Structural genomics: beyond the Human Genome Project

Burley, S.K.; Almo, Steven C.; Bonanno, J.B.; Capel, Malcolm; Chance, Mark R.; Gaasterland, Terry; Lin, Dazhen; Šali, Andrej; Studier, F. William; Swaminathan, Subramanyam

doi:10.1038/13783

Cited by 358 publications

(219 citation statements)

References 21 publications

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“…E-mail: asher+@pitt.edu. 1 Abbreviations: UVRR, ultraviolet resonance Raman spectroscopy; R, arginine; G, glycine; W and Trp, tryptophan; S, serine; V, valine; Q, glutamine; N, asparagine; K, lysine; Y and Tyr, tyrosine; T, threonine; E, glutamic acid; PSSRS, pure secondary structure Raman spectra; CD, circular dichroism; NMR, nuclear magnetic resonance; AmI, amide I normal mode; AmII, amide II normal mode; AmIII, amide III normal mode; C R-H, (C)CR-H bending normal mode; Ar str, aromatic ring stretching band. ments, samples were prepared by dissolving the peptide to a concentration of 0.13-0.30 mM in a 5 mM sodium acetate (EM Science, Gibbstown, NJ) buffer.…”

Section: Methodsmentioning

confidence: 99%

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

Boyden

Asher

2001

Biochemistry

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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...

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Section: Methodsmentioning

confidence: 99%

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

Boyden

Asher

2001

Biochemistry

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“…Parameters screened generally include protein concentration, pH (generally a pH range from 3.0 to 9.0 is evaluated in steps of 0.3 pH units), buffer type, precipitating agent type and concentration, temperature, additive type and concentration. This approach, combined with technological developments such as high-throughput protein-expression/purification and automated crystallographic determination protocols, the use of protein engineering to enhance crystallization lattice contacts and robotic liquid-dispensing/crystallization systems, have accelerated the crystallization and structure determination of thousands of new proteins (Blundell & Mizuguchi, 2000;Burley et al, 1999;Mittl & Grü tter, 2001;Montelione & Anderson, 1999;Teichmann et al, 1999;Christendat et al, 2000;Waldo et al, 1999;Terwilliger, 2000;Abola et al, 2000;Hendrickson, 2000;Derewenda, 2004a,b;Rupp et al, 2002;Krupka et al, 2002;Stevens, 2000). However, in spite of the plethora of new protein structures that have resulted from these technological advances, it is clear that robotics alone is not sufficient for the successful crystallization of a significant number of important proteins.…”

Section: Introductionmentioning

confidence: 99%

Applications of the second virial coefficient: protein crystallization and solubility

Wilson

DeLucas

2014

Acta Cryst Sect F

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This article begins by highlighting some of the ground-based studies emanating from NASA's Microgravity Protein Crystal Growth (PCG) program. This is followed by a more detailed discussion of the history of and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (Bvalues) as a diagnostic indicator of solution conditions conducive to protein crystallization. A second application of measuredBvalues involves the determination of solution conditions that improve or maximize the solubility of aqueous and membrane proteins. These two important applications have led to several technological improvements that simplify the experimental expertise required, enable the measurement of membrane proteins and improve the diagnostic capability and measurement throughput.

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“…The number of experimentally determined structures for comparative modeling of most proteins based on at least 30% sequence identity to a known structure is estimated to be Ϸ16,000 (48). A reduction of this number, while keeping the accuracy of the corresponding models constant, would reduce both the cost and time required by structural genomics to fulfill its aim (49)(50)(51)(52). This reduction can be partly achieved by using more sensitive fold detection methods, such as the method described here.…”

Section: Discussionmentioning

confidence: 99%

Detecting remotely related proteins by their interactions and sequence similarity

Espadaler

Aragüés²,

Eswar³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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The function of an uncharacterized protein is usually inferred either from its homology to, or its interactions with, characterized proteins. Here, we use both sequence similarity and protein interactions to identify relationships between remotely related protein sequences. We rely on the fact that homologous sequences share similar interactions, and, therefore, the set of interacting partners of the partners of a given protein is enriched by its homologs. The approach was benchmarked by assigning the fold and functional family to test sequences of known structure. Specifically, we relied on 1,434 proteins with known folds, as defined in the Structural Classification of Proteins (SCOP) database, and with known interacting partners, as defined in the Database of Interacting Proteins (DIP). For this subset, the specificity of fold assignment was increased from 54% for position-specific iterative blast to 75% for our approach, with a concomitant increase in sensitivity for a few percentage points. Similarly, the specificity of family assignment at the e-value threshold of 10-8 was increased from 70% to 87%. The proposed method would be a useful tool for large-scale automated discovery of remote relationships between protein sequences, given its unique reliance on sequence similarity and protein-protein interactions

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Structural genomics: beyond the Human Genome Project

Cited by 358 publications

References 21 publications

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

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

Applications of the second virial coefficient: protein crystallization and solubility

Detecting remotely related proteins by their interactions and sequence similarity

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