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1
Department of Ocular biochemistry, National Institute of Nutrition, Jamai Osmania,
Hyderabad, 500 007, India.
2
Asterace Labs, Windsor plaza 208, Nallakunta, Hyderabad, 500024, India.
3
Dept.of Biotechnology, Aurora Degree College, Chikkadapally, Hyderabad, India-500020.
4
Department of Pharmacy, Sharada College of Pharmacy, Narasarao pet, Gunturu,
Hyderabad, India.
ABSTRACT
Article Received on
19 May 2014, Surfactant protein A (SP-A) constitutes an important part of the innate
Revised on 25 June
2014, immune defense in the lung. The three-dimensional (3D) model of the
Accepted on 22 July 2014
human surfactant protein-A (hSP-A) has been constructed based on the
crystal structure of Rat norvegicus 1R13 protein (Protein Data Bank
*Correspondence for Author ID: 1R13) using MODELLER 9.9 software. Under the process of
Dr. Sreenivas Enaganti
homology modeling 2 models were generated, and the model having
Asterace Labs, Windsor plaza
the lowest modeler objective function value was chosen for further
208, Nallakunta, Hyderabad,
500024, India assessment. The generated model assessed and validated using
PROCHECK, ProSA and RMSD that showed the final refined model
is reliable, with 0.59 as RMSD and has -6.11 as Z-scores. Furthermore, with the generated
model, we carried out binding studies with simple carbohydrate and lipid ligands using the
Molegro Virtual Docker. Docking studies with these ligands into the active site of hSP-A
indicate that maltose and Dipalmitoylphosphatidylcholine are more preferred ligands than
others, with the binding scores of -93.8850 & -103.774 respectively. Docking studies
revealed that Arg58, Arg63, Glu144, Lys34, Ser 98, Asp99, Glu33 and Ile59 of receptor are
important determinant residues as they have strong hydrogen bonding contacts with both
carbohydrate and lipid compounds. This is in good agreement with the experimental results.
Results of the current study will provide a deep insight about the structure and function of
Surfactant Protein-A and how these interactions influence the binding and neutralization of
pulmonary pathogens.
Key Words: Surfactant Protein-A (SPA), Homology Modeling, Docking, Rattus norvegicus,
Lipids, Carbohydrates.
1. INTRODUCTION
The surface area of the lung is expandable approximately the size of a tennis court. The
extremely thin, delicate gas-exchanging epithelium of this large organ allows efficient
diffusion of oxygen and carbon dioxide between inspired air and the pulmonary circulation.
An average person inhales about 10,000 liters of gas per day; which is laden with bacteria,
viruses, oxidants, pollutants and allergens. Fortunately, several immune mechanisms function
in the lung to help maintain its sterility. Pulmonary surfactant proteins are components of the
lungs innate immune system that have been identified in recent times and are the focus of the
present study [1]. Surfactant is mostly composed of phospholipids that are essential for
reducing surface tension at the air-liquid interface of the lung.
SPA is necessary for the formation of tubular myelin [9&10]. These structures do not disrupt
surface activity but optimize the surface properties of lung surfactant. This ability of SP-A to
bind lipids is of relevance in several aspects of pulmonary surfactant biology [11&12].
However, recent evidence shows that SP-A is also a pulmonary host defense protein that
binds to, aggregates, opsonises, and permeabilizes microorganisms. One view that reconciles
these apparently divergent functions of SP-A is that its high affinity for surfactant membranes
is a mechanism for concentrating the protein at the front line of defense against inhaled
pathogens [13].
2. METHODOLOGY
2.1. Sequence Alignment: The FASTA sequence of SP-A (Q8IWL2) from Homo sapiens
was retrieved from the Swiss-prot database and the protein had 248 amino acids (Accession
Comparative modelling usually starts by searching the PDB of known protein structures
using the target sequence as the query [15]. This search is generally done by comparing the
target sequence with the sequence of each of the structures in the database. The target
sequence was searched for similar sequence using the Basic Local Alignment Search Tool
(BLAST) [16] against PDB.
2.2. Homology Modeling: The theoretical structure of SP-A (Q8IWL2) from Homo sapiens
was generated using MODELLER9.9 by comparative modeling of protein structure
prediction. MODELLER implemented comparative protein structure modeling by satisfaction
of spatial restraints. The program was designed to use as many different types of information
about the target sequence as possible [17].
2.3.2. ProSA
Protein Structure Analysis program compares Z-scores between target and template structure.
The Z-scores of model is a measure of compatibility between its sequence and structure. The
model Z-score should be comparable to the Z-scores obtained from the template [20].
2.3.3. RMSD
Root Mean Squared Deviation (RMSD) is commonly used to represent the distance between
two objects. In a structural sense, this value indicates the degree to which two, 3D structures
are similar. The lower the value, the more similar the structures are. The RMSD value [21]
between the template 1R13 and our model structure was calculated using Spdbv.
We used the default settings, including a grid resolution of 0.30 for grid generation and a
15 radius from the template as the binding site. We used the Mol Dock optimizer as a
search algorithm, and the number of runs was set to 10. A population size of 50, maximum
iteration of 2000, scaling factor of 0.50, crossover rate of 0.90 and a variation-based
termination scheme for parameter settings were used. The maximum number of poses to
generate was 5.
Tertiary structure of a protein was built by packing of its secondary structure elements to
form discrete domains or autonomous folding units. Comparative modeling predicts the 3D
structure of surfactant protein A, a given protein sequence (target) based primarily on its
alignment to 1R13 as template (an experimentally determined structure) by using Clustal X
(Fig 1).
Two models of SP-A were generated by MODELLER 9.9 using crystal structure of SP-A
from Rat norvegicus (PDB-ID: 1R13) as a template protein for homology modeling.
Homology protein modelling uses experimentally determined protein structures (templates)
to predict the 3-D structure of another protein that has a similar amino acid sequence (target).
This approach to modelling is possible since a small change in the protein sequence usually
results in a small change in its 3D structure [28]. Homology modelling remains the only
modelling method that can provide models with a root mean square error lower than 2.
In the present study we reported only one best model out of two predicted models, based on
their highest amino acid sequence identity between query sequence, surfactant protein-A
Q8IWL2) from Homo sapiens and the template i.e. 1R13 from Rattus norvegicus. Further,
modeled hSP-A was validated by PROCHECK and ProSA. The hypothetical protein model
created was stored as PDB output file and consists of 96 hydrogen bonds, 3 helices, 13
strands and 14 turns as visualized by Rasmol (Fig 2).
Figure 3. Ramachandrans plot calculations of modeled hSP-A protein (A) and 1R13
from
Rattus norvegicus (B) were carried out using PROCHECK server. The figure 3(A) shows that
all the residues are in core regions of the Ramachandrans plot.
Figure 4. The plan of Z-Score shows spots of Z scores values of proteins determined by
NMR (represented in dark blue color) and by X ray (represented in light blue color)
using ProSA program. The two black dots encircled by red circles represent Z-Scores of
our model (-6.11) and template (-6.0) indicates the overall quality of the modeled 3D
structure of SPA.
Further evaluation was carried out using ProSA. The Z-score indicates overall model quality
and measures the deviation of the total energy of the structure with respect to an energy
distribution derived from random conformations. In order to facilitate interpretation of the Z-
score of the specified protein, its particular value is displayed in a plot that contains the Z-
scores of all experimentally determined protein chains in current PDB. Groups of structures
from different sources (X-ray, NMR) are distinguished by different colors (NMR with dark
blue and X ray with light blue). This plot can be used to check whether the Z-score of the
protein in question is within the range of scores typically found for proteins of similar size
belonging to one of these groups. It can be seen in (Fig 4) that Z-score value of the obtained
model hSP-A (SPA.B99990001_01.pdb) from Homo sapiens is -6.11 and located within the
space of proteins determined by X ray. The value is extremely closed to the value of the
template 1R13 (-6.0) which suggests that the obtained model is reliable and very close to
experimentally determined structures
The overall general similarities and subtle difference among predicted model
SPA.B99990001 and the 3D structure of template 1R13 can be seen from the backbone
superposition (Fig 5). As evident from superposition, general folding topology of the
structure is similar however, some structural differences appear between the predicted model
and template. These differences are mainly due to insertion and deletions in different loop
regions. The RMSD (Root Mean Square Deviation) between predicted model and template is
0.59 . The low RMSD between the target and template reflects the presence of strong
homology (The lower the value, the more similar the structures are).
Figure 6. Electrostatic surface of hSP-A showing the cavities (green mesh) at the active
site.
3.4. Docking of Carbohydrate and Lipid compounds with Modeled hSP-A Protein
Docking of the optimized compounds against modeled hSP-A at the catalytic active site
residues were performed by Molegro Virtual Docker. At the beginning of docking studies,
seven simple carbohydrates and ten lipid compounds were allowed to undergo extensive
flexible docking on hSP-A The optimized 3D structures of carbohydrate and lipid compounds
were given Table 2 & 3 [Supplementary data]. The default parameters were used in the
docking simulations with Mol Dock. Different Poses of protein-ligand complex were
obtained after docking process with their specific mol dock energy and Rerank scores
displayed in output file. The best carbohydrate and lipid ligands were chosen on the basis of
high score as well as interacting amino acid residues of receptor (Table 2 & 3).
Table 2: Modeled hSP-A protein and carbohydrate ligand showing high Mol Dock
energy and H-bond interactions with different amino acid groups
INTERACTING
NAME OF MOLDOCK RERANK
PROTEIN AMINO ACID
LIGAND SCORE SCORE
(H-BONDED)
Asp99, Arg 63 &
Human Glucose -85.5984 -66.0884
Ser 98
Surfactant
Asp99, Ser 98 &
Protein-A Fucose -53.1567 -14.9014
Arg 63
The ligand poses were analyzed and interactions of ligand molecules with the modeled
protein were studied on the basis of H-bonding made by the poses to the receptor (hSP-A)
molecule and close contacts (Vander Waals clashes) between the poses and receptor
molecule. As it is well known, H bonds play an important role for the structure and function
of biological molecules, especially for the enzyme catalysis
Table 3: Modeled hSP-A protein and lipid ligand showing high Mol Dock energy and H-
bond interactions with different amino acid groups.
INTERACTING
NAME OF MOL DOCK RERANK
PROTEIN AMINO ACID
LIGAND SCORE SCORE
(H-BONDED)
Arg63, Arg58,
Dilauroylphosph-
-93.5902 Glu144, Glu33,
atidylcholine -53.0505
Lys34
Arg63, Asp99,
Dipalmitoylphos- -103.77 -48.1512 Arg58, Glu144,
Human phatidylcholine Glu33, Lys34
Surfactant
Asp99, Ser98,
Protein-A
Phosphatidyl -95.652 -67.8862 Arg58, Arg63,
Lys34, Glu144
Arg63, Ser98,
Phosphatidylserine -94.465 -14.36 Gly85, Ile59,
Arg58
To understand the H bonds interaction between receptor and ligand, the Carbohydrate-hSP-A
and lipid-hSP-A complexes were generated using Molgro Virtual Docker (Fig 7 & 8).
Docking studies with carbohydrates showed that Glucose (Fig 7A), Fucose (Fig 7B),
Mannose (Fig 7C), Galactose (Fig 7D), Inositol(Fig 7E), Maltose (Fig 7F) and N-
Acetylmannosamine (Fig 7G) are binding with Moldock score of -85.5984, -53.1567, -
57.9828, -50.1976, -43.3641, -93.8850, and -58.1159 (Table 2). Docking with lipids showed
that Dilauroylphosphatidylcholine (Fig 8A), Phosphatidyl (Fig 8B),
Dipalmitoylphosphatidylcholoine (Fig 8C), Phosphotidylserine (Fig 8D), are binding with
score of -93.5902, -103.77, -95.652 and -94.465 (Table 3). Other ligands such as
Distearoylphosphatidylcholine, Phosphatidylinositol, Palmitoylphosphatidylcholine,
Phoshatidylethnolamine, phatidylglycerol and Tocopherol are binding with total score of -
61.1728, -88.166, -91.528, -86.731, -87.084 and -83.850 Table 3 [supplementary data].
Hydrogen bonding interactions show that carbohydrates like maltose is binding with Ser98,
Arg63, Lys34, Glu144, Arg58 and Asp99; N-acetylmannosamine as ligand molecule interacts
with Ser98, Asp99, Arg63, Arg58, Glu144 and Lys34. All seven docked complexes were
analyzed through MVD for their interaction studies shown in (Fig 7).
Figure 7. Docking models of active site residues of hSP-A with Glucose (A), Fucose (B),
Mannose (C), Galactose (D), Inositol (E), Maltose (F), and N-acetylmannosamine (G).
These sugars are commonly found on fungal and micrococcal surfaces. The C-terminal
globular domain of SP-A seems to be responsible for these interactions. The results obtained
from the present study are well correlated with those of experimental results.
It was evident from this analysis that the best carbohydrates and lipid compounds are located
in the centre of the active site and is stabilized by hydrogen bonding interactions. As it is well
known, hydrogen bonding plays an important role for the structure and function of biological
molecules, especially for inhibition in a complex.
Docking studies revealed that Arg58, Arg63, Glu144, Lys34, Ser 98, Asp99, Glu33, Ile59,
Gly85 and Gly98 are significant binding key residues in the active site of receptor.
Docking the modeled protein with various carbohydrate and lipid compounds provide an
insight into the nature of binding and interaction of ligands with the receptor. Active site
residues such as Arg58, Arg63, Glu144, Lys34, Ser 98, Asp99, Glu33 and Ile59 were found
to be more important residues involved in hydrogen bonding with both carbohydrate and lipid
compounds as shown in (Table 2&3). Hence, from the obtained results, we conclude that
maltose and dipalmitoylphosphatidylcholine (DPPC) are the most preferred ligands out of all
carbohydrate and lipid compounds respectively.
4. CONCLUSION
Lung SP-A is part of the naturally occurring innate immune system which provides an
immediate defense against a wide range of lung pathogens like viruses, bacteria, and fungi.
The high affinity of SP-A to surfactant membranes allows the concentration of this protein in
the alveolar fluid. The binding capabilities of SP-A are involved in its putative biological
functions like improvement of surfactant biophysical function and integrity, defense against
alveolar pathogens and immunomodulation of the inflammatory response. Levels of SP-A
have been reported to fall during infections and lung inflammation. Therefore, the use of
recombinant forms of human SP-A together with surfactant lipids may alleviate the need for
administration of antibiotics and/or anti-inflammatory drugs, especially in the very young and
in the immunocompromised adults. A complete understanding of the structure and function
of human SP-A will allow the production of recombinant SP-A to be used in human
therapies.
Hence, this study could prove useful in further functional characterization of this important
protein in lungs and paves the way to initiate the research on binding affinity of lung proteins
towards microbial membrane lipids for the clearance of different pathogens. We continue to
study the interactions of Sp-A and how these interactions influence the binding and
neutralization of pulmonary pathogens.
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