Designing a 20-residue protein

Neidigh, Jonathan W.; Fesinmeyer, R. Matthew; Andersen, Niels H.

doi:10.1038/nsb798

Cited by 760 publications

(1,447 citation statements)

References 29 publications

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“…Three systems were used for decoy analysis: trpzip2 42 (SWTWENGKWTWK-NH 2 ), Baldwin type 43 alanine based α-helical peptide 44 (Ace-GGG(KAAAA) 3 K-NH 2 ) and trpcage miniprotein 45 (NLYIQWLKDGGPSSGRPPPS). The decoys for the three systems were generated by a number of unrestrained as well as forced MD simulations at 300K as described previously 12 .…”

Section: Decoy Analysismentioning

confidence: 99%

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "AMBER" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems.

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Section: Decoy Analysismentioning

confidence: 99%

“…The Baldwin type alanine-based peptide 44 was designed to adopt α-helix. Lastly, the trpcage mini-protein 45 has a mixture of secondary structure elements (α, 3 10 and polyproline).…”

Section: Force Field Validationmentioning

confidence: 99%

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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“…All geometries were optimized using the 6-31G* basis set (so that the helix is slightly distorted from being perfectly helical). In addition, we studied a small synthetic protein, Trp-Cage Miniprotein Construct (PDB code: 1L2Y, model 1), 35 using the experimental geometry available from the PDB database 36 (the position of H atoms was optimized with the Amber96 force field in Hyperchem) and the removal of crystal water. The geometry of (H 2 O) 1024 was optimized with the TIP3P force field using the Tinker program.…”

Section: Covalently Connected Systems and Water Kilomermentioning

confidence: 99%

Pair interaction energy decomposition analysis

2006

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Abstract:The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H 2 O) 1024 , the helix, turn, and strand of polyalanine (ALA) 10 , as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.

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“…Monomer, native form of D9E and D9S mutants show helical structure, as reported previously. 26,29,30 All the phosphorylated mutant monomers proved to be disordered exhibiting spectra similar to that of D9E at 60 °C ( Fig. 2A and Fig.…”

Section: Monomer Structures From Nmr Chemical Shift Deviation (Csd)mentioning

confidence: 86%

“…Trp-cage is the smallest protein-like molecule which could realistically model larger globular proteins or domains. 26 It consist of only 20 residues but still folds into a well-defined tertiary structure 26 through a complex folding pathway. 27 Due to its small size it is an excellent model system for both experimental 26,[28][29][30][31][32] and computational studies.…”

Section: Introductionmentioning

confidence: 99%

Phosphorylation as Conformational Switch from the Native to Amyloid State: Trp-Cage as a Protein Aggregation Model

et al. 2015

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The 20 residue long Trp-cage miniprotein is an excellent model both for computational and experimental studies of protein folding and stability. Recently, a great attention emerged to study disease-related protein misfolding, aggregation and amyloid formation, with the aim of revealing their structural and thermodynamic background. Trp-cage is sensitive to both environmental and structure-modifying effects, and aggregates with ease upon structure destabilization and thus, it is an ideal model of aggregation and amyloid formation. Here, we characterize the amyloid formation of several sequence modified and side-chain phosphorylated Trp-cage variants. We applied NMR, CD, FTIR spectroscopy, MD simulations, transmission electron microscopy in conjunction with thioflavin-T fluorescence measurements to reveal the structural consequences of side-chain phosphorylation. We demonstrate that the native fold is destabilized upon serine phosphorylation and the resultant highly dynamic structures form amyloid-like ordered aggregates with high intermolecular β-structure content. The only exception is the D9S(P) variant which follows an alternative aggregation process by forming thin fibrils, presenting a CD spectrum of PPII helix, and showing low ThT binding capability. We propose a complex aggregation model for these Trp-cage miniproteins. This model assumes an additional aggregated state, a collagen triple helical form which can precede amyloid formation. The phosphorylation of a single serine residue serves as a conformational switch, triggering aggregation, otherwise mediated by kinases in cell. We show that Trp-cage miniprotein is indeed a realistic model of larger globular systems of composite folding and aggregation landscapes and helps us to understand the fundamentals of deleterious protein aggregation and amyloid formation.3

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Designing a 20-residue protein

Cited by 760 publications

References 29 publications

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Pair interaction energy decomposition analysis

Phosphorylation as Conformational Switch from the Native to Amyloid State: Trp-Cage as a Protein Aggregation Model

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