Protein Design: A Hierarchic Approach

Bryson, James W.; Betz, Stephen F.; Lu, Helen S. M.; Suich, Daniel J.; Zhou, Huan‐Xiang; O’Neil, Karyn T.; DeGrado, William F.

doi:10.1126/science.270.5238.935

Cited by 564 publications

(488 citation statements)

References 165 publications

Supporting

Mentioning

472

Contrasting

Order By: Relevance

“…It is interesting to compare the information measures with results obtained investigating residue a-helix propensities (Bryson et al, 1995), both previous statistical work (e.g., Gibrat et al, 1987;Williams et al, 1987), and the larger literature based on direct experimentation, e.g., using directed mutagenesis (Horovitz et al, 1992;Blaber et al, 1993) and model peptides (Padmanabhan et al, 1990). The correlation of the DSC intraresidue information for the 20 residues with a-helix propensities of the other methods is: Gibrat et al (1987) surveys has the advantage over physical-based methods in being based on many more proteins, and thus averaged over all types of protein environment.…”

Section: Discussionmentioning

confidence: 99%

Identification and application of the concepts important for accurate and reliable protein secondary structure prediction

1996

View full text Add to dashboard Cite

A protein secondary structure prediction method from multiply aligned homologous sequences is presented with an overall per residue three-state accuracy of 70.1 %. There are two aims: to obtain high accuracy by identification of a set of concepts important for prediction followed by use of linear statistics; and to provide insight into the folding process. The important concepts in secondary structure prediction are identified as: residue conformational propensities, sequence edge effects, moments of hydrophobicity, position of insertions and deletions in aligned homologous sequence, moments of conservation, auto-correlation, residue ratios, secondary structure feedback effects, and filtering. Explicit use of edge effects, moments of conservation, and auto-correlation are new to this paper. The relative importance of the concepts used in prediction was analyzed by stepwise addition of information and examination of weights in the discrimination function. The simple and explicit structure of the prediction allows the method to be reimplemented easily. The accuracy of a prediction is predictable a priori. This permits evaluation of the utility of the prediction: 10% of the chains predicted were identified correctly as having a mean accuracy of >80%. Existing high-accuracy prediction methods are "black-box" predictors based on complex nonlinear statistics (e.g., neural networks in PHD: Rost & Sander, 1993a). For medium-to short-length chains ( 2 9 0 residues and

show abstract

Section: Discussionmentioning

confidence: 99%

Identification and application of the concepts important for accurate and reliable protein secondary structure prediction

1996

View full text Add to dashboard Cite

show abstract

“…To date, synthetic schemes have been successfully developed for the synthesis of R-helix-forming peptides, and much has been uncovered about their folding dynamics (6)(7)(8)(9)(10)(11)(12)(13). In contrast, only limited progress has been made toward understanding the synthesis of and the dynamics of -sheet peptides.…”

mentioning

confidence: 99%

UV Raman Studies of Peptide Conformation Demonstrate That Betanova Does Not Cooperatively Unfold

Boyden

Asher

2001

Biochemistry

View full text Add to dashboard Cite

We used UV resonance Raman spectroscopy (UVRR) excited within the peptide bond π f π* electronic transitions and within the aromatic amino acid π f π* electronic transitions to examine the temperature dependence of the solution conformation of betanova, a 20-residue -sheet polypeptide [Kortemme, T., Ramirez-Alvarado, M., and Serrano, L. (1998) Science 281, 253-256]. The 206.5 nm excited UVRR enhances the amide vibrations and demonstrates that betanova has a predominantly -sheet structure between 5 and 82°C. The 229 nm excited UVRR, which probes the tyrosine and tryptophan side chain vibrations, shows an increase in the solvent exposure of the tryptophan side chains as the temperature is increased. Our results are consistent with the existence of an intermediate state similar to that calculated by Bursulaya and Brooks [Bursulaya, B. D., and Brooks, C. L. (1999) J. Am. Chem. Soc. 121, 9947-9951] and exclude the previously proposed two-state cooperative folding mechanism. Betanova's structure appears to be molten globule over the 3-82°C temperature range of our study.The completion of the human genome sequence makes available the primary sequence of all proteins synthesized by the human body. This represents only the first stage in the development of an understanding of the protein structural basis of disease. The next stage in this development requires an ability to predict the structure and function of proteins from their primary sequences. At present this is impossible, since not enough is known about the dynamics and thermodynamics of protein folding (1-5).The understanding of protein folding mechanisms is advancing as experimentalists develop better strategies for the de novo design of model peptides and better methodologies for characterizing equilibrium secondary structures, as well as the dynamics of folding. To date, synthetic schemes have been successfully developed for the synthesis of R-helix-forming peptides, and much has been uncovered about their folding dynamics (6-13). In contrast, only limited progress has been made toward understanding the synthesis of and the dynamics of -sheet peptides. Primarily, studies have focused on -hairpins rather than complete sheet structures (14-18). Successful synthesis of three-stranded -sheet structures has been accomplished only recently. However, these model peptides only form complete -sheet structures under limited conditions, in the presence of organic solvents and with the use of unnatural amino acids (19)(20)(21)(22). Thus, there remains much to learn about -sheet folding.Significant advances have also occurred in the theoretical understanding of protein folding (23-28). Such work includes molecular dynamics simulations of energy landscapes that describe folding thermodynamics. Currently, some of these models accurately predict experimental results. Thus, theory can now impact how experimental data are interpreted. It seems likely that the most powerful insights into the rules of protein folding will result from combined experimental and theoreti...

show abstract

“…[6][7][8] This approach aims to minimize structural complexity with a view to maximize visualization of a designed function that is so often obscured in natural proteins. We are using these simplified synthetic protein maquettes 9 to identify the requirements for protein assembly and incorporation of electron-transfer cofactors and to determine what controls in situ electrochemistry, kinetic activity, and the nature of coupled chemistry.…”

Section: Introductionmentioning

confidence: 99%

De Novo Design of a CytochromebMaquette for Electron Transfer and Coupled Reactions on Electrodes

et al. 2001

View full text Add to dashboard Cite

Experimental explorations of functional mechanisms in natural electron-transfer proteins are often frustrated by their fragility and extreme complexity. We have designed and synthesized four-R-helix-bundle redox proteins, maquettes, that are much simplified and more robust than natural redox proteins and can be designed to bind onto electrode surfaces to facilitate systematic investigations. The points of interest that can be now assessed are not only the processes that govern biological assembly of equilibrium structures, electrochemistry, and electron tunneling rates but also how these factors are coupled together to effect redox driven catalysis. Here we describe maquettes that bis-histidine ligate protoporphyrin IX (heme), much like native b cytochromes, as well as contain charged surface patches, much like native cytochrome c. The positively charged residues aid adsorption to negatively charged surfaces, such as gold electrodes modified by 11-mercaptoundecanoic acid, and facilitate cyclic voltammetry (CV) measurements. CV demonstrates the reversible electrochemistry typical for cytochrome b as well as the coupling of the b-heme oxidation and reduction to proton exchange. The pH dependency of redox midpoint potentials reveals a major (three pH units) shift of the pK a which matches the shift previously shown to originate in nearby glutamates 1 . The redox potentials correspondingly shift from -0.24 (pH > pK red , deprotonated) to -0.11 V (pH < pK ox , protonated). The rate of electron transfer at zero driving force between the hemes and the gold electrode was determined to be 120 s -1 , a rate consistent with tunneling through the mercaptoundecanoic acid spacer and suggesting that the coupled proton exchange is not rate limiting. Reduction of the heme in the presence of CO-saturated buffer shifted the oxidation peak from -0.2 to +0.35 V, indicating massive preferential CO binding to the reduced heme. Consistent with solution spectroscopy, CO must displace one axial histidine to the heme to form the His-CO form of the ferrous heme. The CO is released upon heme oxidation at high potentials. In contrast to coupled proton exchange, CO binding/release and ligand exchange are slow on the time scale of electron tunneling between the heme edge and the electrode.

show abstract

Protein Design: A Hierarchic Approach

Cited by 564 publications

References 165 publications

Identification and application of the concepts important for accurate and reliable protein secondary structure prediction

Identification and application of the concepts important for accurate and reliable protein secondary structure prediction

UV Raman Studies of Peptide Conformation Demonstrate That Betanova Does Not Cooperatively Unfold

De Novo Design of a CytochromebMaquette for Electron Transfer and Coupled Reactions on Electrodes

Contact Info

Product

Resources

About