Limits...
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family.

Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ - Chem Cent J (2008)

Bottom Line: Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.This inference is consistent with well-known results that show allosteric response within a family generally varies significantly.Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Bioinformatics Research Center, University of North Carolina at Charlotte, Charlotte, NC, USA. drlivesa@uncc.edu

ABSTRACT

Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding.

Results: We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.

Conclusion: Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.

No MeSH data available.


Related in: MedlinePlus

(a) Phylogenetic tree of representatives from the 29 protein classes within the bPBP family. The four proteins investigated herein are highlighted (Blue = LAOBP, Green = HBP, Purple = GBP, and Red = PhBP). (b) Structure superposition of the four binding proteins (color-coding the same). PhBP has been removed in (c) to highlight the conservation within the three amino acid binding proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2533333&req=5

Figure 2: (a) Phylogenetic tree of representatives from the 29 protein classes within the bPBP family. The four proteins investigated herein are highlighted (Blue = LAOBP, Green = HBP, Purple = GBP, and Red = PhBP). (b) Structure superposition of the four binding proteins (color-coding the same). PhBP has been removed in (c) to highlight the conservation within the three amino acid binding proteins.

Mentions: Within the Structural Classification of Proteins (SCOP) database [31], there are 29 different binding protein classes within the bPBP family, which SCOP calls the phosphate binding protein-like family. Several classes within the family include multiple species orthologs, and within each ortholog, many binding proteins have been crystallized within different states (i.e., presence/absence of ligand, wild-type vs. mutant, etc.). Fig. 2a shows the neighbor-joining phylogenetic tree built from the Probalign [32,33] multiple sequence alignment of 29 representative structures. Ideally, we would like to perform a comparative QSFR analysis across all 29 binding protein classes; however, pragmatic considerations make this impractical for manual manipulations. Since a large scale comparison will need automation based on prior experience, we extend our previous comparative QSFR analysis of a mesophilic/thermophilic RNase H pair [22] to four different binding proteins. There is experimental Cp data for only one member of the family, the histidine binding protein (HBP). Three of the homologs, which include lysine/arginine/ornithine binding protein (LAOBP) [34], glutamine binding protein (GBP) [35] and HBP [36], represent a closely related subfamily of amino acid binding proteins. Juxtaposed to this close-knit group is the distantly related phosphate binding protein (PhBP) [37], the namesake of the SCOP family, which provides a point of reference over larger evolutionary distances. In order to circumvent parameterization issues, we apply the HBP parameterization to all four homologs, which we have previously demonstrated to be a satisfactory option [22], especially when considering mechanical response. Two of the binding proteins have been crystallized in both the presence and absence of ligand, whereas the other two have only been crystallized in the presence of ligand. Table 2 lists the PDB ID's and other relevant information of the six structures investigated herein.


Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family.

Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ - Chem Cent J (2008)

(a) Phylogenetic tree of representatives from the 29 protein classes within the bPBP family. The four proteins investigated herein are highlighted (Blue = LAOBP, Green = HBP, Purple = GBP, and Red = PhBP). (b) Structure superposition of the four binding proteins (color-coding the same). PhBP has been removed in (c) to highlight the conservation within the three amino acid binding proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2533333&req=5

Figure 2: (a) Phylogenetic tree of representatives from the 29 protein classes within the bPBP family. The four proteins investigated herein are highlighted (Blue = LAOBP, Green = HBP, Purple = GBP, and Red = PhBP). (b) Structure superposition of the four binding proteins (color-coding the same). PhBP has been removed in (c) to highlight the conservation within the three amino acid binding proteins.
Mentions: Within the Structural Classification of Proteins (SCOP) database [31], there are 29 different binding protein classes within the bPBP family, which SCOP calls the phosphate binding protein-like family. Several classes within the family include multiple species orthologs, and within each ortholog, many binding proteins have been crystallized within different states (i.e., presence/absence of ligand, wild-type vs. mutant, etc.). Fig. 2a shows the neighbor-joining phylogenetic tree built from the Probalign [32,33] multiple sequence alignment of 29 representative structures. Ideally, we would like to perform a comparative QSFR analysis across all 29 binding protein classes; however, pragmatic considerations make this impractical for manual manipulations. Since a large scale comparison will need automation based on prior experience, we extend our previous comparative QSFR analysis of a mesophilic/thermophilic RNase H pair [22] to four different binding proteins. There is experimental Cp data for only one member of the family, the histidine binding protein (HBP). Three of the homologs, which include lysine/arginine/ornithine binding protein (LAOBP) [34], glutamine binding protein (GBP) [35] and HBP [36], represent a closely related subfamily of amino acid binding proteins. Juxtaposed to this close-knit group is the distantly related phosphate binding protein (PhBP) [37], the namesake of the SCOP family, which provides a point of reference over larger evolutionary distances. In order to circumvent parameterization issues, we apply the HBP parameterization to all four homologs, which we have previously demonstrated to be a satisfactory option [22], especially when considering mechanical response. Two of the binding proteins have been crystallized in both the presence and absence of ligand, whereas the other two have only been crystallized in the presence of ligand. Table 2 lists the PDB ID's and other relevant information of the six structures investigated herein.

Bottom Line: Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.This inference is consistent with well-known results that show allosteric response within a family generally varies significantly.Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Bioinformatics Research Center, University of North Carolina at Charlotte, Charlotte, NC, USA. drlivesa@uncc.edu

ABSTRACT

Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding.

Results: We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.

Conclusion: Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.

No MeSH data available.


Related in: MedlinePlus