Protein dynamics derived from clusters of crystal structures

Aalten, D.M.F. van; Conn, D.A.; Groot, Bert L. de; Berendsen, H.J.C.; Findlay, John B. C.; Amadei, Andrea

doi:10.1016/s0006-3495(97)78317-6

Cited by 84 publications

(72 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The application of PCA to both distributions of experimental structures and MD trajectories, along with its ability to provide considerable insight into the nature of conformational differences in a range of protein families has been previously discussed (23)(24)(25)(26). Briefly, PCA is based on the diagonalization of the variance-covariance matrix, ⌺, with elements ⌺ ij calculated from the Cartesian coordinates of C␣ atoms, r, after the superposition of all structures under analysis,…”

Section: Methodsmentioning

confidence: 99%

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Yao¹,

Malik

Griggs

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

G protein ␣ subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of G␣ i . Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function.Heterotrimeric G proteins are key mediators of intracellular signaling pathways that control diverse cellular processes ranging from movement and division to differentiation and neuronal activity (1). G proteins consist of three subunits: G␣, G␤, and G␥. Bound with GDP, G␣ forms an inactive complex with its G␤␥ subunit partners. Interaction with activated receptor (GPCR) 3 promotes the exchange of GDP for GTP on G␣ and its separation from G␤␥. Both isolated G␣ and G␤␥ can then bind and activate or inhibit downstream effectors. GTP hydrolysis deactivates G␣, which subsequently reassociates with G␤␥ completing the cycle. This cycle is further regulated by two classes of additional proteins called regulators of G protein signaling. These function as either GTPase-activating proteins (which promote GTP hydrolysis) or GDP dissociation inhibitors (GDIs, which hinder exchange of GDP for GTP) (2). Important conformational transitions occurring at each stage of this regulated cycle have been characterized from extensive crystallographic studies. These include GDP, GTP analogue, G␤␥, GTPase-activating protein, GDI and most recently GPCR bound complex structures of G␣. However, the link between the observed conformations and the atomic level mechanisms involved in coupling receptor association, G protein activation, and effector interaction remain unclear.All G␣ proteins consist of a catalytic GTP binding Ras-like domain (termed RasD) and a heterotrimeric G protein specific helical domain (HD). Recent principal component analysis (PCA) of 53 available G␣ crystallographic structures identified three major conformationally distinct groups ( Fig. 1 and Ref. 3). These groups correspond to structures with bound GTP analogues, GDP, and GDI (red, green, and blue points in Fig. 1a, respectively). The major variation in the accumulated structures is the concerted displacements of three nucleotide-binding site loops termed the switch regions (SI, SII, and SIII), as well as a relatively small...

show abstract

Section: Methodsmentioning

confidence: 99%

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Yao¹,

Malik

Griggs

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…37,53 The algorithm involves the calculation of the covariance matrix of the fluctuations of each atomic coordinate from a reference structure, taken in these calculations as residues in the conserved core of the MalG or MalK subunit (for the TM or NBD analysis, respectively), following superposition onto the MalF core of the 3PUY structure. 27 The eigenvectors of this matrix represent directions with correlated changes in coordinates between all structures.…”

Section: Principal Components Analysis Of Structuresmentioning

confidence: 99%

Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition

et al. 2011

View full text Add to dashboard Cite

Two new crystal structures of the Escherichia coli high affinity methionine uptake ATP Binding Cassette (ABC) transporter MetNI, purified in the detergents cyclohexyl-pentyl-b-Dmaltoside (CY5) and n-decyl-b-D-maltopyranoside (DM), have been solved in inward facing conformations to resolutions of 2.9 and 4.0 Å , respectively. Compared to the previously reported 3.7 Å resolution structure of MetNI purified in n-dodecyl-b-D-maltopyranoside (DDM), the higher resolution of the CY5 data enabled significant improvements to the structural model in several regions, including corrections to the sequence registry, and identification of ADP in the nucleotide binding site. CY5 crystals soaked with selenomethionine established details of the methionine binding site in the C2 regulatory domain of the ABC subunit, including the displacement of the side chain of MetN residue methionine 301 by the exogenous ligand. When compared to the CY5 or DDM structures, the DM structure exhibits a significant repositioning of the dimeric C2 domains, including an unexpected register shift in the intermolecular b-sheet hydrogen bonding between monomers, and a narrowing of the nucleotide binding space. The immediate proximity of the exogenous methionine binding site to the conformationally variable dimeric interface provides an indication of how methionine binding to the regulatory domains might mediate the phenomenon of transinhibition.

show abstract

“…Previous studies of concerted motions on the basis of molecular dynamics computer simulations (29,30,36), NMR ensembles (38, 54, 55), and crystal structures (34,35) have shown that such motions may play a role in protein function. (67) electrostatics calculations were performed using the appropriate full charges assigned to Asp, Gly, Lys, and Arg and a charge of +2.0 on the zinc ion.…”

Section: D-cysteine Interaction With Cpdmentioning

confidence: 99%

Crystal Structure of Carboxypeptidase A Complexed with d-Cysteine at 1.75 Å − Inhibitor-Induced Conformational Changes^,

2000

View full text Add to dashboard Cite

D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the -carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyzes metal removal. To investigate the structural basis for this difference, we solved the crystal structure of carboxypeptidase A complexed with D-cysteine (D-Cys) at 1.75-Å resolution. D-Cys binds the active site zinc with a sulfur ligand and forms additional interactions with surrounding side chains of the enzyme. The structure explains the difference in potency between D-Cys and L-Cys and provides insight into the mechanism of D-penicillamine inhibition. D-Cys binding induces a concerted motion of the side chains around the zinc ion, similar to that found in other carboxypeptidase-inhibitor crystal structures and along a limited path. Analysis of concerted motions of CPD and CPD-inhibitor crystal structures reveals a clustering of these structures into distinct groups. Using the restricted conformational flexibility of a drug target in this type of analysis could greatly enhance efficiency in drug design.

show abstract

Protein dynamics derived from clusters of crystal structures

Cited by 84 publications

References 40 publications

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition

Crystal Structure of Carboxypeptidase A Complexed with d-Cysteine at 1.75 Å − Inhibitor-Induced Conformational Changes^,

Contact Info

Product

Resources

About

Protein dynamics derived from clusters of crystal structures

Cited by 84 publications

References 40 publications

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins

Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition

Crystal Structure of Carboxypeptidase A Complexed with d-Cysteine at 1.75 Å − Inhibitor-Induced Conformational Changes,

Contact Info

Product

Resources

About

Crystal Structure of Carboxypeptidase A Complexed with d-Cysteine at 1.75 Å − Inhibitor-Induced Conformational Changes^,