Name: protein families and superfamilies
Uploaded: 2023-04-30T18:28:42.000Z
Duration: 2 min 47 s
Channel: JoVE

K12 Standards

Next Generation Science Standards

High School

Life Science

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

From Molecules to Organisms: Structures and Processes

HS-LS1-1

Protein Families

A protein family is a group of proteins that have evolved from a common genetic ancestor.&#160; These proteins have similarities in their three-dimensional structures and the functions they perform.&#160;&#160;
Proteins within a family are called homologs.&#160;&#160;
Orthologs are homologous proteins in different species that evolved from the same protein in a common ancestor. Generally, orthologous proteins perform similar functions in the different species.
Alpha hemoglobin in humans and alpha hemoglobin in mice are orthologous proteins. In contrast, paralogs are homologous proteins produced by gene duplication and can be present in the same or different species. Alpha and beta hemoglobin in humans are paralogous proteins.
A superfamily is composed of two or more families that have evolved from a more distant common ancestor than that of a protein family. Proteins in a superfamily have larger variations in structure and function.
Protein families can help us make a hypothesis about the function of a protein with a known amino acid sequence, but unknown shape or function. These proteins can be compared to other proteins in the family to help predict the three-dimensional structure and help determine the

protein families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.&#160;&#160; Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.&#160;&#160; If these new proteins contain similar amino acids in key locations, protein domains, and possibly the overall three-dimensional structure, can remain similar.&#160;&#160; Proteins within a family can have as low as 30% amino acid sequence homology but still perform related functions.
Protein Superfamilies
Protein superfamilies are larger groups of proteins that have evolved from a more distant ancestor. They generally have lower sequence homology as compared to a protein family but still have significant structural features in common. Each superfamily can contain several protein families with more closely related structures and functions.&#160; Some larger families are even further divided into sub-families.&#160; The exact distinction as to whether proteins belong to a superfamily, family, or subfamily can vary between classification systems and is still changing as the amount of protein sequence and structural data continues to grow.
The immunoglobulin protein superfamily (IgSF) is one of the largest protein superfamilies; over 700 superfamily members are found in the human genome.&#160; All members of the superfamily contain one or more immunoglobulin (Ig) domains. This domain has a unique three-dimensional structure composed of a sandwich of two anti-parallel beta-sheets, and most are involved in cell adhesion or ligand binding. The IgSF contains many families including antigen receptors, cell adhesion molecules (CAMs), cytoskeletal proteins, and several growth-factor and cytokine receptor groups. Several of the larger families are further divided into subfamilies.&#160;&#160; The antigen receptor family can be further divided into subfamilies: the antibody or immunoglobulin family and the T- cell receptor family; the CAMs can be divided into the NCAM, ICAM, and CD2 related protein families.
Classification Databases
Protein family classifications allow scientists to understand functional and evolutionary relationships between proteins. Several online resources can be used to search for known protein families or classify newly discovered proteins.&#160; Pfam is one of several online databases where a scientist can search for known proteins and their family members.&#160; A researcher can also enter the amino acid sequence of a newly discovered protein to see if it might belong to a known family of proteins due to sequence similarity.&#160; This can provide a testable hypothesis as to the possible role of the novel protein as&#160; family members often have similar structures and functions.

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

Education

JoVE Core

Cell Biology

Unit 1

Protein Structure

KEY TERMS AND CONCEPTS

protein families and superfamilies

Protein families and superfamilies group proteins with shared features. These groups help scientists organize proteins by common structure, function, or evolutionary history. The classification can show how related proteins are connected across different organisms.

A protein family usually includes proteins that are closely related. A superfamily is a broader group that can include several families with more distant relationships. These categories help explain why some proteins share similar shapes or roles even when they are not identical.

Researchers use protein families and superfamilies to compare proteins and study how they evolved. This approach is useful for tracking conserved features, which are parts that remain similar over time. It also helps scientists build clearer databases for protein research.

Protein Families and Superfamilies

what are proteins?

Protein Building Blocks and Folding

Proteins are built from amino acids linked by peptide bonds. Long chains of amino acids are often called polypeptides, and the terms proteins and polypeptides are sometimes used the same way. In this context, polypeptides with a molecular weight below 10,000 daltons are called polypeptides, while proteins have a higher molecular weight. Very short chains with fewer than 20 amino acids are called peptides or oligopeptides. Amino acids are the basic units of proteins. Each amino acid has a...

protein organization

Protein Folding Levels and Bonds

Proteins are built from amino acids and folded into shapes that support many cell jobs. They help with DNA replication, molecular transport, catalysis, and structural support. Their function depends on how their amino acids are arranged and folded. Protein structure is organized in levels. The primary structure is the amino acid sequence in a polypeptide chain. Amino acids are joined by peptide bonds, and the chain has two ends: the amino terminus, or N-terminus, and the carboxyl terminus, or...

protein folding

How Amino Acid Sequence Shapes Proteins

Proteins get their shape from the order of amino acids in a polypeptide chain. After a protein is made, the chain folds into a three-dimensional form that is needed for it to work. The way amino acids interact with one another guides this folding. Protein structure matters because proteins do many jobs in cells. They can speed up chemical reactions, help with immune defense, store materials, carry substances, send cell signals, support movement, and provide structure. A protein usually works...

Protein families and superfamilies group proteins with shared features. These groups help scientists organize proteins by common structure, function, or evolutionary history. The classification can show how related proteins are connected across different organisms. A protein family usually includes proteins that are closely related. A superfamily is a broader group that can include several families with more distant relationships. These categories help explain why some proteins share similar...

conservation of protein domains

Protein Domains Shared Across Proteins

Protein domains are shared structural and functional parts of proteins. A domain is a region that can often be found in more than one protein, even when the full proteins are different. This conservation means that a protein domain may keep a similar shape or role across related proteins. Because of that, scientists can compare proteins by looking for domains that stay the same. Conserved domains help reveal how proteins are related and how they may work. The topic of protein domain...

globular and fibrous proteins

Protein Shapes: Globular vs Fibrous

Proteins can have globular or fibrous shapes, and these shapes help explain how they work in the body. Globular proteins are compact and usually fold into rounded forms. Fibrous proteins are long, extended molecules that often provide support and structure. The shape of a protein is tied to its function. Globular proteins often take part in chemical jobs in cells, while fibrous proteins are better suited for strength and stability. These structural differences make the two groups easy to...

intrinsically disordered proteins

Flexible Protein Regions and Disorder

Intrinsically disordered proteins have flexible regions that do not settle into one fixed shape. Instead, these proteins can remain dynamic and change form as they move through the cell. This flexibility is an important part of their structure and function. Many proteins need a stable folded shape to work properly. Intrinsically disordered proteins are different because they may lack a single rigid structure under normal conditions. Their shifting shape can help them take part in cell...

protein complex assembly

Protein Complex Formation and Function

Protein complex formation explains how proteins join together to carry out specific jobs in cells. These groups are called protein complexes, and they can form in more than one way. Some complexes are homomeric, which means they contain the same kind of protein subunit. Others are heteromeric, which means they contain different protein subunits. The assembly process helps show how protein shape and subunit choice affect function. When proteins combine, the resulting complex can behave...

conjugated proteins

Conjugated Proteins and Their Bound Groups

Conjugated proteins are proteins that include a nonprotein part called a prosthetic group. This added group helps give the protein its full structure or function. The video explains how the protein part and the bound group work together. Several common types of conjugated proteins are named by the kind of group attached. Nucleoproteins contain nucleic acids. Glycoproteins contain carbohydrate groups, and lipoproteins contain lipid groups. Other examples include phosphoproteins, which have...

amyloid fibrils

Amyloid Fibrils and Protein Aggregation

Amyloid fibrils are protein aggregates with a very specific structure. They are made when proteins misfold and stick together in long, ordered fibers. This structure makes them different from many other protein clumps. Amyloid fibrils are important in biology because they are linked to protein aggregation. Protein aggregation means proteins build up into groups instead of staying properly folded and separate. In many cases, this process is associated with disease and abnormal cell function. <br...

key terms and concepts

Explore how protein families and superfamilies group related proteins by structure, function, and evolution for high school biology students.

Protein Families and Superfamilies | JoVE K12

cell biology

JoVE Core Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

Characteristics of Life

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Cell Structure

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The Central Dogma

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Conservation of Protein Domains

Transcription

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Globular and Fibrous Proteins

Translation

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Intrinsically Disordered Proteins

Ribosomes

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Protein Complex Assembly

Protein and Protein Structures

Conjugated Proteins

Proteins: From Genes to Degradation

Amyloid Fibrils

What are Proteins?

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Ligand Binding Sites

Protein Organization

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Protein-Protein Interfaces

Protein Folding

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Conserved Binding Sites

Cofactors and Coenzymes

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Cooperative Allosteric Transitions

Protein Kinases and Phosphatases

GTPases and their Regulation

Covalently Linked Protein Regulators

protein-complexes-with-interchangeable-parts

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Structural Protein Function

Protein Networks

Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells. [Assessment Boundary: Assessment does not include identification of specific cell or tissue types, whole body systems, specific protein structures and functions, or the biochemistry of protein synthesis.]

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The Parasympathetic Nervous System

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Homeostasis
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HS-LS1-2

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HS-LS1-3

Protein Families and Superfamilies

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