Geometrically Reduced Number of Protein Ground State Candidates

Ejtehadi, Mohammad Reza; Hamedani, Nona Ghasemi; Shahrezaei, Vahid

doi:10.1103/physrevlett.82.4723

Cited by 20 publications

(14 citation statements)

References 22 publications

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“…These results show some connection to the work of Ejtihadi et al. [20] With a purely geometrical approach, they were able to reduce largely the candidates of structures that can be chosen as the ground states of sequences. They found that for the case of HP protein model the number of ground state candidates grows only as N 2 , N being the sequence length.…”

Section: The Statistical Properties Of Partnumssupporting

confidence: 57%

“…[18,19,20] In this article we present one way to break the symmetry, to distinguish the compact structures of lattice model without explicitly considering concrete interaction form. However, since only compact structures are considered here, an loose constraint is actually set on interactions: interactions under which compact structures are preferred as ground energy states.…”

Section: Introductionmentioning

confidence: 99%

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One way to characterize the compact structures of lattice protein model

Wang

Zhou

2000

The Journal of Chemical Physics

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On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact structure. The Partnum is compared with the concept Designability of protein structures emerged recently. It is shown that the highly designable structures have, on average, an atypical number of local degree of freedom. The statistical property of Partnum and its dependence on sequence length is also studied.

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Section: The Statistical Properties Of Partnumssupporting

confidence: 57%

Section: Introductionmentioning

confidence: 99%

One way to characterize the compact structures of lattice protein model

Wang

Zhou

2000

The Journal of Chemical Physics

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“…Several authors have investigated the effect of the two‐body pairing term in Eq. 5 on designability 35, 42–45. In particular, Shahrezaei and Ejtehadi showed in the case of a two‐letter code that the set of highly designable structures is robust with respect to potential parameters and is largely determined by the structures' geometry 25.…”

Section: Discussionmentioning

confidence: 99%

Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix

Li¹,

Tang²,

Wingreen³

2002

Proteins

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We study the designability of all compact 3×3×3 and 6×6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e. sequences that have that structure as their unique lowest-energy state. Previous studies of hydrophobic -polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a 2-letter (HP) code in such studies. Here we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix), and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model--and vice versa--with the associated sequences having enhanced thermodynamic stability.

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“…33,52,53 Additional work has shown that some paircontact structures can remain stable and highly designable across an entire range of mixing parameters ␥ M for any twoletter amino-acid alphabet. 54,55 More recently, an analytical, statistical mechanical treatment for calculating the volume of two-letter HP sequence space folding into particular 2D pair-contact structures has been presented by Kussell and Shakhnovich. 56 Upon decomposing structures into various strings of pair-contacts, which in 2D can form either strands or loops, Kussell and Shakhnovich established that highly designable 2D structures for two-letter amino-acid alphabets should have the following properties: ͑1͒ No loops, ͑2͒ a maximum number of twolength strands, and ͑3͒ a minimum number of larger-length strands.…”

Section: Introductionmentioning

confidence: 99%

Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus

Buchler

Goldstein

2000

The Journal of Chemical Physics

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A variety of analytical and computational models have been proposed to answer the question of why some protein structures are more ''designable'' ͑i.e., have more sequences folding into them͒ than others. One class of analytical and statistical-mechanical models has approached the designability problem from a thermodynamic viewpoint. These models highlighted specific structural features important for increased designability. Furthermore, designability was shown to be inherently related to thermodynamically relevant energetic measures of protein folding, such as the foldability F and energy gap ⌬ 10 . However, many of these models have been done within a very narrow focus: Namely, pair-contact interactions and two-letter amino-acid alphabets. Recently, two-letter amino-acid alphabets for pair-contact models have been shown to contain designability artifacts which disappear for larger-letter amino-acid alphabets. In addition, a solvation model was demonstrated to give identical designability results to previous two-letter amino-acid alphabet paircontact models. In light of these discordant results, this report synthesizes a broad consensus regarding the relationship between specific structural features, foldability F, energy gap ⌬ 10 , and structure designability for different energy models ͑pair-contact vs solvation͒ across a wide range of amino-acid alphabets. We also propose a novel measure Z d k which is shown to be well correlated to designability. Finally, we conclusively demonstrate that two-letter amino-acid alphabets for pair-contact models appear to be solvation models in disguise.

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Geometrically Reduced Number of Protein Ground State Candidates

Cited by 20 publications

References 22 publications

One way to characterize the compact structures of lattice protein model

One way to characterize the compact structures of lattice protein model

Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix

Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus

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