Structural Characterization of Human Parathyroid Hormone 1 Receptor

LIN Ke-Jiang ZHU Dong-Ji LENG Yong-Gan YOU Qi-Dong

(Department of Medicinal Chemistry,China Pharmaceutical University,Nanjing 210009,P.R.China)

Structural Characterization of Human Parathyroid Hormone 1 Receptor

LIN Ke-Jiang ZHU Dong-Ji LENG Yong-Gan YOU Qi-Dong*

(Department of Medicinal Chemistry,China Pharmaceutical University,Nanjing 210009,P.R.China)

Parathyroid hormone 1 receptor(PTH1R)is a member of the class B G-protein coupled receptor(B-GPCR)family and is involved in bone formation.Its substrate parathyroid hormone(PTH)and its analogues are being developed as anti-osteoporosis therapeutics.The structure-based rational drug design of PTH1R substrates has been hampered by the lack of experimentally determined three-dimensional(3D)structures from techniques such as nuclear magnetic resonance(NMR)and X-ray crystallography.Here,we have constructed a 3D model of PTH1R including its extracellular domain(ECD),transmembrane(TM)domain,and other domains using a homology modeling approach.In addition,to capture the ligand-receptor interactions,we have manually docked human parathyroid hormone(1-34)into the top scoring receptor model,and subjected the PTH-PTH1R complex to an unconstrained energy minimization.The integral 3D receptor model provides an easier way to understand the interactions involved at the TM,ECD,and other domains.Furthermore,the parameters of hydrogen bonding,hydrophobic,and other interactions from the ligand-receptor model,enabled us to elucidate the important interactions between PTH(1-34)and PTH1R.This ligand-receptor model could potentially serve as a tool for structure-based virtual screening in the development of non-peptide based anti-osteoporosis drugs.

Parathyroid hormone 1 receptor;Parathyroid hormone;Homology modeling;PTH-PTH1R complex

1 lntroduction

Parathyroid hormone(PTH)is an 84-amino acid polypeptide endocrine hormone.It is produced by the chief cells of parathyroid glands in response to either low calcium or high phosphate levels in the circulation.1-3The N-terminus(1-34 residues of PTH)is fully active,reproducing all biological responses characterized by the native intact PTH.The biologic effects of PTH are primarily mediated through its binding to the parathyroid hormone 1 receptor(PTH1R).4,5PTH1R is a member of the B family of G-protein coupled receptors(GPCRs),a class of receptors for many therapeutically important peptide hormones,such as secretin,glucagon,and calcitonin.6PTH has been used in clinics as a treatment for osteoporosis,which further sparks interest in developing non-peptide PTH1R substrates as anti-osteoporosis drugs.

However,the progress in PTH1R drug design is hamperedby the scarcity of its structural information.As a class of B GPCR,PTH1R contains an N-terminal extracellular domain (ECD)with three conserved disulfide bonds and a C-terminal with seven transmembrane helices(TMs).4Although,the crystal structure of the extracellular domain of PTH1R engineered as a fusion protein with maltose-binding protein was published,7it did not provide information about the N terminus of PTH with the TM helices of PTH1R.Recently,researchers have created PTH1R models by homology modeling using the crystal structure of bacteriorhosopsin as a template for the seven TMs.8,9However,the models were generated only with the TMs,and they may not adequately describe the possible interactions among domains without modeling the ECD of PTH1R.

In this work,we presented an integral PTH1R model with ECD,TM,and extracellular loop 1(ECL1)using different structures as template.PTH(1-34)was then docked into the receptor model manually and the interactions between PTH (1-34)and PTH1R were thoroughly analyzed.Given its pharmaceutical importance,the PTH1R model may provide a rational structure for designing new non-peptide anti-osteoporosis drugs.

2 Experimental

Three-dimensional(3D)model of PTH1R was built using Discovery Studio 2.5(DS2.5)10with details described below.

2.1 Template preparation

Templates with the highest sequence identity to the target sequence were identified and used to generate homology models. 3C4M(PDB code),71BL1(PDB code)11and human β2-adrenergic receptor(PDB code:2RH1)12were used to model ECD, ECD/TM junction,and TM domain of PTH1R,respectively. For ECL1,the protein 1CYI(PDB code)13was employed as template.

2.2 Sequence alignment

The program Align Multiple Sequences was used for aligning multiple sequences via a progressive pairwise alignment algorithm based on the ClustalW program named Align123.In Align123,the term for scoring a match of secondary structure can be added to the original ClustalW multiple sequence alignment score.14The matrix assigns BLOSUM as score.Sequence alignment of TMs region is accomplished by ADD MEMBRANE AND ORIENT MOLECULE module.This module optimizes the position and the orientation of a molecule relative to an implicit membrane.The optimization algorithm has a stepwise search for the minimum solvation energy of the molecule,calculated by CHARMm modules GBIM and ASPENMB15or GBSW16.The solvent model with implicit membrane is selected in GBIM.The default settings were applied for other parameters.

2.3 Homology modeling

The MODELER module was used to build homology models based on the sequence alignment between templates and target.All template structures discussed above were set as template while the default values for other parameters were kept constant.Subsequently,3D models were created and the top 5 scoring models were collected.

2.4 Optimization and quality assessment of 3D models

Energy minimization was carried out using a none implicit solvent model by the CHARMm forcefield.Then,the Verify Protein(MODELER)protocol was used to assess the quality of protein molecules with the Discrete Optimized Protein Energy(DOPE)method.Afterwards,the 3D model scores and the Ramachandran plot of PTH1R model were generated to identify the residues in the regions of unrealistic conformation for further refinement.

The Verify Protein(Profiles-3D)protocol was used to measure the compatibility between an amino acid sequence and its 3D protein structure.The effect of a lipid membrane was included in the calculation of Profile-3D scores.17

The Ramachandran plot provides a graphical representation of the local backbone conformation of each residue in a protein.Each point on the Ramachandran plot represents the φ and ψ torsion angles of a residue.The plot also includes a representation of the favorable and unfavorable regions for residues,so that one can determine whether individual residues are likely to be built correctly.The Ramachandran plot computed here is as updated by Richardson and coworkers.18

2.5 Docking

PTH(1-34)was docked into the top scoring receptor model manually by constraining the distance(1 nm)between Ser1 of PTH and Met425 of PTH1R,Lys13 of PTH and Arg186 of PTH1R,and Arg20 of PTH,and Asp137 of PTH1R according to the literature.19The PTH-PTH1R complex was then subjected to dynamics simulation without any constraints.The Standard Dynamics Cascade simulation was performed which included minimizations,heating,dynamics,and production with a set of defined simulation procedures.For energy minimizations,the steepest descent method20was employed first to a 418400 J·mol-1·nm-1root mean square(RMS)energy gradient and followed by the Polak and Ribiere conjugate gradient method21until the final convergence criterion reached 418.4 J· mol-1·nm-1RMS gradient.Then the whole system was heated from 100 to 300 K in 2 ps and equilibrated in 300 K for 100 ps.One hundred conformations were collected in 20 ps production phase at 300 K.The conformation with the lowest potential energy was further minimized.The final refined model of the complex was calculated by using MOE program.22

2.6 lnteraction between PTH and receptor

Mapping receptor-ligand interaction was performed using MOE.The method was fully described by Clark et al.23Briefly, the method captures and displays selected receptor ligand interacting entities including hydrogen bonds(HB),solvent interactions,metal ligation,and nonbonded residues.The HB scores were expressed by percentage and the HB directionality was noted.The ligand and residue solvent accessibility metricswere estimated by measuring the exposed surface area when each of the atoms had been assigned a van der Waals radius of +0.14 nm(water solvent).The solvent exposure of receptor residues was calculated by examining the difference between the solvent-exposed surface areas of the receptor with and without the presence of the ligand.The solvent-accessible surface area and the ligand proximity outline were also estimated.For the ligands,the surface accessibility calculation was carried out on the ligand-receptor complex.The default settings were applied for the definition of hydrogen-bonded and proximity interactions.

3 Results and discussion

3.1 Sequence alignment

PTH1R contains a N-terminal ECD with three conserved disulfide bonds,a C-terminal domain with seven transmembrane helices,and a connection domain including the residues 168-198.We used multiple templates including 3C4M,1BL1, and 2RH1 to model PTH1R structure.The templates were aligned with the target individually and then compared by the percentage of their sequence identities.The alignment of the final model with all templates is shown in Fig.S1 in Supporting Information.All three templates showed acceptable sequence identities.

3.1.1 Sequence alignment of ECD

3C4M(PDB code)7was selected as a template because of its partly containing the maltose-binding ECD of PTH1R fusion protein.The interactions between the residues 56-105 of PTH1R and PTH remained unknown.Thus,the sequence of 3C4M was aligned with the sequence of PTH1R after deleting the residues 56-105.The identity is 79.8%while similarity is 83.1%.

3.1.2 Sequence alignment of the connection domain between ECD and TM

The ECD/TM junction includes the residues 169-189 of ECD and the residues 190-196 of TM.After a BLAST search, a 31-amino acid fragment(PDB code:1BL1)11was found with highest similarity to the connection domain between ECD and TM.The 31-amino acid fragment includes the residues 169-189 of PTH1R ECD,containing two helix both of which are amphipathic on the surface of the micelle.The fragment also includes the residues 190-196 of TM1 of PTH1R,which is very hydrophobic and embedded in the lipid core.11Thus,the fragment structure would be the perfect template for modeling the connection domain between ECD and TM.The sequences of 1BL1 and our target share 93.5%sequence identity and similarity.

3.1.3 Sequence alignment of TM

PTH1R belongs to class B GPCR with seven transmembrane helices.The position of each TM helix of PTH1R was predicted before sequence alignment.The TM helix sequence of human β2-adrenergic receptor(PDB code:2RH1)12were aligned with the TM helices of PTH1R(Fig.S1).Despite the low overall sequence homology(identity:8.5%,similarity: 25.5%)between human β2-adrenergic receptor and PTH1R, they share similarly seven TM secondary helical structures. Therefore,the parameters of secondary structure were set as“TRANSMEM”when applying aligning sequence in DS2.5. Despite the relatively low sequence identity/similarity(Fig. S1),the secondary structures were closely aligned and used for modeling the TMs structure of PTH1R.

3.1.4 Sequence alignment of ECL1

In transmembrane,the main difference between PTH1R and template is a long loop domain located at the residues 240-280 region of PTH1R,also named the first extracellular domain(ECL1)of PTH1R.Previous studies have identified Leu261,in the ECL1 of PTH1R,as a putative contact site for Lys27 in the principal bonding domain of PTH(1-34).24So the modeling of ECL1 is very important for PTH1R-PTH structural characterization.A new template(PDB code:1CYI)13was identified to model the tertiary structure of ECL1 according to identity and similarity.Both of the identity and similarity between 1CYI and ECL1 are 88.7%.

3.2 Construction,optimization and evaluation of PTH1R model

3.2.1 Homology modeling of PTH1R

The sequence alignment results discussed above were aligned with the target sequence sequentially.The structures of 3C4M,1BL1,2RH1,and 1CYI were all set as templates for modeling the tertiary structure of PTH1R.Five models were constructed and the results were satisfactory.Eventually,the best one was selected for further optimization(Table 1).

Table 1 lists the probability density function(PDF)total energy(in ascending order),PDF physical energy,and DOPE scores of output models.Smaller PDF energy indicates that the model satisfies the homology restraints better.Lower DOPE score also indicates a better model.25Based on the smallest PDF energy and lowest DOPE scores,the model target. B99990005 was selected for further study(Fig.1).

3.2.2 Validation and evaluation of PTH1R models

To assess the reliability of the chosen model,we carried out further loop refinement and optimization.The Verify(Profile-3D)Scores improved significantly from 98.5701 to 155.36 and was close to the Expected High Score(181.516).In Ramachandran plot,most residues are in the favorable regions(Fig.2). The results show that the model of PTH1R is reliable.

Table 1 Results of PTH1R model

Fig.1 The best model target.B99990005 in Table 1The PTH1R model includes the ECD,ECL1,and TM shown in different styles.The ECD of PTH1R is indicated in line ribbon.The ECL1 is shown in tube on the top surface of juxtamembrane domain.The remaining part in solid ribbon is the TM of PTH1R.

An integral 3D structure of PTH1R was constructed above, which contains complete ECD,TM,especially the ECL1 and the connection domain between ECD and TM(Fig.3).

3.3 Structure characterization for ligand binding to PTH1R

3.3.1 Structure characterization of ligand binding to ECD of PTH1R

The C-terminal fragment of PTH(residues 15-34)binds to the ECD of PTH1R with high affinity and specificity.26The interactions between PTH and PTH1R are mainly H-bonds and hydrophobic interactions.The Asn16 of PTH(15-34)forms a direct H-bond with the residue Asp30 of PTH1R.Most importantly,Arg20 of PTH(15-34)forms a pair of charged interaction with Asp137 and two H-bonds with Asp29 and Met32 of PTH1R,7which provides a significant insight for designing better PTH mimics.The dramatic effects on binding affinity seen with NH methylations near Trp23 at Leu24 and Arg25 provide evidence to support an important role for this interaction in the stability of the complex.27When the flexibility site residues Arg20 are substituted,the PTH reduces affinity for the intact PTH1R by at least～200-fold.Similar effects were observed for Glu substitution at Trp23,Leu24,and Leu28.26,28

The integrated ligand receptor model discussed above was subjected to dynamics simulation without any constraints.The ligand-receptor interactions including H-bonds(Fig.4)and hydrophobic interactions(Fig.S2 in Supporting Information) were calculated.Using this model,we confirmed the interaction sites which have been previously reported.9,29-35In addition,we identified additional contact sites between the ligand and receptor.For example,Glu19,Arg25,His32 of PTH formed H-bond respectively to Lys34,Leu174,Arg162 of PTH1R,which may be used as additional binding sites for ligand design.

3.3.2 Structure characterization for ligand binding to the TM of PTH1R

Fig.2 Ramachandran plot of PTH1R model before(A)and after (B)optimizationThe plot includes a representation of the favorable and unfavorable regions for residues,so that one can determine whether individual residues are likely to be built correctly.Amino acid types are represented graphically as follows:glycine as a triangle,proline as a square,and all other types as a circle.

The ligand-receptor interactions between the PTH(1-14) and TM of PTH1R including H-bonds(Fig.5)and hydrophobic interaction(Fig.S3 in Supporting Information)were calculated. Interestingly,new contact sites were also identified.For example,Gly12 and His16 of PTH interacted with Phe184,Asp185, Arg186,and Val183,which may provide new binding sites for further research.

Fig.3 Complex diagram of PTH(1-34)binding to PTH1R model in different views(A)the side view of receptor/ligand complex;(B)the top view of receptor/ligand complex with the PTH1R indicated in schematic.The PTH(1-34)is shown in line type with N-terminal and C-terminal labeled,of which the N-terminal is inserted in the cavity of PTH1R.

Fig.4 Interaction diagram of PTH(15-34)binding to the ECD of PTH1R with H-bondsThe PTH(15-34)is displayed in 2D chemical structure and the residues of PTH1R are shown in circle.

Fig.5 Interaction diagram of PTH(1-14)binding to the TM of PTH1R with H-bondsThe PTH(1-14)is displayed in 2D chemical structure and the residues of PTH1R are shown in circle.

Our results validated the existence of the interaction recognized previously. Studies using receptor/ligand photo cross-linking indicated that the N-terminal fragment of PTH (residues 1-14)bound with the low affinity.36,37The C-terminal of PTH,on the other hand,interacted with PTH1R through H-bonds and hydrophobic interactions.The Ser1 of PTH was found generating interaction with the Met425 and Phe375 of PTH1R by the photo affinity cross-linking approach.38Val2, Ile5,and Met8 were proved as key amino acids to activation.29Gln6 and Asn10 of PTH binding to the hydrophobic pocket that generated by Phe447,Phe238 were important for activating the receptor.39

3.3.3 Structure characterization of connection domain and the ECL1 of PTH1R

The connection domain(residues 168-198)between ECD and TM is an important fragment of PTH1R for ligand receptor interaction.This fragment includes the residues 169-189 of PTH1R ECD,containing two amphipathic helices.This fragment also includes the residues 190-196 of TM1 of PTH1R,which is hydrophobic and embedded in the lipid core.11There is a bend in the mid-region of this fragment and the direction and degree of the bend would decide the position of ECD.In addition,Lys13 of PTH forms a direct H-bond with Arg186 of PTH1R,which is a critical contact point between the ligand and receptor in this connection domain.19These structural characteristics could affect the C-terminal of PTH binding to the ECD of PTH1R.

The ECL1 domain(residues 240-280)of PTH1R contains more than 40 residues,which is different from other GPCRs. Piserchio et al.31suggested that the ECL1 was embedded into the membrane.Our model predicts that the ECL1(Fig.1)is perpendicular to rather than embedded into the TM,in parallel with the ECD.This explains the observation that Glu19 of PTH interacted with Lys240 of PTH1R situated in ECL1 region,and Lys27 of PTH interacted with Leu261 of PTH1R.40Both Glu19 and Lys27,which pertain to C-terminus of PTH, were anticipated to interact with the ECD instead of extracellular loop ECL1.However,from the interaction calculation,no interaction between the two parts was shown.This may be because the ECL1 is more flexible and far away from the C-terminal fragment of PTH.

4 Conclusions

This study is intended to elucidate the structural characterization of PTH1R.The integral 3D model encompasses major structure components of the ligand receptor binding and activation,and helps to describe the interactions among the TM, ECD,and ECL1.

Although the TM and ECD domains of PTH1R have been modeled separately in literature,the complete structure of PTH1R has not been reported.Our study comes first to define an integral 3D structure of PTH1R upon binding with the PTH (1-34).

Our ligand-receptor model has the potential to serve as a tool for structure-based virtual design as well as screening of novel PTH analogues and mimics for the treatment of osteoporosis.

Supporting Information Available: The sequence alignments and the hydrophobic interaction diagrams of PTH (1-14)and PTH(15-34)binding to PTH1R have been included.This information is available free of charge via the internet at http://www.whxb.pku.edu.cn.

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人甲狀腺旁素1型受體的結構特征

林克江 朱冬吉 冷勇敢 尤啟冬*

(中國藥科大學藥物化學教研室,南京210009)

人甲狀腺旁素1型受體(PTH1R)是骨形成相關的B類G蛋白偶聯受體,其底物甲狀腺旁腺素(PTH)及類似物具有抗骨質疏松作用.由于此類受體的三維結構難以進行實驗測定,本文采用同源模建的方法,完整構建了胞外區、跨膜區及其它相關區域,并通過對接研究,闡明復合物的氫鍵、疏水性相互作用及其與底物的相互作用關系和關鍵位點.為進一步設計和發展此類藥物提供理論依據.

甲狀腺旁素1型受體; 甲狀腺旁素; 同源模建; 甲狀腺旁素復合物

O641

10.1196/annals.1402.088

10.1677/ joe.1.06057

Received:February 22,2012;Revised:April 19,2012;Published on Web:April 19,2012.?

.Email:Youqd@163.com;Tel:+86-25-83271351

?Editorial office ofActa Physico?Chimica Sinica

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