A powerful tool for biomolecular communication and a 3d

Proteopedia is widely used in scientific research, in the preparation of papers for publication and teaching from secondary level to post-graduate. Teaching Strategies Using Proteopedia:. Of course, you can use existing pages in Proteopedia. Be sure to consider those specifically designed for and by educators, which are listed at Teaching Scenes, Tutorials, and Educators' Pages.

If you create your own pages, you will have scenes of the molecules that you are emphasizing in your teaching -- scenes that show exactly the structural features you wish to emphasize. See the Main Page Fig. Customizing molecular scenes is amazingly easy with Proteopedia's Scene Authoring Tool. Main Page of Proteopedia showing the green hyperlinks that when clicked result in a change in the 3D Jmol figure to reflect what is described in the text.

3D Printing of Biomolecular Models for Research and Pedagogy

A low tech, but quick-to-prepare lesson plan involves distributing worksheets of questions regarding the molecular scenes on a particular Proteopedia page.

These worksheets can be on paper, a web page which could be on a page in Proteopediaor within your local courseware system. Students in a computer lab can do such worksheets in class, concurrently, perhaps in pairs, which fosters discussion. The questions can be purposefully vagueto encourage discussion -- in which case completion could be simply "checked off" rather than graded in detail.

Such worksheets give focus and a finite completion goal to each student. In contrast, simply assigning students to read a Proteopedia page may leave them less focused and perhaps uncertain about whether they have absorbed what you intend from the page.

Proteopedia has a mechanism to include quizzes on pages you prepare for your students. See Help:Quiz. Upper level undergraduates, e. A particularly outstanding example, Photosystem II Fig. Professor Oberholser reported "I think that Emily's work on Photosystem II shows that Proteopedia is a system that a Jmol novice can use with good effect. Emily had no experience with using Jmol. The other students in the class Thank you for a great product!

Any student planning to author a permanent page should request a personal user account in their own real name, identifying themselves as a student, and their college.

See, for example, Emily Forschler. The use of the protected pages insures that the page will be editable only by the student and not subject to alterations possible for typical sandbox pages. The project could then later always be copied to standard Proteopedia page so others can improve it.

Some educators have assigned their students to try out authoring a Proteopedia molecular scene or two, just to learn the process, without making permanent pages in Proteopedia. Proteopedia has Sandbox pages where you or your students are invited to try authoring. The contents of these pages are not permanent, and will be erased or replaced at a later time. FirstGlance makes it easy to explore the molecular structure in more detail and, like Proteopedia, it can use Java but also works without Java.

You can click on any of these to find them.

a powerful tool for biomolecular communication and a 3d

Sequences can be displayed and short sequences can be found. With one click each you can see secondary structure, amino and carboxyl termini, hydrophobic cores two clicks, one to slice through the center with "Slab"positive and negative charges, and much more. Tools locate disulfide bonds, salt bridges, cation-pi interactions, and non covalent bonds to any moiety you specify.

Help and color keys appear automatically. When students are given a worksheet or a list of suitable questions, FirstGlance provides an easy way to see answers.

Here are 20 questions assigned to students in a workshop. These questions apply to any protein; each student chose a different protein to investigate.

a powerful tool for biomolecular communication and a 3d

Jaswal, O'Hara, Williamson and Springer [1] describe in detail how they use ProteopediaFirstGlance in Jmol and student-authored presentations about their structure-function analysis projects in a one-semester biochemistry course at Amherst College Amherst, Massachusetts, USA.

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User Reviews Be the first to post a review of Biomolecule Toolkit! Report inappropriate content. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. Sign Up No, Thank you.We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery.

We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur.

Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future. Molecular recognition is of paramount importance in biology—without it life would not exist.

Before the first 3D structures of biomolecules were determined Watson and Crick ; Kendrew et al. Over time, an appreciation of the structural changes that can occur upon binding led to the related induced fit Koshland and fluctuation fit Straub and Szabolcsi models.

At about the same time two complementary models for describing allostery, a key biological mechanism that is responsible for information transfer, were also proposed, the concerted model Monod et al.

These models were proposed before the development of molecular dynamics MD simulations McCammon et al. Molecular dynamics has provided significant insight into the details of molecular motion, but the significant contributions from experimental techniques cannot be overlooked. Indeed experiments provide direct evidence for dynamic processes, often at an atomic level, and can be used to validate the predictions of MD.

Nuclear magnetic resonance NMR spectroscopy is a particularly powerful tool in the experimental analysis of macromolecular dynamics, because it furnishes information about both structure and motion at atomic resolution. This can be analysed by use of MD to generate conformational ensembles that enumerate the conformations adopted by a given macromolecule Torda et al.

These methods have recently been used to study molecular recognition and allostery and have provided new insights into their underlying mechanisms that are, importantly, supported by experimental results Lange et al. To illustrate the types of representation of structural heterogeneity that can be obtained by use of NMR in combination with MD, in Fig. Structures and ensembles of ubiquitin showing the ability of ensemble approaches to capture structural heterogeneity. In addition to being important for fundamental reasons, theoretical or hybrid theoretical—experimental methods for characterisation of structural heterogeneity can be very important in structure-based drug discovery.

In the near future, as recently demonstrated by the Al-Hashimi laboratory Stelzer et al. Here we review the advances that have been made in the understanding of the motion, molecular recognition, and allostery of biomolecules by use of conformational ensembles and discuss how these powerful techniques will continue to guide our understanding of these and related important biological phenomena.

Given that molecular motion undoubtedly occurs under physiological conditions it is perhaps not surprising that functional roles have been attributed to it. Henzler-Wildman and Kern have recently reviewed this subject, emphasising the importance of motion for protein function. Examples include cytoskeletal function, antibody—antigen recognition, small molecule signalling, and information storage.

Coarse-grained MD simulations have, for example, shown that the motion of actin filaments is important in dictating the structural and functional properties of the cytoskeleton Chu and Voth and, similarly, two-dimensional correlation Fourier Transform Infrared FTIR spectroscopy has shown that structural flexibility is an inherent property of immunoglobulins Kamerzell and Middaugh ; such flexibility is required for function because monoclonal IgG molecules must recognize antigens of various shapes and sizes.

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Finally, a role of motion in the function of DNA has also been proposed Blagoev et al. In Fig. Motion of biological interest is often challenging to study because it occurs on timescales ps to ms that are accessible to a limited number of techniques such as NMR and dielectric relaxation spectroscopy Fig. Timescales of biological motion above and experimental and theoretical methods below.

Protein and nucleic acid dynamic timescales are shown in green and redrespectively. Timescales common to all biomolecules are shown in black. Motion on faster timescales averages during the experiments. Although it is well-established, both from theoretical predictions and experimental observations, that macromolecules are highly dynamic at physiological temperatures, characterization of the motion is very challenging.

McCammon et al. Increases in computer power have enabled study of the motion of systems of much larger size Jensen et al. Shaw Research, which observed slow motion, occurring on timescales longer than the rotational diffusion correlation time, of the backbone of a globular protein. This work shows that the motion of the backbone of BPTI occurs on longer timescales than that of the side chains, and suggests this is a general property of proteins.

Taken from Shaw et al. Normal mode analysis, a theoretical tool that is complementary to MD, and its coarse-grained equivalents, the Gaussian network model Bahar et al. Normal mode analysis produces projections of the modes rather than conformational ensembles but can, in principle, probe longer timescales.

Although relating the frequencies of motion of biomolecules to biological function has remained contentious Kamerlin and Warshel ; Karplus the motion of biomolecules is likely to be related to their function.Physical models of biomolecules can facilitate an understanding of their structure-function for the researcher, aid in communication between researchers, and serve as an educational tool in pedagogical endeavors.

Here, we provide detailed guidance for the 3D printing of accurate models of biomolecules using fused filament fabrication desktop 3D printers.

a powerful tool for biomolecular communication and a 3d

The construction of physical three-dimensional 3D models of biomolecules can uniquely contribute to the study of the structure-function relationship. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction.

Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules.

Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance.

Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. A thorough understanding of the function and activity of a biomolecule requires the determination of its three-dimensional 3D structure.

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This is routinely achieved using X-ray crystallography, NMR, or electron microscopy. Historically, the construction of physical 3D models was necessary for investigators to validate, explore, and communicate the resulting hypotheses regarding function of biomolecules. These models, such as Watson-Crick's DNA double helix and Pauling's alpha helix, provided unique insight into structure-function relationships and were pivotal to our early understanding of nucleic acid and protein structure-function 234.

Although complex protein and nucleic acid models can be created, the time and cost of building a physical model was eventually outweighed by the relative ease of computer-aided molecular visualization.

The development of 3D printing, also known as additive manufacturing, has again enabled the construction of physical models of biomolecules 5. A variety of mechanisms are used in this process. Until recently, the machines used to produce physical models of biomolecules were too expensive to be widely used. However, in the last decade, 3D printing technology, fused filament fabrication FFF in particular, has advanced significantly, making it accessible for consumer use 6.

FFF printers are now commonly available in high schools, libraries, universities, and laboratories. The greater affordability and accessibility of 3D printing technology has made it possible to convert digital 3D biomolecular models into accurate, physical 3D biomolecular models 789.

Such models include not only simple representations of single biomolecules, but also complex macromolecular assemblies, such as the ribosome and virus capsid structures. However, the process of printing individual biomolecules and macromolecular assemblies poses several challenges, particularly when using thermoplastic extrusion methods.

In particular, representations of biomolecules often have complex geometries that are difficult for printers to produce, and creating and processing digital models that will print successfully requires skill with molecular modelling, 3D modelling, and 3D printer software.

The 3D workflow for printing a biomolecule broadly occurs in four steps: 1 preparing a biomolecular model from its coordinate file for 3D printing; 2 importing the biomolecular model into a "slicing" software to segment the model for the printer and to generate a support structure that will physically prop up the biomolecular model; 3 selecting the correct filament and printing the 3D model; and 4 post-production processing steps, including removing support material from the model Figures 1 and 2.

The first step in this process, computationally manipulating the coordinate file of the biomolecule, is critical. At this stage, the user may build model reinforcements in the form of struts, as well as remove structures that are extraneous to what the user chooses to display. Next, the file is opened in a second software program to convert the model into a 3D print file that can be printed, layer by layer, into a plastic replica of the biomolecule.

The goal of our protocol is to make the fabrication of molecular models accessible to the large numbers of users who have access to FFF printers but not to more expensive 3D printing technologies.

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Here, we provide a guide for the 3D printing of biomolecules from 3D molecular data, with methods that are optimized for FFF printing. We detail how to maximize the printability of complex biomolecular structures and ensure the simple post-processing of physical models.Software for interactive molecular exploration in High School Biology courses.

DNA New resource added! This table draws together the 3d resources with background information for your convenience. Each molecule is descibed briefly in a summary, which is followed by links to the 3d displays, bullet points of features of each display, and finally links to background information for lesson planning purposes. To rotate a molecule in the 3d display, click and drag on it with the mouse. To identify an atom, let the mouse cursor rest on top of it for a few seconds.

Use buttons and controls next to or below the molecule to change the display. To access more functions, click on the Jmol logo in the corner of the structure area for a pop-up menu.

All 3d resources open in a new window. Guided Tutorials and Animations are authored by Eric Martz unless otherwise noted. We hope you enjoy exploring! Antibody production is one part of a complex response mounted by the immune systems of vertebrates to an unwelcome molecular guest. Antibodies, also called immunoglobulins, are soluble proteins secreted by specialized cells called B lymphocytes.

Antibodies can recognize and bind very specifically to foreign molecules, such as toxins or parts of invading microbes. Toxins are neutralized when antibodies bind. Microbes marked with bound antibodies are killed by white blood cells. People who lack antibodies get recurrent, severe infections, and are treated by injecting antibodies from healthy donors.

Antibodies Format: Guided Tutorial. Composed entirely of carbon, hydrogen, and oxygen, carbohydrates are literally hydrated carbonas seen by their generalized formula, C x H 2 O y. Carbohyrates range from simple sugars to complex assemblies of sugars, and have diverse functions.

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

Their most famous functions are those of energy storage and providing cellular structure. Carbohydrates Format: Biomodel. Collagen literally holds us together. Collagen is a relatively simple protein, made of three separate chains of amino acids that twist together.

Just as strong rope is made of small strands twisted together, collagen is strong, yet flexible.

Biomolecule Toolkit

Collagen provides flexible strength to our skin, tendons, and internal organs, and underlying structure for bones and teeth. Rare genetic diseases and scurvy from vitamin C deficiency are due to defects in collagen. The DNA double helix carries genetic information in the sequence of the nucleotide building blocks of which it is composed.

DNA holds the genes for all life on Earth. The structure of DNA is uniquely suited to its purpose as an information-carrying molecule capable of faithful duplication. Although the structure of DNA was proposed by Watson and Crick init was not directly observed as you will see here until over 25 years later by X-ray crystallography. Also see The Nucleosome. Respiration depends on the presence of the protein hemoglobin in red blood cells. Hemoglobin picks up oxygen in the lungs, where oxygen concentration is highest, and releases the oxygen at the tissues, where, due to the continual use of oxygen, the oxygen concentration is lowest.

When oxygen is bound, the heme adopts a bright red color. Inherited mutations in hemoglobin may cause diseases, such as sickle cell anemia. Breathing carbon monoxide is fatal because it binds tightly to the iron in heme and is never released, thereby blocking the transport of oxygen. Hemoglobin Format: Guided Tutorial. A protease is a protein enzyme that can break a bond in another protein at a specific point.

Without the function of this protease, the AIDS virus cannot spread.These metrics are regularly updated to reflect usage leading up to the last few days. Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.

Find more information on the Altmetric Attention Score and how the score is calculated. Dynamic light scattering DLS is an analytical tool used routinely for measuring the hydrodynamic size of nanoparticles and colloids in a liquid environment.

Gold nanoparticles GNPs are extraordinary light scatterers at or near their surface plasmon resonance wavelength. In this study, we demonstrate that DLS can be used as a very convenient and powerful tool for gold nanoparticle bioconjugation and biomolecular binding studies. The conjugation process between protein A and gold nanoparticles under different experimental conditions and the quality as well as the stability of the prepared conjugates were monitored and characterized systematically by DLS.

Furthermore, the specific interactions between protein A-conjugated gold nanoparticles and a target protein, human IgG, can be detected and monitored in situ by measuring the average particle size change of the assay solution. For the first time, we demonstrate that DLS is able to directly and quantitatively measure the binding stoichiometry between a protein-conjugated GNP probe and a target analyte protein in solution.

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a powerful tool for biomolecular communication and a 3d

Cite this: Anal. Article Views Altmetric. Citations Abstract Dynamic light scattering DLS is an analytical tool used routinely for measuring the hydrodynamic size of nanoparticles and colloids in a liquid environment. Cited By. This article is cited by publications. Konopka, Tzu-Wen L. Cross, Kelly S. Swanson, Lawrence W. Dobrucki, Andrew M. ACS Nano14 1 ACS Omega4 12 Journal of Agricultural and Food Chemistry67 32Ready to promote your business online. Create a free website with Wix.

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