Relaxation of structural constraints during Amicyanin unfolding

Kozak, John J.; Gray, Harry B.; Garza-López, Roberto A.

doi:10.1016/j.jinorgbio.2017.11.016

Cited by 2 publications

(6 citation statements)

References 45 publications

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“…Three recent publications illustrating the method of analysis are noted: our study of the structural stability of intelectin-1 [7] , a comparative study of three cytochromes [ cyt c, cyt-b562, and cyt c' in Ref. ( 8) ], and a study of the thermal denaturation of amicyanin [9], including comparisons with experimental evidence.…”

Section: Methodsmentioning

confidence: 99%

“…The changing environment of each residue as the protein unfolds from the native state to one of these linearly-extended reference states is followed quantitatively via direct application of classical Euclidean geometry and trigonometry [See Refs. (7)(8)(9) and Appendix].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…As noted, the linear extended state in our geometrical model is representative of one of many possible states in the near neighborhood of the globally-optimized native state that are accessible energetically as the protein is destabilized . The configurations represented by the six stages of unfolding considered here can be realized in a sequence of stepwise transitions starting from native state or (with a lower probability) to an advanced stage in a single transition [9].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…(8), the blue copper proteins amicyanin in Ref. (9) and azurin in Refs. (11)(12)(13), or the proteins studied here], unfolding processes can be systematically compared.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…The metric of 10 Å, noted above, is totally arbitrary. It is the same metric we used in our studies of the cytochromes [8] and amicyanin [9], thereby allowing comparisons of the relative stabilization of residue segments in the neighborhood of the metal ion(s) in different proteins in the same family and in different families. Thus, we can assess the relative influence of the iron ion in the cytochromes, the Cu ion in amicyanin, as well as the Ca ions in the intelectin family.…”

Section: Regional Comparisonsmentioning

confidence: 99%

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Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL

Kozak

Gray

Garza-López

et al. 2018

Journal of Inorganic Biochemistry

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We extend our study of the structural stability of helical and nonhelical regions in chain A of human intelectin-1 to include a second human intelectin (4WMY) and the frog protein "Xenopus embryonic epidermal lectin" (XEEL). These unique lectins have been shown to recognize carbohydrate residues found exclusively in microbes, thus they could potentially be developed into novel microbe detection and sequestration tools. We believe that by studying the structural stability of these proteins we can provide insights on their biological role and activities. Using a geometrical model introduced previously, we perform computational analyses of protein crystal structures that quantify the resiliency of the native state to steric perturbations. Based on these analyses, we conclude that differences in the resiliency of the human and frog proteins can be attributed primarily to differences in non-helical regions and to residues near Ca ions. Since these differences are particularly pronounced in the vicinity of the ligand binding site, they provide an explanation for the finding that human intelectin-1 has a higher affinity for a ligand than XEEL. We also present data on conserved and position-equivalent pairs of residues in 4WMY and XEEL. We identify residue pairs as well as regions in which the influence of neighboring residues is nearly uniform as the parent protein denatures. Since the structural signatures are conserved, this identification provides a basis for understanding why both proteins exhibit trimeric structures despite poor sequence conservation at the interface.

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Section: Methodsmentioning

confidence: 99%

Section: Accepted Manuscriptmentioning

confidence: 99%

Section: Accepted Manuscriptmentioning

confidence: 99%

“…(8), the blue copper proteins amicyanin in Ref. (9) and azurin in Refs. (11)(12)(13), or the proteins studied here], unfolding processes can be systematically compared.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Section: Regional Comparisonsmentioning

confidence: 99%

See 3 more Smart Citations

Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL

Kozak

Gray

Garza-López

et al. 2018

Journal of Inorganic Biochemistry

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Geometrical Description of Protein Structural Motifs

2018

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We present a geometrical method that can identify secondary structural motifs in proteins via angular correlations. The method uses crystal structure coordinates to calculate angular and radial signatures of each residue relative to an external reference point as the number of nearest-neighbor residues increases. We apply our approach to the blue copper protein amicyanin using the copper cofactor as the external reference point. We define a signature termed Δβ which describes the change in angular correlation as the span of nearest neighbor residues increases. We find that three turn regions of amicyanin harbor residues with Δβ near zero, while residues in other secondary structures have Δβ greater than zero: for β-strands, Δβ changes gradually residue by residue along the strand. Extension of our analysis to other blue copper proteins demonstrated that the noted structural trends are general. Importantly, our geometrical description of the folded protein accounts for all forces holding the structure together. Through this analysis, we identified some of the turns in amicyanin as symmetrical anchor points.

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Relaxation of structural constraints during Amicyanin unfolding

Cited by 2 publications

References 45 publications

Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL

Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL

Geometrical Description of Protein Structural Motifs

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