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

العديد من العمليات البيولوجية تعتمد على تفاعلات البروتين مع البروتين فى الحقيقة, عدد كبير من البروتينات بحاجة إلى تكوين مركب معقد بروتينى أو مجموعات قليلة الوحدات, لأداء وظائفها أحيانًا اثنان أو أكثر من البروتينات المتطابقة تشكل مركب معقدًا،مثل هذا الكينسن ثنائى الوحدات الذى يتكون من اثنان من سلاسل البروتين المتطابقة. في حالات أخرى،البروتينات أو متعددة الببتيد المختلفة تتجمع معا لتشكيل وحدة وظيفية على سبيل المثال،الانبيبات الدقيقة فى الهيكل الخلوى تتكون من ثنائيات الفا وبيتا تيوبلين الأسطح الرابطة لوحدات ألفا وبيتا تيوبلين بها أشكال تكميلية. هذه الأشكال المتوافقة تمكّن الوحدات من تكوين عدد كبير من التفاعلات غير التساهمية،التي تمسك لفا وبيتا تيوبلين معًبعضهم هذا النوع من السطح البينى مثال لتفاعل الأسطح مع الأسطح تشابها مع مواقع ربط الليجاند تفاعلات السطح البينى فى البروتين مع البروتين الآخر قد يتضمن روابط غير تساهمية وقوى ناتجه من كره الماء ومع ذلك،الروابط ثنائية الكبريت التساهمية بين الأحماض الأمينية سيستيين على سطح كل بروتين قد تلعب أيضًا دورًا لإبقائها معا.ولكن ليس كل الأسطح البينية للبروتين تظهر توافق سطحى بشكل وثيق على سبيل المثال،العديد من الإنزيمات،مثل البروتين كايناز أ هنا تكوّن شق بواسطته يمكن التعرف على حلقات عديد البيبتايد لمشاركينهم فى التفاعل والربط به. هذا النوع من السطح البينى معروف بتفاعل السلاسل السطحية. نوع آخر من السطح البينى،معروف بالتفاعل بين حلزون-حلزون أو لولب لولب يتكون عندما اثنان من الحلزونات من البروتينات يلتفوا حول بعض هذا السطح البينى يتم مراقبته بشكل متكرر في البروتينات التي تحتوي على مجموعات كبيرة من نطاقات ليوسين زيبر مثل عوامل نسخ حقيقيات النوى في الختام, التركيب الفيزيائى والخواص الكيميائية للأجزاء المتفاعلة تحدد نوع السطح البينى بين اثنان من البروتين

<ol>
	<li>كوه GC ، بوراس بي ، أراندا ب ، هيرمجاكوب إتش ، أورشارد إس إي. تحليل شبكات تفاعل البروتين والبروتين. مجلة أبحاث البروتينات. 2012 أبريل; 11 (4): 2014-2031.</li>
	<li>لاريا L, ماكنزي G, الربيع DR, فينكيتارامان AR, هوغينز دي جي. التغلب على التحديات الكيميائية والبيولوجية والحسابية في تطوير مثبطات تستهدف تفاعلات البروتين والبروتين. كيم بيول. 2015; 22 (6): 689-703.</li>
	<li>De Las Rivas J، Fontanillo C. أساسيات تفاعلات البروتين والبروتين: المفاهيم الأساسية لبناء وتحليل شبكات interactome. PLoS Comput Biol. 2010; 6 (6): e1000807.</li>
	<li>S لالوند ، إيرهارت دوي دبليو ، د لوكيه ، تشين ي ، ري ساي ، فرومر دبليو بي. الأساليب الجزيئية والخلوية للكشف عن تفاعلات البروتين والبروتين: أحدث التقنيات والقيود الحالية. مصنع J. 2008 فبراير ؛ 53 (4): 610-35.</li>
	<li>Amos-Binks A و Patulea C و Pitre S و al. التنبؤ بموقع الربط لتفاعلات البروتين والبروتين واكتشاف الشكل الجديد باستخدام تسلسلات عديد الببتيد التي تكرر. المعلوماتية الحيوية BMC. 2011;12:225. تم النشر في 2011 يونيو 2.</li>
</ol>

واجهات البروتين والبروتين

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تشكل العديد من البروتينات مجمعات للقيام بوظائفها، مما يجعل تفاعلات البروتين البروتين (PPIs) ضرورية لبقاء الكائن الحي. يتم تثبيت معظم واجهات البروتين -بروتين بواسطة العديد من القوى الكيميائية غير التساهمية الضعيفة. يحدد الشكل المادي للواجهات الطريقة التي يتفاعل بها البروتينان. العديد من البروتينات الكروية لها أشكال متطابقة بشكل وثيق على أسطحها، والتي تشكل عددًا كبيرًا من الروابط الضعيفة. بالإضافة إلى ذلك، تحدث العديد من تفاعلات البروتين- بروتين بين حلزونين أو بين شق سطحي وسلسلة أو سلسلة متعددة الببتيد.

يتم استخدام طرق حسابية وكيميائية حيوية مختلفة لدراسة واجهات البروتين. يمكن استخدام الأساليب المختبرية، مثل تنقية الألفة، وقياس الطيف الكتلي، والمصفوفات الدقيقة للبروتين، لتحديد التفاعلات الجديدة. يتم استخدام الترسيب المناعي المشترك للبروتينات وفحص الخميرة ثنائي الهجين على نطاق واسع لتقديم أدلة على ما إذا كان هناك بروتينان يتفاعلان في المختبر. يمكن لبرامج الكمبيوتر التنبؤ بتفاعلات البروتين-بروتين بناءً على تفاعلات مماثلة موجودة في بروتينات أخرى من خلال مقارنة تسلسلات البروتين والهياكل ثلاثية الأبعاد. تتنبأ الأساليب الحسابية الأخرى، مثل التنميط التطوري، بتفاعلات البروتين بناءً على التطور المشترك للشركاء الملزمين. بالإضافة إلى ذلك، يتم استخدام تحليل دمج الجينات للتنبؤ بشركاء التفاعل من خلال إيجاد أزواج البروتين المندمجة في جينوم الكائنات الحية الأخرى.

تتفاعل البروتينات عادةً مع شركاء متعددين إما في نفس الوقت أو في أوقات مختلفة، وقد تحتوي على أكثر من واجهة تفاعل واحدة. تشكل العديد من البروتينات مجمعات كبيرة تؤدي وظائف محددة لا يمكن تنفيذها إلا بواسطة المجمع الكامل. وفي بعض الحالات، يتم تنظيم هذه التفاعلات البروتينية؛ أي أن البروتين قد يتفاعل مع شركاء مختلفين بناءً على الاحتياجات الخلوية. تقوم المزيد من التحليلات الحسابية والإحصائية بفرز هذه التفاعلات في شبكات، والتي يتم تنظيمها في قواعد البيانات التفاعلية عبر الإنترنت. تمكن قواعد البيانات القابلة للبحث هذه المستخدمين من دراسة تفاعلات بروتينية معينة، بالإضافة إلى تصميم الأدوية التي يمكن أن تعزز أو تعطل التفاعلات في الواجهة.

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تشكل العديد من البروتينات مجمعات للقيام بوظائفها ، مما يجعل تفاعلات البروتين والبروتين (PPIs) ضرورية لبقاء الكائن الحي. معظم PPIs ...

Education

JoVE Core

Cell Biology

بيولوجيا الخلية

Unit 1

الوحدة الأولى

Protein Function

وظيفة البروتين

KEY TERMS AND CONCEPTS

المصطلحات والمفاهيم الأساسية

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

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

Cell Structure

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Visualizing Onion and Cheek Cells
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Cytoplasm

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The Nucleus

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The Central Dogma

The DNA Helix

Nucleic Acids

DNA as a Genetic Template

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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

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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
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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
ExpandTo prepare for the blood pressure exercise, simply place the appropriate number of alcohol swabs, sphygmomanometers, and ...

Anatomy of the Heart

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Measuring Circulatory System Function in Humans
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Blood Flow

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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
Blood collection is a common requirement for ...

Kidney Structure

The kidneys are two large bean-shaped organs located in the upper abdomen. They filter the blood several times a day to remove toxins and rebalance water ...

Blood Withdrawal II

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
The collection of blood from mice and rats for ...

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

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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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