Name: predicting protein ligand-binding pockets
Uploaded: 2020-11-23T11:47:34.000Z
Duration: 1 min 49 s
Channel: JoVE

K12 Standards

Tennessee Academic Standards

High School

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

BIO1.LS1.3

Conserved Binding Sites

Generally, ligand binding sites are located within specific amino acid clusters or domains, dedicated to a certain type of interaction.&#160;&#160;
Parts that are crucial to the function of a domain, such as ligand binding, remain unchanged during evolution because, as a rule, mutations that eliminate vital functions are eliminated by natural selection.&#160;
For instance, many nuclear proteins, including transcription factors, contain FF domains that bind to RNA polymerase II. These domains get their name from the two phenylalanine amino acids they contain on separate helices.&#160;
These phenylalanine amino acids, together with a few other highly-conserved amino acids form the hydrophobic core of the binding site.
Replacing these amino acids would disrupt the formation of this specific structure, hence affect its ability to bind to RNA polymerase II.&#160;
Scientists use evolutionary tracing to find conserved regions of domains. This is performed by comparing genome and protein sequences of similar domains and identifying the amino acids that remain unchanged.
Subsequent analyses of these related sequences allow identification of clusters formed by the conserved amino acids. These data can be used to create 3D models to determine the shapes of proteins as well as the optimal structures of their binding sites.
Analyzing conserved sequences and structures helps scientists understand evolutionary relationships between proteins but also allows them to predict binding sites of novel proteins containing comparable clusters.

conserved binding sites

Many proteins&#8217; biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein&#8217;s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the interaction energy of different amino acid residues with the ligand and predicts the ones where binding energy is at a minimum to be potential binding sites. However, examining conserved sequences is often used in conjunction with other methodologies to enhance this prediction further. Structurally conserved residues can be used to distinguish between binding sites and exposed protein surfaces. The amino acids, Trp, Phe, and Met, are highly conserved in binding sites, and no such conservation is observed in the case of exposed protein surfaces.
Various computational tools can predict binding sites using a mix of structural, energetic, and conserved binding site methodologies.&#160; ConCavity is a tool that can be used to predict 3D ligand-binding pockets and individual ligand-binding residues. The algorithm used directly integrates evolutionary sequence conservation estimates with structure-based prediction. Another tool, MONKEY, is used to identify conserved transcription-factor binding sites in multispecies alignments. It employs factor specificity and binding-site evolution models to compute the likelihood that putative sites are conserved and assign statistical significance to each prediction.

Many proteins&#8217; biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein ...

Education

JoVE Core

Molecular Biology

Unit 1

Protein Function

KEY TERMS AND CONCEPTS

predicting protein ligand-binding pockets

Protein ligand-binding pockets help explain how proteins work. A ligand is a small molecule that binds to a specific spot on a protein. These sites are often conserved in related proteins because they are important for function.

When the exact site on a protein surface is not known, it can be predicted. One approach is the energetic method. It examines how amino acid residues interact with the ligand and looks for positions where the binding energy is lowest. Those low-energy regions are likely binding sites.

Conserved sequence analysis can improve these predictions. Structurally conserved residues help separate true binding sites from exposed protein surfaces. In binding sites, amino acids such as Trp, Phe, and Met are often highly conserved. Exposed protein surfaces do not show the same conservation pattern.

Computational tools combine these ideas to find binding sites more accurately. ConCavity predicts 3D ligand-binding pockets and individual binding residues by combining evolutionary sequence conservation with structure-based prediction. MONKEY is used for conserved transcription-factor binding sites in multispecies alignments. It uses factor specificity and binding-site evolution models to estimate how likely a site is conserved and to assign statistical significance to each prediction.

Predicting Protein Ligand-Binding Pockets

predicting-protein-ligand-binding-pockets

ligand binding sites

How Ligands Attach to Proteins

Ligands attach to proteins at specific binding sites on the protein surface. These sites let proteins interact with other molecules or ions and help them carry out important cell functions. Although many possible ligands may be nearby, only a matching ligand can bind to a given protein. A ligand-binding site has a shape and chemical pattern that fit its ligand. This fit comes from the protein’s amino acid chain, which gives the site its structure and reactivity. The ligand stays in place...

protein-protein interfaces

How Proteins Connect to Form Complexes

Proteins connect with other proteins to form complexes that carry out cell functions. These protein-protein interactions, or PPIs, are important for an organism's survival. Most PPIs are held together by many weak, noncovalent chemical forces rather than one strong bond. The shape of the interaction surface helps determine how two proteins fit together. Many globular proteins have surface shapes that match closely and can form many weak bonds. Other PPIs happen between two helices or between a...

Protein ligand-binding pockets help explain how proteins work. A ligand is a small molecule that binds to a specific spot on a protein. These sites are often conserved in related proteins because they are important for function. When the exact site on a protein surface is not known, it can be predicted. One approach is the energetic method. It examines how amino acid residues interact with the ligand and looks for positions where the binding energy is lowest. Those low-energy regions are...

the equilibrium binding constant and binding strength

the-equilibrium-binding-constant-and-binding-strength

Measuring Protein-Ligand Binding Strength

Protein-ligand binding strength can be measured with the equilibrium binding constant, Kb. This value describes how strongly a protein binds a ligand when the reaction has reached equilibrium. In a bound complex, the protein and ligand are joined as PL, while P and L are the unbound forms. Kb can be determined in two main ways. One approach uses equilibrium concentrations. The other uses reaction kinetics, which are the rates of binding and unbinding. Kb can also be related to the binding rate...

cofactors and coenzymes

Protein Helpers: Cofactors and Coenzymes

Cofactors and coenzymes help enzymes work. Many enzymes need these helper molecules to carry out chemical reactions. Without them, the enzyme may not function properly. A cofactor is a helper molecule that can be either an inorganic ion or an organic molecule. Coenzymes are organic cofactors. They often move between enzymes and help transfer chemical groups or electrons during a reaction. Some cofactors are vitamins or come from vitamins. These molecules are important because they support...

allosteric regulation

How Allosteric Control Changes Enzymes

Allosteric control changes how enzymes work by using a site other than the active site. A small molecule binds to this separate allosteric site and changes the enzyme’s shape. That shape change can alter how well the enzyme binds its substrate and how fast the reaction runs. Many enzymes use this kind of regulation to turn activity up or down when the cell needs it. In some cases, the allosteric molecule acts as an activator and improves enzyme function. In other cases, it acts as an inhibitor...

ligand binding and linkage

Allosteric Proteins: Positive and Negative Effects

Allosteric proteins have more than one ligand binding site. A ligand is a molecule that binds to a protein. When a ligand binds at one site, it can affect binding at the other sites. These sites are called coupled or linked because they influence one another. In enzymes, the site that binds the substrate is the active site. The other site is the regulatory site. When a ligand binds to the regulatory site, it can change the protein’s shape. This conformational change can then alter how the...

cooperative allosteric transitions

Allosteric Switching in Multimeric Proteins

Allosteric switching in multimeric proteins helps explain how ligand binding at one site can change the behavior of the whole protein. In these proteins, each subunit has its own ligand-binding site. When a ligand binds to one subunit, it can cause a shape change that affects the other subunits and their binding sites. This change in shape comes from the protein’s structure, which includes both flexible and stable segments. A molecule that causes the shift is called a modulator. Because the...

phosphorylation

Phosphorylation in Cell Signaling

Phosphorylation is a key step in cell signaling. It changes how a molecule behaves by adding a phosphate group. In many cells, this modification helps control activity, shape, and interactions with other molecules. Phosphorylation is carried out by enzymes called kinases. These enzymes transfer a phosphate group to a target molecule. A phosphatase can remove that phosphate group and reverse the change. Together, kinases and phosphatases help cells turn signals on and off in a controlled way. <br...

protein kinases and phosphatases

Phosphorylation Switches in Protein Control

Protein control often depends on chemical changes that alter a protein’s charge, shape, and conformation. These changes can include phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis. In cells, these modifications are usually driven by enzymes. Phosphorylation is one of the most important protein modifications. It adds a phosphate group to a protein and often changes how that protein works. A family of enzymes called kinases...

gtpases and their regulation

GTPase Signaling Switches in Cells

GTPases are cell proteins that act as signaling switches. They help control cell signaling, vesicle transport, cell shape, and cell movement. When these proteins change or stop working properly, disease can result. There are about 40,000 known G-proteins. They are usually grouped into two main types. Small G-proteins have one domain, while large G-proteins have multiple domains. Large G-proteins are also called heterotrimeric G-proteins. They have three subunits: alpha, beta, and gamma. The...

covalently linked protein regulators

How Protein Tags Change Cell Signaling

Proteins can be changed after they are made by adding small chemical tags or small proteins. These post-translational modifications help control protein function and stability when the cell environment changes. Common covalent regulators include methyl, acetyl, and phosphate groups, as well as small proteins such as ubiquitin. About 200 types of covalent regulators have been identified. These tags attach to specific amino acids in a protein. Phosphate groups can attach only to serine,...

protein complexes with interchangeable parts

protein-complexes-with-interchangeable-parts

SCF Ubiquitin Ligase and F-Box Variants

The SCF ubiquitin ligase is a protein complex that uses an F-box protein to help choose which target proteins get marked for destruction. This complex is made of five separate proteins, and each one has a different job. Together, they attach ubiquitin to target proteins so the cell can send those proteins to be degraded. The F-box protein is the part that binds the substrate, or target protein. That binding step lets the ubiquitin-conjugating enzyme reach the target and attach ubiquitin. In...

mechanical protein functions

Protein Force: Cell Movement and Support

Proteins can create and respond to mechanical force in cells. Some proteins generate force, while others are pulled or stretched by it. Proteins such as keratin provide structural support and are subjected to mechanical force. Proteins such as ion pumps help move molecules across cell membranes and can generate mechanical force. Cell movement and muscle contraction depend on turning chemical energy into motion. This often happens through conformational change, which is a shift in a protein’s...

structural protein function

Collagen and the Cell Skeleton

Structural proteins give cells and tissues shape, support, and strength. They help build bones, cartilage, hair, and muscles. Important examples include collagen, actin, myosin, and keratin. Collagen is the most abundant protein in mammals. It is found throughout the body. In skin, ligaments, and tendons, collagen adds tensile strength and elasticity. In bones and teeth, it helps form hard, load-bearing tissue through mineralization. Collagen also does more than provide support. It can...

protein networks

Mapping Protein Interactions

Mapping protein interactions shows how proteins work together in a cell. Many proteins must connect with other proteins to carry out their jobs and keep an organism healthy. These connections can be shown as protein-protein interaction networks, also called protein maps. In these maps, proteins are shown as nodes, or circles. Lines called edges connect two proteins that interact. The network can include stable interactions, such as those in protein complexes, and transient interactions that...

allosteric proteins-atcase

ATCase Feedback Inhibition in Pyrimidine Synthesis

ATCase is a key enzyme in pyrimidine synthesis. It is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl-L-aspartate. This reaction starts the pathway that makes pyrimidines. ATCase is regulated by feedback inhibition. The end products UTP and CTP bind to the enzyme and reduce its activity when pyrimidine levels are high compared with purines in the cell. This binding at one site affects the linked catalytic site, which helps keep...

key terms and concepts

Learn how conserved residues, energy models, and tools like ConCavity and MONKEY help predict protein ligand-binding pockets and binding sites.

Predicting Protein Ligand-Binding Pockets | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

Arizona Science Standards

Life Science

HS+B.L1

HS+B.L1U1.5

Characteristics of Life

Biology is a natural science that studies life and living organisms, including their structure, function, development, interactions, evolution, ...

https://cloudfront.jove.com/files/media/science-education/science-education-thumbs/10647.jpg

Levels of Organization

Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth&#x27;s biosphere. ...

the-tree-of-life-bacteria-archaea-and-eukaryotes

The Tree of Life - Bacteria, Archaea, and Eukaryotes

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains &#8212; Archaea and Bacteria. Bacteria include many common microorganisms, such as ...

Introduction to Virus

Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic ...

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. ...

Compare and contrast existing models, identify patterns, and use structural and functional evidence to analyze the characteristics of life. Engage in argument about the designation of viruses as non-living based on these characteristics.
EXPLANATION: Students begin to develop patterns of living and non-living organisms in kindergarten and build on detailed characteristics of different classifications of living organisms throughout elementary and middle school. Biology 1 discussions introduce viral particles and viral cycles, building on student understanding of living organisms to engage in an argument regarding the classification of a viral particle as either living or non-living.

BIO1.LS1.1

What are Cells?

Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium, or trillions of them, ...

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry ...

Eukaryotic Evolution

The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the ...

Animal and Plant Cell Structure

Animal and plant cells not only differ in their structure, function, and mode of nutrition but also in how they reproduce, specialize, and organize into ...

Evaluate comparative models of various cell types with a focus on organic molecules that make up cellular structures.
EXPLANATION: Students explicitly discuss the structure and function of major cellular organelles in seventh grade. Building on this understanding, Biology I students should shift their focus to the different types of cells found in organisms and how the role of each cell type relates to its composition and the prevalence of different organelles within that cell. An example might include the absence (or enucleation) of the nucleus in red blood cells in mammals providing for increased levels of oxygen transport in organisms or the lack of centrioles in most neurons. Varying cell types can include both prokaryotic and eukaryotic cell types.

BIO1.LS1.2

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and carry instructions for its ...

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA ...

DNA Base Pairing

Erwin Chargaff&#x2019;s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff&#x2019;s rules state that in a ...

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between ...

DNA Packaging

Overview

Eukaryotes have large genomes compared to prokaryotes. In order to fit their genomes into a cell, eukaryotes must pack their DNA tightly inside ...

Organization of Genes

Overview

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. ...

Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by ...

Replication in Prokaryotes

Overview

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to ...

Replication in Eukaryotes

Overview

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high ...

Mutations

Overview

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. ...

Transcription

Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene ...

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following ...

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form ...

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations ...

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or ...

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs ...

MicroRNAs

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional ...

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while ...

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect ...

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding ...

What are Proteins?

Protein Organization

Protein Folding

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein ...

conservation-of-protein-domains-over-different-proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.&#160; Although these domains are often structurally ...

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular ...

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows ...

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.&#160; Most protein complexes ...

Conjugated Proteins

Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with ...

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein&#39;s function.&#160; For example, enzyme activity is often regulated through a feedback mechanism where the ...

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.&#160; Under most circumstances, misfolded proteins are either refolded by chaperone proteins or ...

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand ...

Antibody Structure

Phosphorylation

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their ...

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, ...

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism&#39;s survival. Most PPIs ...

GTPases and their Regulation

Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell ...

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an ...

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at ...

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex&#8217;s function. ...

Cofactors and Coenzymes

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical ...

Allosteric Regulation

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures ...

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other ...

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other ...

Integrate evidence to develop a structural model of a DNA molecule. Using the model, develop and communicate an explanation for how DNA serves as a template for self-replication and encodes biological information.
EXPLANATION: Discussions of DNA in earlier grades have been limited to discussions of genes and the role of genes in the appearance and activities of an organism. Biology 1 represents a student's introduction to a molecular model of a DNA as well as the organization of DNA into genes and genes subsequently into chromosomes. Students should address interactions between genes in proteins which regulate both the shape and reproduction of DNA molecules. It is important to note that not all segments of DNA are transcribed for proteins. Portions of DNA are involved in regulating the expression of genes or affect the structure of the chromosomes (replication origin, centromeres, and telomeres).

What is the Cell Cycle?

The cell cycle refers to the sequence of events occurring throughout a typical cell&#8217;s life. In eukaryotic cells, the somatic cell cycle has two ...

Interphase

The cell cycle occurs over approximately 24 hours (in a typical human cell) and in two distinct stages: interphase, which includes three phases of the ...

Create a model for the major events of the eukaryotic cell cycle, including mitosis. Compare and contrast the rates of cell division in various eukaryotic cell types in multicellular organisms.
EXPLANATION: Students first discuss mitosis in seventh grade, specifically focusing on the role of mitosis in creating genetically identical daughter cells. Biology 1 discussions should connect a student's understanding of gene expression and protein function with the process of mitosis to explore the differentiation of cell types from otherwise identical daughter cells. Discussions should also include varying rates of mitotic division and the relationship between these rates of division and the function of specific cell types within eukaryotic organisms. Examples may include the extremely limited use of mitosis by neurons due to their interconnectedness within neural networks or the rapid rates of mitosis with growing root tips.

BIO1.LS1.6

Predicting Protein Ligand-Binding Pockets

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