X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly)

Kramer, Rachel Z; Vitagliano, Luigi; Bella, Jordi; Berisio, Rita; Mazzarella, L.; Brodsky, Barbara; Zagari, Adriana; Berman, Helen M.

doi:10.1006/jmbi.1998.1881

Cited by 163 publications

(192 citation statements)

References 24 publications

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“…The rmsd of the main-chain atoms from their position in triple-helical ðProHypGlyÞ 10 [1v7h (42)] or in ðProProGlyÞ 10 (35) is 0.2 Å. This value holds for comparison with both 1k6f (35), our molecular replacement model, and 1a3i (43), an independent ProProGly structure, providing assurance against phasing model bias in our structure determination. Similar values have been reported for comparisons between various ProProGly and ProHypGly structures (43).…”

mentioning

confidence: 67%

“…This value holds for comparison with both 1k6f (35), our molecular replacement model, and 1a3i (43), an independent ProProGly structure, providing assurance against phasing model bias in our structure determination. Similar values have been reported for comparisons between various ProProGly and ProHypGly structures (43). This conservation of main-chain structure is evident from the congruence of ϕ, ψ, and ω with those in natural CRPs (Table 3).…”

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confidence: 78%

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Stereoelectronic and steric effects in side chains preorganize a protein main chain

Shoulders¹,

Satyshur²,

Forest³

et al. 2009

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

152

142

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Preorganization is shown to endow a protein with extraordinary conformational stability. This preorganization is achieved by installing side-chain substituents that impose stereoelectronic and steric effects that restrict main-chain torsion angles. Replacing proline residues in ðProProGlyÞ 7 collagen strands with 4-fluoroproline and 4-methylproline leads to the most stable known triple helices, having T m values that are increased by >50°C. Differential scanning calorimetry data indicate an entropic basis to the hyperstability, as expected from an origin in preorganization. Structural data at a resolution of 1.21 Å reveal a prototypical triple helix with insignificant deviations to its main chain, even though 2∕3 of the residues are nonnatural. Thus, preorganization of a main chain by subtle changes to side chains can confer extraordinary conformational stability upon a protein without perturbing its structure.collagen triple helix | nonnatural amino acid | preorganization | protein stability | x-ray crystallography T he three-dimensional structures of proteins are stable because of a delicate balance of forces (1). Increases in the conformational stability of a protein-desirable in many contexts (2)-can be realized by enhancing the hydrophobic effect (3, 4), introducing or shielding a hydrogen bond (5) or electrostatic interaction (6-8), or introducing a disulfide crosslink (9-11) or metal ion-binding site (12). These strategies are often frustrated by enthalpy-entropy compensation, whereby enthalpic stabilization is offset entirely by entropic destabilization, or vice versa (13). Moreover, the strategies often lack subtlety and can lead to a misshapen and hence dysfunctional protein.As elaborated by Cram (14), the principle of preorganization states that, "the more highly hosts and guests are organized for binding and low solvation prior to their complexation, the more stable will be their complexes." In a typical manifestation, a conformational constraint is imposed upon a receptor or ligand during its chemical synthesis. This principle can also yield biopolymers with increased conformational stability (Fig. 1). For example, the stability of a DNA duplex correlates with the helicity of its single strands (15, 16), and a bicyclic ("locked") derivative of ribose enhances that stability (17, 18). The stability of β-turns within protein structures can be increased by incorporating Dproline (19) and certain β-amino acids (20) that bias the conformations occupied by the unfolded polypeptide. Likewise, proteins containing a cis-peptide bond can be stabilized by constrained amides or isosteres (21-23). The utility of these substitutions is limited, however, by the difficulty of modifying the backbone of proteins as well as concomitant effects on structure and function (24-27).We suspected that alterations to proline residues could provide a particularly incisive means to preorganize the conformation of a polypeptide chain. In classic work, Matthews and coworkers substituted proline, which is the least flexible residu...

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confidence: 67%

mentioning

confidence: 78%

Stereoelectronic and steric effects in side chains preorganize a protein main chain

Shoulders¹,

Satyshur²,

Forest³

et al. 2009

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

152

142

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“…We used published data for modeling the structures of the isolated components (11,55,56). The most reliable and powerful conclusion from these modeling studies is the orientation of the extended collagen peptide relative to the enzyme.…”

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confidence: 99%

The 1.8-Å Crystal Structure of a Matrix Metalloproteinase 8-Barbiturate Inhibitor Complex Reveals a Previously Unobserved Mechanism for Collagenase Substrate Recognition

Brandstetter

Grams

Glitz

et al. 2001

Journal of Biological Chemistry

124

103

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The individual zinc endoproteinases of the tissue degrading matrix metalloproteinase (MMP) family share a common catalytic architecture but are differentiated with respect to substrate specificity, localization, and activation. Variation in domain structure and more subtle structural differences control their characteristic specificity profiles for substrates from among four distinct classes (Nagase, H., and Woessner, J.

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“…6,7 In the collagen model made of PRO-PRO-GLY triplets, prolines at the Xaa positions usually pucker DOWN and those at the Yaa positions usually pucker UP. 8,9 These features of proline puckering, along with the other factors have been attributed to influence the conformational stability of collagen structures. 2,4,[10][11][12] In molecular simulations, the HYP puckering parameters have been proposed by Mooney et al 13 and by Park et al 14 Based on the Amber 99 force field, 15 Park et al proposed the HYP parameters that produced good results.…”

Section: Introductionmentioning

confidence: 99%

“…However, the PDB results show the DOWN puckering preference of proline at the Xaa position. 8 Therefore, in this study we try to improve the proline puckering populations by introducing the proline puckering parameters into the Charmm22 force field.…”

Section: Introductionmentioning

confidence: 99%

Proline puckering parameters for collagen structure simulations

2015

AIP Advances

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The puckering free-energy surface of proline AIP Advances 3, 032141 (2013) Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion-proline puckering-becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations. Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

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X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly)

Cited by 163 publications

References 24 publications

Stereoelectronic and steric effects in side chains preorganize a protein main chain

Stereoelectronic and steric effects in side chains preorganize a protein main chain

The 1.8-Å Crystal Structure of a Matrix Metalloproteinase 8-Barbiturate Inhibitor Complex Reveals a Previously Unobserved Mechanism for Collagenase Substrate Recognition

Proline puckering parameters for collagen structure simulations

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