman three-strand beta-sheet model with the aim of measuring the entropic advantage associated with aligning an additional strand onto an existing hairpin versus aligning the same two strands in an initial hairpin formation. In a four-state analysis (unfolded, 2 single hairpins, and the double hairpin fold in equilibrium) a cooperativity index can be defined as the factor by which the equilibrium constant for hairpin formation is improved when one strand is prestructured. This cooperativity index is 2.7 +/- 0.7 for hairpin formation about a stable D-Pro-Gly turn locus and increases to 7.6 +/- 1.2 for an Asn-Gly turn locus. The latter corresponds to a cooperativity induced DeltaDeltaG increment of 4.9 kJ/mol for the folding of a hairpin. Although larger than previous experimental measures of folding cooperativity in three-stranded sheets, the magnitude of this effect (which is considerably less than the TDeltaDeltaS expectation for prestructuring three or more beta-strand residue sites) likely reflects the intrinsic preference of these designed sequences for extended conformations. If similar or larger effects apply to protein beta-sheet folding, it is not surprising that particularly favorable hairpin alignments serve as nucleation sites in protein folding pathways.
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Affiliation(s)
- F Michael Hudson
- Department of Chemistry, University of Washington, Seattle, 98195 USA
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38
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Wang WL, Xu J, Sun Z, Zhang X, Lu Y, Lai YH. Effect of Transannular π−π Interaction on Emission Spectral Shift and Fluorescence Quenching in Dithia[3.3]paracyclophane−Fluorene Copolymers. Macromolecules 2006. [DOI: 10.1021/ma060510z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei-Ling Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
| | - Jianwei Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
| | - Zhe Sun
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
| | - Xinhai Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
| | - Yong Lu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
| | - Yee-Hing Lai
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, and Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602
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39
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Fernández-Escamilla AM, Ventura S, Serrano L, Jiménez MA. Design and NMR conformational study of a beta-sheet peptide based on Betanova and WW domains. Protein Sci 2006; 15:2278-89. [PMID: 16963647 PMCID: PMC2242380 DOI: 10.1110/ps.062186506] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A good approach to test our current knowledge on formation of protein beta-sheets is de novo protein design. To obtain a three-stranded beta-sheet mini-protein, we have built a series of chimeric peptides by taking as a template a previously designed beta-sheet peptide, Betanova-LLM, and incorporating N- and/or C-terminal extensions taken from WW domains, the smallest natural beta-sheet domain that is stable in absence of disulfide bridges. Some Betanova-LLM strand residues were also substituted by those of a prototype WW domain. The designed peptides were cloned and expressed in Escherichia coli. The ability of the purified peptides to adopt beta-sheet structures was examined by circular dichroism (CD). Then, the peptide showing the highest beta-sheet population according to the CD spectra, named 3SBWW-2, was further investigated by 1H and 13C NMR. Based on NOE and chemical shift data, peptide 3SBWW-2 adopts a well defined three-stranded antiparallel beta-sheet structure with a disordered C-terminal tail. To discern between the contributions to beta-sheet stability of strand residues and the C-terminal extension, the structural behavior of a control peptide with the same strand residues as 3SBWW-2 but lacking the C-terminal extension, named Betanova-LYYL, was also investigated. beta-Sheet stability in these two peptides, in the parent Betanova-LLM and in WW-P, a prototype WW domain, decreased in the order WW-P > 3SBWW-2 > Betanova-LYYL > Betanova-LLM. Conclusions about the contributions to beta-sheet stability were drawn by comparing structural properties of these four peptides.
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40
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Mayewski S. A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing. Proteins 2006; 59:152-69. [PMID: 15723360 DOI: 10.1002/prot.20397] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new multibody, whole-residue potential for protein tertiary structure is described. The potential is based on the local environment surrounding each main-chain alpha carbon (CA), defined as the set of all residues whose CA coordinates lie within a spherical volume of set radius in 3-dimensional (3D) space surrounding that position. It is shown that the relative positions of the CAs in these local environments belong to a set of preferred templates. The templates are derived by cluster analysis of the presently available database of over 3000 protein chains (750,000 residues) having not more than 30% sequence similarity. For each template is derived also a set of residue propensities for each topological position in the template. Using lookup tables of these derived templates, it is then possible to calculate an energy for any conformation of a given protein sequence. The application of the potential to ab initio protein tertiary structure prediction is evaluated by performing Monte Carlo simulated annealing on test protein sequences.
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Affiliation(s)
- Stefan Mayewski
- Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.
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41
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Simpson ER, Meldrum JK, Searle MS. Engineering Diverse Changes in β-Turn Propensities in the N-Terminal β-Hairpin of Ubiquitin Reveals Significant Effects on Stability and Kinetics but a Robust Folding Transition State. Biochemistry 2006; 45:4220-30. [PMID: 16566596 DOI: 10.1021/bi052495g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the N-terminal 17-residue beta-hairpin of ubiquitin as a "host" for mutational studies, we have investigated the influence of the beta-turn sequence on protein stability and folding kinetics by replacing the native G-bulged turn (TLTGK) with more flexible analogues (TG3K and TG5K) and a series of four-residue type I' beta-turn sequences, commonly found in beta-hairpins. Although a statistical analysis of type I' turns demonstrates residue preferences at specific sites, the frequency of occurrence appears to only broadly correlate with experimentally determined protein stabilities. The subsequent engineering of context-dependent non-native tertiary contacts involving turn residues is shown to produce large changes in stability. Relatively few point mutations have been described that probe secondary structure formation in ubiquitin in a manner that is independent of tertiary contacts. To this end, we have used the more rigorous rate-equilibrium free energy relationship (Leffler analysis), rather than the two-point phi value analysis, to show for a family of engineered beta-turn mutants that stability (range of approximately 20 kJ/mol) and folding kinetics (190-fold variation in refolding rate) are linearly correlated (alpha(f) = 0.74 +/- 0.08). The data are consistent with a transition state that is robust with regard to a wide range of statistically favored and disfavored beta-turn mutations and implicate a loosely assembled beta-hairpin as a key template in transition state stabilization with the beta-turn playing a central role.
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Affiliation(s)
- Emma R Simpson
- Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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42
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Camara-Campos A, Hunter CA, Tomas S. Cooperativity in the self-assembly of porphyrin ladders. Proc Natl Acad Sci U S A 2006; 103:3034-8. [PMID: 16492786 PMCID: PMC1413879 DOI: 10.1073/pnas.0508071103] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cooperativity is a general feature of intermolecular interactions in biomolecular systems, but there are many different facets of the phenomenon that are not well understood. Positive cooperativity stabilizes a system as progressively more interactions are added, and the origin of the beneficial free energy may be entropic or enthalpic in origin. An "enthalpic chelate effect" has been proposed to operate through structural tightening that improves all of the functional group interactions in a complex, when it is more strongly bound. Here, we present direct calorimetric evidence that no such enthalpic effects exist in the cooperative assembly of supramolecular ladder complexes composed of metalloporphyrin oligomers coordinated to bipyridine ligands. The enthalpic contributions of the individual coordination interactions are 35 kJ.mol(-1) and constant over a range of free energies of self-assembly of -35 to -111 kJ.mol(-1). In rigid well defined systems of this type, the enthalpies of individual interactions are additive, and no enthalpic cooperative effects are apparent. The implication is that in more flexible, less well defined systems such as biomolecular assemblies, the enthalpy contributions available from specific functional group interactions are well defined and constant parameters.
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Affiliation(s)
- Amaya Camara-Campos
- Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Christopher A. Hunter
- Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
- *To whom correspondence may be addressed. E-mail:
or
| | - Salvador Tomas
- Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
- *To whom correspondence may be addressed. E-mail:
or
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Fesinmeyer RM, Hudson FM, Olsen KA, White GWN, Euser A, Andersen NH. Chemical shifts provide fold populations and register of beta hairpins and beta sheets. JOURNAL OF BIOMOLECULAR NMR 2005; 33:213-31. [PMID: 16341751 DOI: 10.1007/s10858-005-3731-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 09/29/2005] [Indexed: 05/05/2023]
Abstract
A detailed analysis of peptide backbone amide (H(N)) and H alpha chemical shifts reveals a consistent pattern for beta hairpins and three-stranded beta sheets. The H alpha's at non-hydrogen-bonded strand positions are inwardly directed and shifted downfield approximately 1 ppm due largely to an anisotropy contribution from the cross-strand amide function. The secondary structure associated H alpha shift deviations for the H-bonded strand positions are also positive but much smaller (0.1-0.3 ppm) and the turn residues display negative H alpha chemical shift deviations (CSDs). The pattern of (H(N)) shift deviations is an even better indicator of both hairpin formation and register, with the cross-strand H-bonded sites shifted downfield (also by approximately 1 ppm) and with diagnostic values for the first turn residue and the first strand position following the turn. These empirical observations, initially made for [2:2]/[2:4]-type-I' and -II' hairpins, are rationalized and can be extended to the analysis of other turns, hairpin classes ([3:5], [4:4]/[4:6]), and three-stranded peptide beta-sheet models. The H alpha's at non-hydrogen-bonded sites and (H(N))'s in the intervening H-bonded sites provide the largest and most dependable measures of hairpin structuring and can be used for melting studies; however the intrinsic temperature dependence of (H(N)) shifts deviations needs to reflect the extent of solvent sequestration in the folded state. Several observations made in the course of this study provide insights into beta-sheet folding mechanisms: (1) The magnitude of the (H(N)) shifts suggests that the cross-strand H-bonds in peptide hairpins are as short as those in protein beta sheets. (2) Even L-Pro-Gly turns, which are frequently used in unfolded controls for hairpin peptides, can support hairpin populations in aqueous fluoroalcohol media. (3) The good correlation between hairpin population estimates from cross-strand H-bonded (H(N)) shift deviations, H alpha shift deviations, and structuring shifts at the turn locus implies that hairpin folding transitions approximate two-state behavior.
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Roe DR, Hornak V, Simmerling C. Folding cooperativity in a three-stranded beta-sheet model. J Mol Biol 2005; 352:370-81. [PMID: 16095612 PMCID: PMC4805115 DOI: 10.1016/j.jmb.2005.07.036] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 07/08/2005] [Accepted: 07/13/2005] [Indexed: 12/22/2022]
Abstract
The thermodynamic behavior of a previously designed three-stranded beta-sheet was studied via several microseconds of standard and replica exchange molecular dynamics simulations. The system is shown to populate at least four thermodynamic minima, including two partially folded states in which only a single hairpin is formed. Simulated melting curves show different profiles for the C and N-terminal hairpins, consistent with differences in secondary structure content in published NMR and CD/FTIR measurements, which probed different regions of the chain. Individual beta-hairpins that comprise the three-stranded beta-sheet are observed to form cooperatively. Partial folding cooperativity between the component hairpins is observed, and good agreement between calculated and experimental values quantifying this cooperativity is obtained when similar analysis techniques are used. However, the structural detail in the ensemble of conformations sampled in the simulations permits a more direct analysis of this cooperativity than has been performed on the basis of experimental data. The results indicate the actual folding cooperativity perpendicular to strand direction is significantly larger than the lower bound obtained previously.
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Affiliation(s)
- Daniel R Roe
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
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Vaz de Andrade E, Freitas SM, Ventura MM, Maranhão AQ, Brigido MM. Thermodynamic basis for antibody binding to Z-DNA: comparison of a monoclonal antibody and its recombinant derivatives. Biochim Biophys Acta Gen Subj 2005; 1726:293-301. [PMID: 16214293 DOI: 10.1016/j.bbagen.2005.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 08/24/2005] [Accepted: 08/31/2005] [Indexed: 10/25/2022]
Abstract
Antibody engineering represents a promising area in biotechnology. Recombinant antibodies can be easily manipulated generating new ligand and effector activities that can be used as prototype magic bullets. On the other hand, an extensive knowledge of recombinant antibody binding and stability features are essential for an efficient substitution. In this study, we compared the stability and protein binding properties of two recombinant antibody fragments with their parental monoclonal antibody. The recombinant fragments were a monomeric scFv and a dimeric one, harboring human IgG1 CH2-CH3 domains. We have used fluorescence titration quenching to determine the thermodynamics of the interaction between an anti-Z-DNA monoclonal antibody and its recombinant antibody fragments with Z-DNA. All the antibody fragments seemed to bind DNA similarly, in peculiar two-affinity states. Enthalpy-entropy compensation was observed for both affinity states, but a marked entropy difference was observed for the monomeric scFv antibody fragment, mainly for the high affinity binding. In addition, we compared the stability of the dimeric antibody fragment and found differences favoring the monoclonal antibody. These differences seem to derive from the heterologous expression system used.
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Dyer RB, Maness SJ, Franzen S, Fesinmeyer RM, Olsen KA, Andersen NH. Hairpin Folding Dynamics: The Cold-Denatured State Is Predisposed for Rapid Refolding. Biochemistry 2005; 44:10406-15. [PMID: 16042418 DOI: 10.1021/bi050698z] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cold denaturation is a general phenomenon in globular proteins, and the associated cold-denatured states of proteins have important fundamental and practical significance. Here, we have characterized the cold-denatured state of a beta-hairpin forming peptide, MrH3a, in 8% hexafluoro-2-propanol (HFIP) and the dynamics of its refolding following a laser-induced T-jump. Beta-hairpins constitute an important class of protein structural elements, yet their folding mechanisms are not fully understood. Characterization of MrH3a using NMR, CD, and IR spectroscopies reveals residual structure in the cold-denatured state, in contrast with the highly disordered heat-denatured state. The residual structure in the cold-denatured state comprises relatively compact and solvent protected conformations. Furthermore, we find a substantial acceleration in the rate of folding from the cold-denatured state compared to that of the heat-denatured state. In addition, the cold-denatured state is not populated in 20% HFIP; folding occurs only from the fully unfolded state and is significantly slower. We interpret the acceleration of the folding rate of MrH3a in 8% HFIP as a direct consequence of the collapsed conformations of the cold-denatured state. Finally, there may be some reduction of the loop search cost when starting from the cold-denatured state, since this state may have some of the stabilizing cross-strand interactions already formed.
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Affiliation(s)
- R Brian Dyer
- Bioscience Division, Mail Stop J586, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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Zhao Y, Truhlar DG. Multicoefficient Extrapolated Density Functional Theory Studies of π···π Interactions: The Benzene Dimer. J Phys Chem A 2005; 109:4209-12. [PMID: 16833747 DOI: 10.1021/jp050932v] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report tests of new (2005) and established (1999-2003) multilevel methods against essentially converged benchmark results for nonbonded interactions in benzene dimers. We found that the newly developed multicoefficient extrapolated density functional theory (DFT) methods (which combine DFT with correlated wave function methods) give better performance than multilevel methods such as G3SX, G3SX(MP3), and CBS-QB3 that are based purely on wave function theory (WFT); furthermore, they have a lower computational cost. We conclude that our empirical approach for combining WFT methods with DFT methods is a very efficient and effective way for describing not only covalent interactions (as shown previously) but also nonbonded interactions.
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48
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Westerlund K, Berry BW, Privett HK, Tommos C. Exploring amino-acid radical chemistry: protein engineering and de novo design. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:103-16. [PMID: 15721609 DOI: 10.1016/j.bbabio.2004.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 02/26/2004] [Indexed: 11/21/2022]
Abstract
Amino-acid radical enzymes are often highly complex structures containing multiple protein subunits and cofactors. These properties have in many cases hampered the detailed characterization of their amino-acid redox cofactors. To address this problem, a range of approaches has recently been developed in which a common strategy is to reduce the complexity of the radical-containing system. This work will be reviewed and it includes the light-induced generation of aromatic radicals in small-molecule and peptide systems. Natural redox proteins, including the blue copper protein azurin and a bacterial photosynthetic reaction center, have been engineered to introduce amino-acid radical chemistry. The redesign strategies to achieve this remarkable change in the properties of these proteins will be described. An additional approach to gain insights into the properties of amino-acid radicals is to synthesize de novo designed model proteins in which the redox chemistry of these species can be studied. Here we describe the design, synthesis and characteristics of monomeric three-helix bundle and four-helix bundle proteins designed to study the redox chemistry of tryptophan and tyrosine. This work demonstrates that de novo protein design combined with structural, electrochemical and quantum chemical analyses can provide detailed information on how the protein matrix tunes the thermodynamic properties of tryptophan.
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Affiliation(s)
- Kristina Westerlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Abstract
Beside alpha-helices, beta-sheets are the most common secondary structure elements of proteins. In this article, the question of structure and stability of parallel and antiparallel sheets of various lengths is addressed. All data obtained are compared to a selected set of protein structures. In antiparallel beta-sheets, one of the two possible H-bonded structures (containing 14 atoms in the H-bonded pseudoring) is energetically more favored and also more abundant in proteins than the other one (with 10 atoms involved in the pseudoring). Parallel beta-sheets and their subunits are energetically less stable and indeed found to occur more rarely in proteins. Antiparallel hairpins are disfavored compared to beta-sheets formed by sequentially separated strands. Agreement between theory and experimental data indicates that characterization of structural building blocks at an appropriately accurate level of theory is a useful tool to get insight into fundamentals of protein structure.
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Affiliation(s)
- András Perczel
- Department of Organic Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary.
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50
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Zhao Y, Truhlar DG. How well can new-generation density functional methods describe stacking interactions in biological systems? Phys Chem Chem Phys 2005; 7:2701-5. [PMID: 16189582 DOI: 10.1039/b507036h] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
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