1
|
Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates. Angew Chem Int Ed Engl 2023; 62:e202303943. [PMID: 37170337 PMCID: PMC10592574 DOI: 10.1002/anie.202303943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.
Collapse
Affiliation(s)
- Alex Nazzaro
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Brandon Lu
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | | | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| |
Collapse
|
2
|
Moharana TR, Nagaraj R. In silico folding of hydrophobic peptides that form β-hairpin structures in solution. J Pept Sci 2022; 28:e3427. [PMID: 35595709 DOI: 10.1002/psc.3427] [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: 01/19/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Peptides designed with residues that have a high propensity to occur in β-turns form β-hairpin structures in apolar as well as in polar organic solvents such as dimethyl sulfoxide (DMSO). Due to limited solubility, their conformations have not been investigated experimentally in water. We have examined the conformations of four of such designed peptides that fold into well-defined β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by molecular dynamics simulations (MDS). The peptides folded into β-hairpin structures in water, starting from the fully extended conformation. However, in DMSO, neither folding nor unfolding was observed during MDS, when the starting structures were unfolded and folded, respectively. The lack of folding in DMSO was investigated by constructing folding free energy landscapes by umbrella sampling. The folding free energy landscape is smooth in water while in DMSO folded and unfolded structures are separated by high-energy barriers. The folding free energy is less in DMSO compared to water due to a more stable unfolded structure in DMSO compared to water, which in turn is due to stabilization of the unfolded state by hydrophobic interactions in DMSO. This finding will be helpful to researchers to accurately model and/or design small peptide structures in water and organic solvents.
Collapse
|
3
|
Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
Collapse
Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
4
|
Abstract
RNA structures play a pivotal role in many biological processes and the progression of human disease, making them an attractive target for therapeutic development. Often RNA structures operate through the formation of complexes with RNA-binding proteins, however, much like protein-protein interactions, RNA-protein interactions span large surface areas and often lack traditional druggable properties, making it challenging to target them with small molecules. Peptides provide much greater surface areas and therefore greater potential for forming specific and high affinity interactions with RNA. In this chapter, we discuss our approach for engineering peptides that bind to structured RNAs by highlighting methods and design strategies from previous successful projects aimed at inhibiting the HIV Tat-TAR interaction and the biogenesis of oncogenic microRNAs.
Collapse
Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, United States.
| |
Collapse
|
5
|
Lin CY, Cheng YS, Liao TY, Lin C, Chen ZT, Twu WI, Chang CW, Tan DTW, Liu RS, Tu PH, Chen RPY. Intranasal Administration of a Polyethylenimine-Conjugated Scavenger Peptide Reduces Amyloid-β Accumulation in a Mouse Model of Alzheimer's Disease. J Alzheimers Dis 2018; 53:1053-67. [PMID: 27340844 DOI: 10.3233/jad-151024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Amyloid-β (Aβ) aggregation in the brain plays a central and initiatory role in pathogenesis and/or progression of Alzheimer's disease (AD). Inhibiting Aβ aggregation is a potential strategy in the prevention of AD. A scavenger peptide, V24P(10-40), designed to decrease Aβ accumulation in the brain, was conjugated to polyethylenimine (PEI) and tested as a preventive/therapeutic strategy for AD in this study. This PEI-conjugated V24P(10-40) peptide was delivered intranasally, as nasal drops, to four-month-old APP/PS1 double transgenic mice for four or eight months. Compared with control values, peptide treatment for four months significantly reduced the amount of GdnHCl-extracted Aβ40 and Aβ42 in the mice's hippocampus and cortex. After treatment for eight months, amyloid load, as quantified by Pittsburgh compound B microPET imaging, was significantly decreased in the mice's hippocampus, cortex, amygdala, and olfactory bulb. Our data suggest that this intranasally delivered scavenger peptide is effective in decreasing Aβ accumulation in the brain of AD transgenic mice. Nasal application of peptide drops is easy to use and could be further developed to prevent and treat AD.
Collapse
Affiliation(s)
- Chih-Yun Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yu-Sung Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tai-Yan Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Zih-Ten Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Woan-Ing Twu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Wei Chang
- Biomedical Imaging Research Center, Department of Nuclear Medicine, National Yang Ming University and Taipei Veterans General Hospital, Taipei, Taiwan
| | - David Tat-Wei Tan
- Biomedical Imaging Research Center, Department of Nuclear Medicine, National Yang Ming University and Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ren-Shyan Liu
- Biomedical Imaging Research Center, Department of Nuclear Medicine, National Yang Ming University and Taipei Veterans General Hospital, Taipei, Taiwan.,Molecular and Genetic Imaging Core, Taiwan Mouse Clinic, Academia Sinica, Taipei, Taiwan
| | - Pang-Hsien Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
6
|
Ingole TS, Vijayadas KN, Chaitanya KN, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Disruption of Native β-Turns: Consequence of Folding Competition between Native and Orthanilic Acid Proline-BasedPseudoβ-Turn. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
7
|
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.
Collapse
Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
| |
Collapse
|
8
|
Tsai M, Yuan J, Yamaki M, Lin C, Lin SH. Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta‐Hairpin Peptide. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Min‐Yeh Tsai
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617, ROC
| | - Jian‐Min Yuan
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Masahiro Yamaki
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
| | - Chih‐Kai Lin
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
| | - Sheng Hsien Lin
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
| |
Collapse
|
9
|
Chuang CC, Liao TY, Chen EHL, Chen RPY. How do amino acid substitutions affect the amyloidogenic properties and seeding efficiency of prion peptides. Amino Acids 2013; 45:785-96. [PMID: 23736988 PMCID: PMC3776267 DOI: 10.1007/s00726-013-1522-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 05/22/2013] [Indexed: 11/28/2022]
Abstract
The amino acid sequences in the amyloidogenic region (amino acids 108–144) of several mammalian prion proteins were compared and variations were found to occur at residues 109 (M or L), 112 (M or V), 129 (M, V, or L), 135 (N or S), 138 (M, L, or I), 139 (M or I), and 143 (N or S). Using the bovine PrP peptide (residues 108–144 based on the numbering of the human prion protein sequence) as a control peptide, several peptides with one amino acid differing from that of the bovine PrP peptide at residues 109, 112, 135, 138, 139, or 143 and several mammalian PrP peptides were synthesized, and the effects of these amino acid substitutions on the amyloidogenic properties of these peptides were compared and discussed on the basis of the chemical and structural properties of amino acids. Our results showed that the V112M substitution accelerated nucleation of amyloidogenesis, while the N143S and I139M substitutions retarded nucleation. These effects tended to cancel each other out when two substitutions with opposite effects were present on the same peptide. Moreover, acceleration or inhibition of nucleation was not necessarily correlated with effect on seeding efficiency. Using amyloid fibrils prepared from the bovine PrP peptide as seeds, the seeding efficiency for the monomer peptides with the M129L, S135N, N143S, or I139M substitution was decreased compared to that for bPrP peptide. Of all the mammalian peptides used in this study, the dog, mule deer, and pig PrP peptides had the lowest seeding efficiencies.
Collapse
Affiliation(s)
- Chi-Chen Chuang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 106, Taiwan, ROC
| | | | | | | |
Collapse
|
10
|
Chien CY, Liu TY, Kuo WH, Wang MJ, Tsai WB. Dopamine-assisted immobilization of hydroxyapatite nanoparticles and RGD peptides to improve the osteoconductivity of titanium. J Biomed Mater Res A 2012; 101:740-7. [DOI: 10.1002/jbm.a.34376] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/23/2012] [Accepted: 07/12/2012] [Indexed: 12/16/2022]
|
11
|
Tsai WB, Chen RPY, Wei KL, Tan SF, Lai JY. Modulation of RGD-Functionalized Polyelectrolyte Multilayer Membranes for Promoting Osteoblast Function. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2012; 21:377-94. [DOI: 10.1163/156856209x419095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Wei-Bor Tsai
- a Department of Chemical Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
| | - Rita Pei-Yeh Chen
- b Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuang-Ling Wei
- c Department of Chemical Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
| | - Su-Fang Tan
- d Department of Chemical Engineering, National Taiwan University, No. 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
| | - Juin-Yih Lai
- e R&D Center for Membrane Technology and Department of Chemical Engineering, Chung Yuan Christian University, Chungli, Taoyuan, Taiwan
| |
Collapse
|
12
|
Engin O, Sayar M. Adsorption, Folding, and Packing of an Amphiphilic Peptide at the Air/Water Interface. J Phys Chem B 2012; 116:2198-207. [DOI: 10.1021/jp206327y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ozge Engin
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
| | - Mehmet Sayar
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
| |
Collapse
|
13
|
Huang JJT, Larsen RW, Chan SI. The interplay of turn formation and hydrophobic interactions on the early kinetic events in protein folding. Chem Commun (Camb) 2012; 48:487-97. [DOI: 10.1039/c1cc13278d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
14
|
Wu L, McElheny D, Setnicka V, Hilario J, Keiderling TA. Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy. Proteins 2011; 80:44-60. [DOI: 10.1002/prot.23140] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/28/2011] [Accepted: 07/21/2011] [Indexed: 12/28/2022]
|
15
|
Shanmugam G, Phambu N, Polavarapu PL. Unusual structural transition of antimicrobial VP1 peptide. Biophys Chem 2011; 155:104-8. [DOI: 10.1016/j.bpc.2011.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/06/2011] [Accepted: 03/07/2011] [Indexed: 11/16/2022]
|
16
|
Effects of Turn Stability and Side-Chain Hydrophobicity on the Folding of β-Structures. J Mol Biol 2010; 402:595-609. [DOI: 10.1016/j.jmb.2010.08.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/10/2010] [Accepted: 08/19/2010] [Indexed: 11/24/2022]
|
17
|
Tsai WB, Chen RPY, Wei KL, Chen YR, Liao TY, Liu HL, Lai JY. Polyelectrolyte multilayer films functionalized with peptides for promoting osteoblast functions. Acta Biomater 2009; 5:3467-77. [PMID: 19497392 DOI: 10.1016/j.actbio.2009.05.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 05/24/2009] [Accepted: 05/26/2009] [Indexed: 01/20/2023]
Abstract
Layer-by-layer deposition of polyelectrolyte multilayer (PEM) thin films has recently been applied to biomaterial applications. This simple and versatile technique provides a wide variety of potential utilization by insertion of biomolecules such as cell adhesion peptides. In this work dual peptides containing RGD (a cell-binding domain) and LHRRVKI (a heparin-binding domain) were immobilized onto polystyrene by the PEM technique and the effects on osteoblast cell culture were investigated. These peptides were conjugated to the amino groups of poly(allylamine hydrochloride) and then adsorbed onto the top of a 10 layer poly(allylamine hydrochloride)/poly(acrylic acid) film assembled at either pH 2.0 or pH 6.5. Osteoblasts, isolated from neonatal rat calvariae, were then seeded and cultured on the peptide-conjugated surfaces. We found that the cells adhered and grew better on the RGD-conjugated PEM films. The osteoblasts exhibited a better differentiated phenotype on the pH 2.0 films than the pH 6.5 films with respect to calcium deposition. The incorporation of LHRRVKI did not support cell adhesion, growth and matrix mineral deposition. Our results showed that the efficacy of RGD conjugation on osteoblast behavior was affected by the base PEM film.
Collapse
|
18
|
Chang ESH, Liao TY, Lim TS, Fann W, Chen RPY. A new amyloid-like beta-aggregate with amyloid characteristics, except fibril morphology. J Mol Biol 2008; 385:1257-65. [PMID: 19041877 DOI: 10.1016/j.jmb.2008.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 11/06/2008] [Accepted: 11/10/2008] [Indexed: 11/26/2022]
Abstract
Amyloid plaques, formed from amyloid beta (Abeta) peptides (mainly Abeta40 or Abeta42), are one of the most important pathological characteristics of Alzheimer's disease. Here, a single D-form proline substitution in the 40-amino-acid Abeta40 peptide can totally change the aggregation behavior of this peptide. The residue immediately preceding each glycine in Abeta40 (S8, V24, I32, and V36) was individually replaced by D-form proline ((D)Pro). The resulting (D)P-G sequence (the (D)Pro residue and the following Gly residue) was designed as a "structural clip" to force the formation of a bend in the peptide, as this sequence has been reported to be a strong promoter of beta-hairpin formation. The mutant peptide with Val24-to-(D)Pro substitution, named V24P, formed a new amyloid-like beta-aggregate at high peptide concentration. The aggregate has most of the characteristics of amyloid fibrils, except fibril morphology. Moreover, the mutant peptide V24P, when mixed with Abeta40, can attenuate the cytotoxicity of Abeta40.
Collapse
Affiliation(s)
- Evan S-H Chang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec 2, Academia Road, Nankang, Taipei 115, Taiwan, ROC
| | | | | | | | | |
Collapse
|
19
|
Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding. J Mol Biol 2008; 381:1184-201. [PMID: 18616947 DOI: 10.1016/j.jmb.2008.06.046] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 06/16/2008] [Accepted: 06/17/2008] [Indexed: 11/21/2022]
Abstract
Position-specific denatured-state thermodynamics were determined for a database of human proteins by use of an ensemble-based model of protein structure. The results of modeling denatured protein in this manner reveal important sequence-dependent thermodynamic properties in the denatured ensembles as well as fundamental differences between the denatured and native ensembles in overall thermodynamic character. The generality and robustness of these results were validated by performing fold-recognition experiments, whereby sequences were matched with their respective folds based on amino acid propensities for the different energetic environments in the protein, as determined through cluster analysis. Correlation analysis between structure and energetic information revealed that sequence segments destined for beta-sheet in the final native fold are energetically more predisposed to a broader repertoire of states than are sequence segments destined for alpha-helix. These results suggest that within the subensemble of mostly unstructured states, the energy landscapes are dominated by states in which parts of helices adopt structure, whereas structure formation for sequences destined for beta-strand is far less probable. These results support a framework model of folding, which suggests that, in general, the denatured state has evolutionarily evolved to avoid low-energy conformations in sequences that ultimately adopt beta-strand. Instead, the denatured state evolved so that sequence segments that ultimately adopt alpha-helix and coil will have a high intrinsic structure formation capability, thus serving as potential nucleation sites.
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
Affiliation(s)
- Daniel R Roe
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | | |
Collapse
|
22
|
Santiveri CM, Pantoja-Uceda D, Rico M, Jiménez MA. β-Hairpin formation in aqueous solution and in the presence of trifluoroethanol: A1H and13C nuclear magnetic resonance conformational study of designed peptides. Biopolymers 2005; 79:150-62. [PMID: 16078190 DOI: 10.1002/bip.20345] [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: 11/07/2022]
Abstract
In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE.
Collapse
Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid, Spain
| | | | | | | |
Collapse
|
23
|
Kim J, Lee J, Brych SR, Logan TM, Blaber M. Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor. Protein Sci 2005; 14:351-9. [PMID: 15632285 PMCID: PMC2253408 DOI: 10.1110/ps.041094205] [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: 10/26/2022]
Abstract
The beta-turn is the most common type of nonrepetitive structure in globular proteins, comprising ~25% of all residues; however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF-1) is a member of the beta-trefoil superfold and contains a total of five beta-hairpin structures (antiparallel beta-sheets connected by a reverse turn). beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild-type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. The results indicate that the beta-turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.
Collapse
Affiliation(s)
- Jaewon Kim
- Kasha Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
| | | | | | | | | |
Collapse
|
24
|
Chen RPY, Huang JJT, Chen HL, Jan H, Velusamy M, Lee CT, Fann W, Larsen RW, Chan SI. Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale. Proc Natl Acad Sci U S A 2004; 101:7305-10. [PMID: 15123838 PMCID: PMC409914 DOI: 10.1073/pnas.0304922101] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whether turns play an active or passive role in protein folding remains a controversial issue at this juncture. Here we use a photolabile cage strategy in combination with laser-flash photolysis and photoacoustic calorimetry to study the effects of different turns on the kinetics of beta-hairpin refolding on a nanosecond time scale. This strategy opens up a temporal window to allow the observation of early kinetic events in the protein refolding process at ambient temperature and pH without interference from any denaturants. Our results provide direct evidence demonstrating that even a one-residue difference in the turn region can change the refolding kinetics of a peptide. This observation suggests an active role for turn formation in directing protein folding.
Collapse
Affiliation(s)
- Rita P-Y Chen
- Institutes of Chemistry and Atomic and Molecular Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Santiveri CM, Santoro J, Rico M, Jiménez MA. Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial. Protein Sci 2004; 13:1134-47. [PMID: 15044739 PMCID: PMC2280049 DOI: 10.1110/ps.03520704] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/15/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
We have recently reported on the design of a 20-residue peptide able to form a significant population of a three-stranded up-and-down antiparallel beta-sheet in aqueous solution. To improve our beta-sheet model in terms of the folded population, we have modified the sequences of the two 2-residue turns by introducing the segment DPro-Gly, a sequence shown to lead to more rigid type II' beta-turns. The analysis of several NMR parameters, NOE data, as well as Deltadelta(CalphaH), DeltadeltaC(beta), and Deltadelta(Cbeta) values, demonstrates that the new peptide forms a beta-sheet structure in aqueous solution more stable than the original one, whereas the substitution of the DPro residues by LPro leads to a random coil peptide. This agrees with previous results on beta-hairpin-forming peptides showing the essential role of the turn sequence for beta-hairpin folding. The well-defined beta-sheet motif calculated for the new designed peptide (pair-wise RMSD for backbone atoms is 0.5 +/- 0.1 A) displays a high degree of twist. This twist likely contributes to stability, as a more hydrophobic surface is buried in the twisted beta-sheet than in a flatter one. The twist observed in the up-and-down antiparallel beta-sheet motifs of most proteins is less pronounced than in our designed peptide, except for the WW domains. The additional hydrophobic surface burial provided by beta-sheet twisting relative to a "flat" beta-sheet is probably more important for structure stability in peptides and small proteins like the WW domains than in larger proteins for which there exists a significant contribution to stability arising from their extensive hydrophobic cores.
Collapse
Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | | | | | | |
Collapse
|
26
|
Dhanasekaran M, Prakash O, Gong YX, Baures PW. Expected and unexpected results from combined β-hairpin design elements. Org Biomol Chem 2004; 2:2071-82. [PMID: 15254635 DOI: 10.1039/b315228f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model beta-hairpin dodecapeptide [EFGWVpGKWTIK] was designed by including a favorable D-ProGly Type II' beta-turn sequence and a Trp-zip interaction, while also incorporating a beta-strand unfavorable glycine residue in the N-terminal strand. This peptide is highly folded and monomeric in aqueous solution as determined by combined analysis with circular dichroism and 1H NMR spectroscopy. A peptide representing the folded conformation of the model beta-hairpin [cyclic(EFGWVpGKWTIKpG)] and a linear peptide representing the unfolded conformation [EFGWVPGKWTIK] yield unexpected relative deviations between the CD and 1H NMR spectroscopic results that are attributed to variations in the packing interactions of the aromatic side chains. Mutational analysis of the model beta-hairpin indicates that the Trp-zip interaction favors folding and stability relative to an alternate hydrophobic cluster between Trp and Tyr residues [EFGYVpGKWTIK]. The significance of select diagonal interactions in the model beta-hairpin was tested by rearranging the cross-strand hydrophobic interactions to provide a folded peptide [EWFGIpGKTYWK] displaying evidence of an unusual backbone conformation at the hydrophobic cluster. This unusual conformation does not appear to be a result of the glycine residue in the beta-strand, as replacement with a serine results in a peptide [EWFSIpGKTYWK] with a similar and seemingly characteristic CD spectrum. However, an alternate arrangement of hydrophobic residues with a Trp-zip interaction in a similar position to the parent beta-hairpin [EGFWVpGKWITK] results in a folded beta-hairpin conformation. The differences between side chain packing of these peptides precludes meaningful thermodynamic analysis and illustrates the caution necessary when interpreting beta-hairpin folding thermodynamics that are driven, at least in part, by aromatic cross strand interactions.
Collapse
|
27
|
DeVane R, Ridley C, Larsen RW, Space B, Moore PB, Chan SI. A molecular dynamics method for calculating molecular volume changes appropriate for biomolecular simulation. Biophys J 2003; 85:2801-7. [PMID: 14581185 PMCID: PMC1303561 DOI: 10.1016/s0006-3495(03)74703-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Accepted: 05/06/2003] [Indexed: 11/28/2022] Open
Abstract
Photothermal methods permit measurement of molecular volume changes of solvated molecules over nanosecond timescales. Such experiments are an important tool in investigating complex biophysical phenomena including identifying transient species in solution. Developing a microscopic understanding of the origin of volume changes in the condensed phase is needed to complement the experimental measurements. A molecular dynamics (MD) method exploiting available simulation methodology is demonstrated here that both mimics experimental measurements and provides microscopic resolution to the thermodynamic measurements. To calculate thermodynamic volume changes over time, isothermal-isobaric (NPT) MD is performed on a solution for a chosen length of time and the volume of the system is thus established. A further simulation is then performed by "plucking" out a solute molecule of interest to determine the volume of the system in its absence. The difference between these volumes is the thermodynamic volume of the solute molecule. NPT MD allows the volume of the system to fluctuate over time and this results in a statistical uncertainty in volumes that are calculated. It is found in the systems investigated here that simulations lasting a few nanoseconds can discern volume changes of approximately 1.0 ml/mole. This precision is comparable to that achieved empirically, making the experimental and theoretical techniques synergistic. The technique is demonstrated here on model systems including neat water, both charged and neutral aqueous methane, and an aqueous beta-sheet peptide.
Collapse
Affiliation(s)
- Russell DeVane
- Department of Chemistry, University of South Florida, Tampa, Florida 33620-5250, USA
| | | | | | | | | | | |
Collapse
|
28
|
Santiveri CM, Rico M, Jiménez MA, Pastor MT, Pérez-Payá E. Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 61:177-88. [PMID: 12605603 DOI: 10.1034/j.1399-3011.2003.00045.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In a previous study we designed a 20-residue peptide able to adopt a significant population of a three-stranded antiparallel beta-sheet in aqueous solution (de Alba et al. [1999]Protein Sci.8, 854-865). In order to better understand the factors contributing to beta-sheet folding and stability we designed and prepared nine variants of the parent peptide by substituting residues at selected positions in its strands. The ability of these peptides to form the target motif was assessed on the basis of NMR parameters, in particular NOE data and 13Calpha conformational shifts. The populations of the target beta-sheet motif were lower in the variants than in the parent peptide. Comparative analysis of the conformational behavior of the peptides showed that, as expected, strand residues with low intrinsic beta-sheet propensities greatly disfavor beta-sheet folding and that, as already found in other beta-sheet models, specific cross-strand side chain-side chain interactions contribute to beta-sheet stability. More interestingly, the performed analysis indicated that the destabilization effect of the unfavorable strand residues depends on their location at inner or edge strands, being larger at the latter. Moreover, in all the cases examined, favorable cross-strand side chain-side chain interactions were not strong enough to counterbalance the disfavoring effect of a poor beta-sheet-forming residue, such as Gly.
Collapse
Affiliation(s)
- C M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | | | | | |
Collapse
|
29
|
Syud FA, Stanger HE, Mortell HS, Espinosa JF, Fisk JD, Fry CG, Gellman SH. Influence of strand number on antiparallel beta-sheet stability in designed three- and four-stranded beta-sheets. J Mol Biol 2003; 326:553-68. [PMID: 12559922 DOI: 10.1016/s0022-2836(02)01304-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe experiments that probe whether antiparallel beta-sheet secondary structure becomes more stable as the number of strands increases. Several groups, including ours, have explored this issue with peptides designed to adopt three-stranded beta-sheet conformations, but the conclusions have not been consistent. In this study, we examine the effect on conformational stability of beta-sheet lengthening perpendicular to the strand direction via analysis of designed peptides that adopt three-stranded or four-stranded antiparallel beta-sheet conformations in aqueous solution. The findings reported here, along with the context provided by earlier studies, suggest that antiparallel beta-sheet does, in general, become more stable when the number of strands is increased from two to three. We show that this conclusion is not influenced by the rigidity of the loop segment used to link adjacent beta-strands (D-Pro-Gly versus Asn-Gly). We show that further extension, from three strands to four, leads to a further increase in antiparallel beta-sheet stability.
Collapse
Affiliation(s)
- Faisal A Syud
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Blandl T, Cochran AG, Skelton NJ. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns. Protein Sci 2003; 12:237-47. [PMID: 12538887 PMCID: PMC2312432 DOI: 10.1110/ps.0228603] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The turn-forming ability of a series of three-residue sequences was investigated by substituting them into a well-characterized beta-hairpin peptide. The starting scaffold, bhpW, is a disulfide-cyclized 10-residue peptide that folds into a stable beta-hairpin with two antiparallel strands connected by a two-residue reverse turn. Substitution of the central two residues with the three-residue test sequences leads to less stable hairpins, as judged by thiol-disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three-residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel beta-hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide-cyclized scaffold and a linear beta-hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.
Collapse
Affiliation(s)
- Tamas Blandl
- Department of Protein Engineering, Genentech, South San Francisco, California 94080, USA
| | | | | |
Collapse
|