**Abstract**

Homology modeling is one of the key discoveries that led to a rapid paradigm shift in the field of computational biology. Homology modeling obtains the three dimensional structure of a target protein based on the similarity between template and target sequences and this technique proves to be efficient when it comes to studying membrane proteins that are hard to crystallize like GPCR as it provides a higher degree of understanding of receptor-ligand interaction. We get profound insights on structurally unsolved, yet clinically important drug targeting proteins through single or multiple template modeling. The advantages of homology modeling studies are often used to overcome various problems in crystallizing GPCR proteins that are involved in major disease-related pathways, thus paving way to more structural insights via in silico models when there is a lack of experimentally solved structures. Owing to their pharmaceutical significance, structural analysis of various GPCR proteins using techniques like homology modeling is of utmost importance.

**Keywords:** membrane protein, bovine rhodopsin, template-based modeling, GPCR-EXP, GPCRdb

### **1. Introduction**

The comparative modeling of proteins, more popularly known as homology modeling among the research community, is a computational procedure that constructs three dimensional atomic resolution structure of a 'target' protein, the structure of it is unknown. A new structure for the target protein is modeled using its own amino acid sequence and a known experimental structure of a homologous protein as a template based upon which the model is constructed. This template-based modeling technique became a plausible computational technique because of the fact that evolutionary related proteins share a similar structure [1]. This undeniable truth led to the famous outbreak of using homology modeling to determine the three dimensional structure of proteins whose structures were otherwise difficult to solve.

One such family of protein that poses a great challenge to study is membrane proteins due to their partially flexibility and lack of stability. The surface of membrane proteins is also comparatively hydrophobic and can only be extracted from the cell membrane with detergents which cause challenges at many levels, including expression, solubilization, purification, crystallization, data collection and structure solution. **Figure 1** shows the total number of membrane protein structures deposited in PDB as of August 2020 and this data was derived from the mpstruc database [2]. There are 2037 published reports of membrane protein structures in this database. It is also very clear that the number of available membrane protein structures is very less compared to the expected exponential growth in the number of available structures [3]. Though approximately 25% of all proteins are membrane proteins, there are less solved structures available due to the difficulty in crystallizing membrane proteins.

Many advances are being made in developing novel methods that can help in solving and studying the structure of membrane proteins in a high-throughput manner. The key to overcome the membrane protein structural biology is the underlying fact that they are structurally homologous to proteins which are evolutionarily related to them. This kindled the structural biologists to try a large number of targets and homologs of each target so that at least a few proteins will show progress through all the steps associated with their structural studies. This is where computational techniques like homology modeling came to the aid of structural biologists in helping solve the structures of membrane proteins by obtaining the three dimensional structure of a target protein based on the similarity between template and target sequences. One arena of such membrane protein structural biology research that has proved to be promising is the G-protein-coupled receptors (GPCRs) which are the largest family of membrane proteins.

The GPCRs constitute a diverse family of proteins in mammalian genomes [4]. The first GPCR for which structure was determined was Rhodopsin, a prototypical class A GPCR. The GPCRs are categorized into five major classes based on their

#### **Figure 1.**

*The number of membrane protein structures deposited each year since the first structure was solved as given by the mpstruc database. The number of structures available is considerably low compared to the expected number of membrane protein structures (red line).*

**57**

studies of GPCRs.

*Importance of Homology Modeling for Predicting the Structures of GPCRs*

sequences as well as on their known or suspected functions in vertebrate: rhodopsin (family A), secretin (family B), glutamate (family C), adhesion and Frizzled/Taste2 [5]. The actual estimate of GPCRs in human genome is still being analyzed. The presence of seven transmembrane (7-TM) spanning α-helical segments separated by alternating intracellular and extracellular loop regions is one of the characteristic features in the structure of GPCRs. They also possess an extracellular N-terminus and an intracellular C-terminus which paved way for GPCRs to be also known as the 7-TM receptors or the heptahelical receptors. The tertiary structure of the GPCR resembles a barrel, with the seven transmembrane helices forming a cavity within the plasma membrane that serves as a ligand-binding domain. With its unique structure, the GPCRs serve many important roles in the human body. Hence the structure function correlation of GPCRs is a vital area of research even today.

The crystal structure of protein plays a pivot role in determining the functional importance of a protein. However membrane proteins are difficult to crystallize. Being a membrane protein, the GPCR structural studies have complexity because of low protein expression level in native tissues and heterologous systems. The poor protein stability and multiple conformational states of the receptors also are major hurdles in the GPCR structural studies. GPCRs have also been notoriously difficult to crystallize owing to their intrinsic flexibility and the above mentioned reasons [6]. For such special cases, homology modeling aids in developing three dimensional models of such proteins. This has been possible through the understanding about the structure of GPCRs facilitated by homology modeling. Since many of these receptors lack experimentally solved structures, in silico methods like homology modeling were applied to gain insights. Template structure with high homology was used for modeling the structures to gain more advance insights on their function. Approximately one-fifth of the total GPCRs structure are solved whereas the remaining GPCR structures can be predicted by homology modeling. Three dimensional model building with the help of template helps us to predict protein structural and functional domains which further aids in drug discovery. .This chapter deals with the contribution of homology modeling to the structural

**2. The importance and multifaceted functionality of GPCRs**

from the perspective of advanced structural research.

The importance of G-protein coupled receptors (GPCRs) in the fields of biology,

medicine and pharmaceutical studies have been extensively studied, well established and properly documented [7]. Due to its significance in playing a crucial role in various normal and pathological processes, GPCRs have become a major field of advanced research and a promising focus for drug discovery processes. The GPCRs have an extensive medical significance owing to their position and function within the human cell spanning the whole cell's plasma membrane. By this way it bridges the extra- and an intracellular environment which enables the GPCRs to act as signal transducers wherein it acclaims a direct mechanism for the transduction of extracellular messages into intracellular responses. In this way and together with their transmitters and effectors, GPCR systems function to modulate a broad spectrum of cellular phenomena dictated by the needs of the tissues and organs they serve. The gradient of GPCR distribution across vast majority of the body's organs and tissues and its primary role as signal transducers like converting transduce extracellular stimuli into intracellular signals at cellular levels makes it fascinating molecules

Other fascinating roles of GPCRs include modulation of neuronal firing, regulation of ion transport across the plasma membrane and within intracellular

*DOI: http://dx.doi.org/10.5772/intechopen.94402*

#### *Importance of Homology Modeling for Predicting the Structures of GPCRs DOI: http://dx.doi.org/10.5772/intechopen.94402*

*Homology Molecular Modeling - Perspectives and Applications*

to the difficulty in crystallizing membrane proteins.

(GPCRs) which are the largest family of membrane proteins.

from the cell membrane with detergents which cause challenges at many levels, including expression, solubilization, purification, crystallization, data collection and structure solution. **Figure 1** shows the total number of membrane protein structures deposited in PDB as of August 2020 and this data was derived from the mpstruc database [2]. There are 2037 published reports of membrane protein structures in this database. It is also very clear that the number of available membrane protein structures is very less compared to the expected exponential growth in the number of available structures [3]. Though approximately 25% of all proteins are membrane proteins, there are less solved structures available due

Many advances are being made in developing novel methods that can help in solving and studying the structure of membrane proteins in a high-throughput manner. The key to overcome the membrane protein structural biology is the underlying fact that they are structurally homologous to proteins which are evolutionarily related to them. This kindled the structural biologists to try a large number of targets and homologs of each target so that at least a few proteins will show progress through all the steps associated with their structural studies. This is where computational techniques like homology modeling came to the aid of structural biologists in helping solve the structures of membrane proteins by obtaining the three dimensional structure of a target protein based on the similarity between template and target sequences. One arena of such membrane protein structural biology research that has proved to be promising is the G-protein-coupled receptors

The GPCRs constitute a diverse family of proteins in mammalian genomes [4]. The first GPCR for which structure was determined was Rhodopsin, a prototypical class A GPCR. The GPCRs are categorized into five major classes based on their

*The number of membrane protein structures deposited each year since the first structure was solved as given by the mpstruc database. The number of structures available is considerably low compared to the expected number* 

**56**

**Figure 1.**

*of membrane protein structures (red line).*

sequences as well as on their known or suspected functions in vertebrate: rhodopsin (family A), secretin (family B), glutamate (family C), adhesion and Frizzled/Taste2 [5]. The actual estimate of GPCRs in human genome is still being analyzed. The presence of seven transmembrane (7-TM) spanning α-helical segments separated by alternating intracellular and extracellular loop regions is one of the characteristic features in the structure of GPCRs. They also possess an extracellular N-terminus and an intracellular C-terminus which paved way for GPCRs to be also known as the 7-TM receptors or the heptahelical receptors. The tertiary structure of the GPCR resembles a barrel, with the seven transmembrane helices forming a cavity within the plasma membrane that serves as a ligand-binding domain. With its unique structure, the GPCRs serve many important roles in the human body. Hence the structure function correlation of GPCRs is a vital area of research even today.

The crystal structure of protein plays a pivot role in determining the functional importance of a protein. However membrane proteins are difficult to crystallize. Being a membrane protein, the GPCR structural studies have complexity because of low protein expression level in native tissues and heterologous systems. The poor protein stability and multiple conformational states of the receptors also are major hurdles in the GPCR structural studies. GPCRs have also been notoriously difficult to crystallize owing to their intrinsic flexibility and the above mentioned reasons [6]. For such special cases, homology modeling aids in developing three dimensional models of such proteins. This has been possible through the understanding about the structure of GPCRs facilitated by homology modeling. Since many of these receptors lack experimentally solved structures, in silico methods like homology modeling were applied to gain insights. Template structure with high homology was used for modeling the structures to gain more advance insights on their function. Approximately one-fifth of the total GPCRs structure are solved whereas the remaining GPCR structures can be predicted by homology modeling. Three dimensional model building with the help of template helps us to predict protein structural and functional domains which further aids in drug discovery.

.This chapter deals with the contribution of homology modeling to the structural studies of GPCRs.
