Name: protein binding surfaces and contacts
Uploaded: 2023-04-30T18:28:43.000Z
Duration: 2 min 4 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-Protein Interfaces

תהליכים ביולוגיים רבים תלויים באינטראקציות חלבון-חלבון. למעשה, מספר רב של חלבונים צריכים ליצור מתחמי חלבון או אוליגומרים כדי לבצע את תפקידיהם.
לפעמים, שני חלבונים זהים או יותר יוצרים קומפלקס, כגון דימר קינזין זה. במקרים אחרים, חלבונים או פוליפפטידים שונים מתאחדים ליצירת יחידה פונקציונלית. 
לדוגמה, מיקרוטובולים cytoskeletal מורכב דימרים אלפא ובטא tubulin. למשטחי הקישור של מונומרים אלפא ובטא-טובולין יש צורות משלימות. 
צורות תואמות אלה מאפשרות למונומרים ליצור מספר רב של קשרים לא קוולנטיים זה עם זה, אשר לאחר מכן מחזיקים את אלפא ובטא-טובולין יחד. סוג זה של ממשק הוא דוגמה לאינטראקציה בין פני השטח למשטח.
בדומה לאתרי קשירת ליגנדים, אינטראקציות בממשק חלבון-חלבון עשויות לכלול קשרים לא קוולנטיים וכוחות הידרופוביים. עם זאת, קשרים דיסולפידים קוולנטיים בין חומצות אמינו ציסטאין על כל משטח חלבון עשויים גם לשחק תפקיד לשמור אותם יחד.
עם זאת, לא כל ממשקי החלבונים כוללים משטחים תואמים זה לזה. לדוגמה, אנזימים רבים, כגון חלבון קינאז A כאן, יוצרים שסע שיכול לזהות ולקשור לולאות פוליפפטיד של שותפיהם הקושרים. סוג זה של ממשק ידוע בשם אינטראקציה משטח-מחרוזת.
סוג אחר של ממשק, המכונה סליל-סליל, או אינטראקציית סליל-סליל, נוצר כאשר סלילים של שני חלבונים עוטפים זה את זה. ממשק זה נצפה לעתים קרובות בחלבונים המכילים תחומי רוכסן לאוצין כגון גורמי שעתוק אאוקריוטיים.
לסיכום, המבנה הפיזיקלי והתכונות הכימיות של החלקים המקיימים אינטראקציה קובעים את סוג הממשק בין שני חלבונים.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. ניתוח רשתות אינטראקציה חלבון-חלבון. כתב עת למחקר פרוטאום. אפריל 2012; 11(4):2014-2031.</li>
	<li>Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. התגברות על אתגרים כימיים, ביולוגיים וחישוביים בפיתוח מעכבים המכוונים לאינטראקציות חלבון-חלבון. כימיה ביול. 2015; 22(6):689–703.</li>
	<li>De Las Rivas J, Fontanillo C. יסודות אינטראקציות חלבון-חלבון: מושגי מפתח לבנייה וניתוח של רשתות אינטראקטומיות. PLoS Comput Biol. 2010; 6(6):e1000807.</li>
	<li>Lalonde S, Ehrhardt DW, Loqué D, חן J, Rhee SY, פרומר WB. גישות מולקולריות ותאיות לזיהוי אינטראקציות חלבון-חלבון: הטכניקות העדכניות ביותר והמגבלות הנוכחיות. צמח J. 2008 פברואר; 53(4):610-35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. חיזוי אתר קשירה לאינטראקציות חלבון-חלבון וגילוי מוטיב חדש באמצעות רצפי פוליפפטידים חוזרים. BMC ביואינפורמטיקה. 2011;12:225. פורסם 2011 יונ 2.</li>
</ol>

ממשקי חלבון-חלבון

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חלבונים רבים יוצרים קומפלקסים לביצוע תפקידיהם, מה שהופך אינטראקציות חלבון-חלבון (PPIs) לחיוניות להישרדות האורגניזם. רוב PPIs מיוצבים על ידי כוחות כימיים לא קוולנטיים רבים. הצורה הפיזית של הממשקים קובעת את האופן שבו שני חלבונים מתקשרים. לחלבונים כדוריים רבים יש צורות תואמות על פני השטח שלהם, היוצרים מספר רב של קשרים חלשים. בנוסף, PPIs רבים מתרחשים בין שני סלילים או בין שסע משטח לשרשרת או מחרוזת פוליפפטידים.

שיטות חישוביות וביוכימיות שונות משמשות לחקר ממשקי חלבון. ניתן להשתמש בשיטות מעבדה, כגון טיהור זיקה, ספקטרומטריית מסה ומיקרו-מערכי חלבון, כדי לזהות אינטראקציות חדשות. שילוב אימוני של חלבונים והקרנה דו-היברידית של שמרים נמצאים בשימוש נרחב כדי לספק ראיות לגבי האם שני חלבונים מקיימים אינטראקציה במבחנה. תוכנות מחשב יכולות לחזות PPIsPPI על סמך אינטראקציות דומות שנמצאות בחלבונים אחרים על ידי השוואת רצפי חלבונים ומבנים תלת מימדיים. גישות חישוביות אחרות, כגון פרופיל פילוגנטי, מנבאות PPIsPPI על סמך האבולוציה המשותפת של שותפים מחייבים. בנוסף, ניתוח היתוך גנים משמש לניבוי שותפי אינטראקציה על ידי מציאת זוגות חלבונים המאוחדים בגנום של אורגניזמים אחרים.

חלבונים בדרך כלל מקיימים אינטראקציה עם מספר שותפים או באותו זמן או בזמנים שונים, והם עשויים להכיל יותר מממשק אינטראקציה אחד. חלבונים רבים יוצרים קומפלקסים גדולים המבצעים פונקציות ספציפיות שיכולות להתבצע רק על ידי הקומפלקס השלם. במקרים מסוימים, אינטראקציות חלבון אלו מוסדרות; כלומר, חלבון עשוי לקיים אינטראקציה עם שותפים שונים על בסיס צרכים תאיים. ניתוחים חישוביים וסטטיסטיים נוספים ממיינים אינטראקציות כאלה לרשתות, אשר נאצרות במאגרי הנתונים של אינטראקטום. מאגרי נתונים אלה הניתנים לחיפוש מאפשרים למשתמשים ללמוד אינטראקציות חלבון ספציפיות, כמו גם לעצב תרופות שיכולות לשפר או לשבש אינטראקציות בממשק.

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חלבונים רבים יוצרים קומפלקסים כדי לבצע את תפקידיהם, מה שהופך אינטראקציות חלבון-חלבון (PPIs) חיוניות להישרדות האורגניזם. רוב ה- PPI ...

Education

JoVE Core

Cell Biology

ביולוגיה של התא

Unit 1

יחידה 1

Protein Function

תפקוד חלבונים

KEY TERMS AND CONCEPTS

מונחים ומושגים מרכזיים

protein binding surfaces and contacts

Protein binding surfaces and contacts help proteins recognize and attach to each other. These interfaces are the regions where two proteins meet and interact. They are important for many cell processes and for how proteins work together.

A protein-protein interface is not just a random touch point. It is shaped by the three-dimensional form of each protein. The matching surfaces allow a stable interaction to form when the proteins fit together well.

Studying these interfaces helps explain how protein complexes form. It also helps scientists understand why some proteins bind strongly while others do not. This knowledge is useful for linking protein structure to protein function.

Protein Binding Surfaces and Contacts

ligand binding sites

Ligand Binding Sites in Proteins

Ligand binding sites are specific parts of a protein where a ligand can attach. A ligand is a molecule that binds to another molecule, often to help start or change a biological process. These sites matter because the shape and chemistry of the protein help determine which ligands can fit and bind. Proteins do not bind every ligand in the same way. The binding site provides a matching surface that supports a close interaction. In many cases, this interaction is important for how cells respond...

protein-protein interfaces

Protein binding surfaces and contacts help proteins recognize and attach to each other. These interfaces are the regions where two proteins meet and interact. They are important for many cell processes and for how proteins work together. A protein-protein interface is not just a random touch point. It is shaped by the three-dimensional form of each protein. The matching surfaces allow a stable interaction to form when the proteins fit together well. Studying these interfaces helps explain how...

conserved binding sites

Conserved Binding Sites in Protein Families

Conserved binding sites are regions on proteins that stay similar across related proteins. These shared areas often help proteins interact with the same molecules. For this reason, they are useful clues when comparing protein families. A conserved site can help identify where a protein binds. It can also show which parts of the protein are important for function. When the same pattern appears in several proteins, it suggests that the site has been kept through evolution. Scientists look at...

cofactors and coenzymes

Enzyme Helpers: Metals and Vitamins

Enzyme helpers include cofactors and coenzymes. Enzymes are proteins made of amino acids, and the functional groups on those amino acids can drive many chemical reactions through ionic interactions or acid-base reactions. But amino acids alone cannot handle oxidation-reduction and group transfer reactions, so they need non-protein helpers called cofactors. Cofactors are often described as the chemical teeth of an enzyme. They can be metal ions or organic molecules called coenzymes. These...

cooperative allosteric transitions

Allosteric Changes in Protein Shape

Allosteric changes in protein shape help explain how some proteins switch between active and inactive states. These transitions are cooperative, which means a change in one part of the protein can affect other parts of the same molecule. The video focuses on how these shifts in shape support protein function. It also shows that allosteric transitions can be described with different models. In the concerted model, the protein changes shape as a whole. In the sequential model, the change happens...

protein kinases and phosphatases

Protein Kinases and Phosphatases in Cell Control

Protein kinases and phosphatases help control how proteins work in cells. Kinases add phosphate groups to proteins. Phosphatases remove those phosphate groups. This phosphorylation and dephosphorylation process can change a protein’s shape and activity. It is one way cells turn protein function on or off at the right time. These changes also help cells respond to signals and manage many cell activities. Together, protein kinases and phosphatases keep cellular signaling balanced. When one adds...

gtpases and their regulation

GTPase Molecular Switches and Control

GTPases are molecular switches that help control cell activity. They bind guanosine triphosphate, or GTP, and can change between active and inactive states. This switch-like behavior makes them important in many cell processes. The protein is active when GTP is bound and inactive when guanosine diphosphate, or GDP, is bound. GTPases can also turn themselves off by breaking down GTP into GDP. This built-in control helps cells regulate when the protein is on or off. Their activity is regulated...

covalently linked protein regulators

Protein Regulation by Covalent Bonds

Protein regulation by covalent bonds helps control how cells respond to changing conditions. A covalent bond is a strong chemical link, and in this context it can change how a protein behaves. Some regulators work by attaching a chemical group directly to a protein. This covalent change can alter the protein's activity, its location in the cell, or how long it stays active. Because the change is built into the protein itself, it can have a strong effect on cell function. Covalently linked...

protein complexes with interchangeable parts

protein-complexes-with-interchangeable-parts

Modular Protein Complexes in Cells

Protein complexes in cells can be built from interchangeable parts. This modular design lets some complexes share common subunits while still changing their behavior. A well-known example is the ubiquitin ligase complex called SCF. SCF stands for Skp1-Cullin-F-box, and it helps attach ubiquitin, a small protein tag, to target proteins. The core of SCF stays the same, but the F-box protein can change. The interchangeable F-box subunit gives the complex its specificity. Different F-box proteins...

mechanical protein function

Proteins That Generate Cell Movement

Mechanical proteins help cells and tissues move. They turn chemical energy into force and motion. This process is important in many biological systems. These proteins are also called motor proteins. They interact with cell structures and can produce directed movement. In muscle cells, they support contraction. In other cells, they help with transport and shape changes. Mechanical protein function is a key part of how living systems work. It links protein activity to movement at the cellular...

structural protein function

Structural Proteins in Cells and Tissues

Structural proteins help cells and tissues keep their shape and strength. They are an important part of living systems because they provide support where it is needed most. Many structural proteins form fibers or other sturdy forms that resist stretching and wear. These proteins work as building materials in the body and help keep structures stable over time. Examples of structural proteins include collagen, actin, myosin, and keratin. Each one supports a different part of the body, but all...

protein networks

Mapping Protein Interaction Networks

Protein interaction networks show how proteins work together inside a cell. These networks help scientists see which proteins connect with each other and how those links support cell activity. Researchers often use online tools to build and study these networks. The transcript points to IntAct and STRING as examples of resources that can help predict and organize protein interactions. These tools make it easier to compare protein links and look for patterns in the network. Protein networks...

key terms and concepts

Learn how protein binding surfaces and contacts let proteins recognize each other, form complexes, and support cell function in a clear high school science format.

Protein Binding Surfaces and Contacts | 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

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

Cell Structure

Background
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Visualizing Onion and Cheek Cells
ExpandImmediately before the experiment, wash and peel onion bulbs for the class.
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Cytoplasm

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The Nucleus

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The Central Dogma

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Nucleic Acids

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Chromosome Structure

Base-pairing and DNA Repair

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RNA Structure

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Protein Families

Types of RNA

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

Conservation of Protein Domains

Transcription

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

Globular and Fibrous Proteins

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes ...

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?

Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino ...

Ligand Binding Sites

Protein Organization

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Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to ...

Conserved Binding Sites

Cofactors and Coenzymes

Enzymes are proteins made of amino acids. The functional group of each constituent amino acid catalyzes a wide variety of chemical reactions via ionic ...

Cooperative Allosteric Transitions

Protein Kinases and Phosphatases

GTPases and their Regulation

Covalently Linked Protein Regulators

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.]

Levels of Organization

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Animal and Plant Cell Structure

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structural-organization-of-the-human-body-an-overview

Structural Organization of the Human Body: An Overview

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Overview of Human Digestion

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Anatomy of the Intestines

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Accessory Organs

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Lipid Digestion

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Protein Digestion

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Carbohydrate Digestion

Carbohydrate digestion and metabolism break down simple and complex carbohydrates from food into saccharides (i.e., sugars) for the body to use as energy. ...

What is a Nervous System?

Overview

The nervous system is the collection of specialized cells responsible for maintaining an organism&rsquo;s internal environment and coordinating ...

The Parasympathetic Nervous System

Overview

The parasympathetic nervous system is one of the two major divisions of the autonomic nervous system. This parasympathetic system is responsible ...

The Sympathetic Nervous System

Overview

The sympathetic nervous system&mdash;one of the two major divisions of the autonomic nervous system&mdash;is activated in times of stress. It ...

Oogenesis

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What is a Sensory System?

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Fertilization

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What is the Skeletal System?

Overview

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an-introduction-to-the-zebrafish-danio-rerio

An Introduction to the Zebrafish: Danio rerio

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Physiology of the Circulatory System

Homeostasis
Conditions in the external environment of an organism can change rapidly and drastically. To survive, organisms must maintain a fairly ...

Anatomy of the Circulatory System

The human circulatory system consists of blood, blood vessels that carry blood away from the heart, around the body, and back to the heart, and the heart ...

Measuring Blood Pressure
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Anatomy of the Heart

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Measuring Circulatory System Function in Humans
ExpandBefore starting the experiment go to the front of the room and collect an alcohol swab, a ...

Blood Flow

Blood is pumped by the heart into the aorta, the largest artery in the body, and then into increasingly smaller arteries, arterioles, and capillaries. The ...

What Are Osmoregulation and Excretion?

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Blood Withdrawal I

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
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Kidney Structure

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Blood Withdrawal II

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
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What is the Immune System?

Overview

The immune system comprises diverse biological structures and processes that protect the body from disease. These processes can be classified ...

Bone Remodeling

Bone remodeling is a continuous and balanced process of bone resorption by osteoclasts and bone formation by osteoblasts. In adults, it helps maintain ...

Spermatogenesis

Spermatogenesis is the process by which haploid sperm cells are produced in the male testes. It starts with stem cells located close to the outer rim of ...

Bone Structure

Within the skeletal system, the structure of a bone, or osseous tissue, can be exemplified in a long bone, like the femur, where there are two types of ...

Breathing

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Develop and use a model to illustrate the hierarchical organization of interacting systems that provide specific functions within multicellular organisms. [Clarification Statement: Emphasis is on functions at the organism system level such as nutrient uptake, water delivery, and organism movement in response to neural stimuli. An example of an interacting system could be an artery depending on the proper function of elastic tissue and smooth muscle to regulate and deliver the proper amount of blood within the circulatory system.] [Assessment Boundary: Assessment does not include interactions and functions at the molecular or chemical reaction level.]

HS-LS1-2

What is Homeostasis?

Maintaining homeostasis requires that the body continuously maintain its internal conditions. Each physiological condition has a particular set point, ...

Negative and Positive Feedback

Homeostatic Imbalance

Homeostasis is the maintenance of a stable internal environment within the body, which is crucial for the proper functioning of cells, tissues, organs, ...

pH Homeostasis

Acid-base homeostasis is essential for maintaining normal physiological activities in humans. The pH of various body fluids is strictly regulated because ...

Plan and conduct an investigation to provide evidence that feedback mechanisms maintain homeostasis. [Clarification Statement: Examples of investigations could include heart rate response to exercise, stomate response to moisture and temperature, and root development in response to water levels.] [Assessment Boundary: Assessment does not include the cellular processes involved in the feedback mechanism.]

HS-LS1-3

Protein Binding Surfaces and Contacts

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