Design, synthesis and characterisation of a 34-residue polypeptide that interacts with nucleic acids

Gutte, Bernd; Däumigen, M.; Wittschieber, Erika

doi:10.1038/281650a0

Cited by 103 publications

(31 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently there have been major advances in protein design [i.e., in the design of amino acid sequences that will fold to desired "target" native conformations (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)]. However, the following several hurdles remain to be overcome.…”

mentioning

confidence: 99%

Inverse protein folding problem: designing polymer sequences.

Yue

Dill

1992

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

178

103

View full text Add to dashboard Cite

We consider the question of how to design proteins. How can we find "good" amino acid sequences (D) that fold to a desired "target" structure as a native conformation of lowest accessible free energy and (ii) that will not simultaneously fold to many other conformations of the same free energy? Current protein designs often focus on helix propensities and turns. We focus here on designing the hydrophobicity. For a model of self-avoiding hydrophobic/polar chains on two-dimensional square lattices, geometric proofs and exhaustive enumerations show the following results. (i) The strategy hydrophobic residues inside/polar residues outside is not optimal. Placement of additional hydrophobic residues on the surface is often necessary. (u) To avoid unwanted conformations, the designed sequence must have neither too many nor too few hydrophobic residues. (iii) The computational complexity of inverse folding appears to be in a different class than folding: unlike the folding problem, the design problem does not scale exponentially with chain length. Some design strategies, described here for the lattice model, produce good sequences and scale only linearly with chain length.Recently there have been major advances in protein design [i.e., in the design of amino acid sequences that will fold to desired "target" native conformations (1-11)]. However, the following several hurdles remain to be overcome. (i) So far, most designed proteins have only simple symmetries-4-helix bundles and all-sheet conformations, for example (2-4, 9, 10).(ii) Most of the "rational" aspects of design currently focus on the interactions among the "connected" neighbors [i.e., on the intrinsic propensities of monomeric and dimeric amino acids to form helices and turns (12-16)]. However, major forces of folding are due to hydrophobic and other "nonlocal" interactions [i.e., among monomers far apart in the sequence (17-19)]. The main design principle currently used for them is hydrophobic (H) residues inside/polar (P) residues outside. Nevertheless, many real proteins have exposed nonpolar and buried polar units (20,21), and some single-site mutations contradict the hydrophobic residues inside/pol~ar residues outside principle (22). Are there more subtle principles that are important? (iii) A major design problem has been how to avoid simultaneous folding to wrong conformations; designed sequences sometimes appear to fold to "gemiche" states, involving multiple or wrong native structures (ref. 4 and T. Handel, personal communication). It is not known how to control the multiplicity of stable structures (i.e., how to design the desired structure uniquely into the sequence). The problem of sequence design is the "inverse protein folding" problem (23)(24)(25). Whereas the input of a protein folding algorithm would be an amino acid sequence and the output would be a native structure, the input for an inverse folding algorithm would be a desired native structure and the output would be a sequence that will fold to it. Can heuristic rules be f...

show abstract

mentioning

confidence: 99%

Inverse protein folding problem: designing polymer sequences.

Yue

Dill

1992

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

178

103

View full text Add to dashboard Cite

show abstract

“…Prediction will be easier if the natural conformation has outstanding stability 5275 The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 (8), and an artificial 34-residue polypeptide designed to interact with RNA has been synthesized and found active (9). It has been proposed to give microcircuitry special sensitivities by adsorbing engineered proteins onto selected surfaces (10).…”

mentioning

confidence: 99%

Molecular engineering: An approach to the development of general capabilities for molecular manipulation

1981

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

502

197

View full text Add to dashboard Cite

Development ofthe ability to design protein molecules will open a path to the fabrication of devices to complex atomic specifications, thus sidestepping obstacles facing. conventional microtechnology. This path will involve construction of molecular machinery able to position;reactive groups to atomic precision. It could lead to great advances in computational devices and in the ability to manipulate biological materials. The existence of this path has implications for the present. Feynman's .1959 talk entitled "There's Plenty of Room at the Bottom" (1) discussed microtechnology as a 'frontier to be pushed back, like the frontiers of high pressure, low temperature, or high vacuum. He suggested that ordinary machines could build smaller machines that could build still smaller machines, working step by step down toward the molecular level; he also suggested using particle beams to. define two-dimensional patterns. Present microtechnology (exemplified by integrated circuits) has realized some ofthe potential outlined by Feynman by following the same basic~approach: working down from the macroscopic level to the microscopic.Present microtechnology (2) handles statistical populations of atoms. As the devices shrink, the atomic graininess of matter increasingly creates irregularities and imperfections, so long as atoms are handled in bulk, rather than individually. Indeed, such miniaturization of bulk processes seems unable to reach the ultimate level of microtechnology-the structuring of matter to complex atomic specifications. In this paper, I will outline a path to this goal, a general molecular engineering technology. The existence of this path will be shown to have implications for the present.Although the capabilities described may not prove necessary to the achievement of any particular objective, they will prove sufficient for the achievement ofan extraordinary range of objectives in which the ;structuringand analysis ofmatter are con--cerned. The claim that devices can be built to complex atomic specifications should not, however, be construed to deny the inevitability of a finite error rate arising from thermodynamic effects (and radiation damage). Such errors can be minimized through.the use of free energy in error-correcting 'procedures (including rejection offaulty components before device assembly); the effects of errors can be minimized through fault-tolerant design, as in macroscopic engineering.The emphasis on devices that have general capabilities should be taken in the spirit of early work on the theoretical capabilities ofcomputers, which did not attempt to predict such practical embodiments as specialized or distributed computation systems. The present argument, however, will -proceed from step to step by close analogies between the proposed steps and past developments in-nature. and technology, rather than by mathematical proof. We commonly accept the feasibility of new devices without formal proof, where analogies to existing systems are close enough: consider the feasibility of making ...

show abstract

“…Our work on the design of novel functional proteins began with the synthesis of a 34-residue polypeptide that interacted with nucleic acids [2]. The proposed secondary structure @%r) of this peptide was partly confirmed by circular dichroism (CD) measurements ([6] and unpublished results).…”

Section: Introductionmentioning

confidence: 99%

An artificial crystalline DDT‐binding polypeptide

1983

View full text Add to dashboard Cite

A hydrophobic U-residue polypeptide that could potentially form a four-stranded antiparallel H-pleated sheet and bind the insecticide DDT was designed and synthesized. The synthetic peptide aggregated in 1 M acetic acid but was monomeric in aqueous W7o ethanol. In the latter solvent the 24-residue polypeptide and DDT formed a complex with an apparent dissociation constant of -2 x lo-' M. The DDT binding of an analogue of this peptide possessing the same amino acid residues in a random sequence was more than 2 orders of magnitude and that of bovine serum albumin at least 3 orders of magnitude weaker. The designed polypeptide could be crystallized. Protein secondary structure prediction Model building Protein design Synthetic DDT-binding polypeptideCrystallization, of artificial polypeptide

show abstract

Design, synthesis and characterisation of a 34-residue polypeptide that interacts with nucleic acids

Cited by 103 publications

References 25 publications

Inverse protein folding problem: designing polymer sequences.

Inverse protein folding problem: designing polymer sequences.

Molecular engineering: An approach to the development of general capabilities for molecular manipulation

An artificial crystalline DDT‐binding polypeptide

Contact Info

Product

Resources

About