| Revision as of 19:41, 9 October 2019 edit2601:246:c700:9b0:48a6:82d4:5919:3b87 (talk) →Roles: Extended the legend of the otherwise incomprehensible animation, giving the color codings, and description of what the reader is seeing. Also, began sourcing this content.← Previous edit |
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{{merge|Biomolecular complex|discuss=Talk:Macromolecular assembly#Merger proposal|date=October 2019}} |
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]'', based on ] from the laboratory of ]. Of the 31 component proteins, 27 are shown (blue), along with its 2 RNA strands (orange, yellow).<ref name=Ban>{{cite journal |vauthors=Ban N, Nissen P, Hansen J, Moore P, Steitz T|title=The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 ångström Resolution |journal=Science |volume=289 |issue=5481 |pages=905–20 |year=2000 |pmid=10937989 | doi = 10.1126/science.289.5481.905|bibcode = 2000Sci...289..905B |citeseerx=10.1.1.58.2271 }}</ref> Animation by D.S. Goodsell of the ].<ref>{{cite web|url=https://ccsb.scripps.edu/goodsell/|title=WELCOME}}</ref> The size of the assembly is approximately 240 Å (24 nm) across, for both the longest vertical and the longest horizontal axes shown in the graphic.<ref>{{dead link|date=October 2019}}</ref>]] |
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]l ] structure, "motor", and partial rod from ''Salmonella''. Digitally printed physical model of some of 40 protein type based on molecular structures, from the laboratory of ]. From bottom to top, repeating FliM and FliN, motor/switch proteins in darker blue, FliG motor/switch proteins in red, FliF transmembrane coupling protein in yellow, L and P ring proteins in light blue, and (at top), the cap, hook-filament junction, hook, and rod proteins all in darker blue.<ref>Legend, cover art, J. Bacteriol., October 2006.{{full}}</ref>]] |
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]'' ] model of 29 of the 33 native compoents, from the laboratory of ]. Of the 31 component proteins, 27 are shown (blue), along with its 2 RNA strands (orange/yellow).<ref name=Ban>{{cite journal |vauthors=Ban N, Nissen P, Hansen J, Moore P, Steitz T|title=The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 ångström Resolution |journal=Science |volume=289 |issue=5481 |pages=905–20 |year=2000 |pmid=10937989 | doi = 10.1126/science.289.5481.905|bibcode = 2000Sci...289..905B |citeseerx=10.1.1.58.2271 }}</ref> Animation by D.S. Goodsell of the ].<ref>http://mgl.scripps.edu/people/goodsell/illustration/index.html</ref> The size of the assembly is approximately 240 Å (24 nm) across, for both the longest vertical and the longest horizontal axes shown in the graphic.<ref>https://web.archive.org/web/20051124223341/www.bio.cmu.edu/courses/03231/LecF03/Lec22/lec22img.html</ref>]] |
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]l ] "motor" and partial rod structure of a ''Salmonella'' species. ] model of some of 40 protein molecular structure types, from the ] group. Bottom to top: dark blue, repeating FliM and FliN, motor/switch proteins; red, FliG motor/switch proteins; yellow, FliF transmembrane coupling protein; light blue, L and P ring proteins; and (at top), dark blue, the cap, hook-filament junction, hook, and rod proteins.<ref>Legend, cover art, J. Bacteriol., October 2006.{{full|date=October 2019}}</ref>]] |
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The term '''macromolecular assembly''' (MA) refers to massive chemical structures such as ]es and non-biologic ]s, cellular ]s and ] and ]s, etc. that are complex mixtures of ], ], ] or other polymeric ]s. They are generally of more than one of these types, and the mixtures are defined spatially (i.e., with regard to their chemical shape), and with regard to their underlying chemical composition and ]. ]s are found in living and nonliving things, and are composed of many hundreds or thousands of ]s held together by ]s; they are often characterized by repeating units (i.e., they are ]). Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term ] is more often applied in non-biologic contexts (e.g., in ] and ]). MAs of macromolecules are held in their defined forms by ] ]s (rather than covalent bonds), and can be in either non-repeating structures (e.g., as in the ] (image) and ] architectures), or in repeating linear, circular, spiral, or other patterns (e.g., as in ] and the ], image). The process by which MAs are formed has been termed ], a term especially applied in non-biologic contexts. A wide variety of physical/biophysical, chemical/biochemical, and computational methods exist for the study of MA; given the scale (molecular dimensions) of MAs, efforts to elaborate their composition and structure and discern mechanisms underlying their functions are at the forefront of modern structure science. |
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The term '''macromolecular assembly''' (MA) refers to massive chemical structures such as ]es and non-biologic ]s, cellular ]s and ] and ]s, etc. that are complex mixtures of ], ], ] or other polymeric ]s. They are generally of more than one of these types, and the mixtures are defined spatially (i.e., with regard to their chemical shape), and with regard to their underlying chemical composition and ]. ]s are found in living and nonliving things, and are composed of many hundreds or thousands of ]s held together by ]s; they are often characterized by repeating units (i.e., they are ]). Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term ] is more often applied in non-biologic contexts (e.g., in ] and ]). MAs of macromolecules are held in their defined forms by ] ]s (rather than covalent bonds), and can be in either non-repeating structures (e.g., as in the ] (image) and ] architectures), or in repeating linear, circular, spiral, or other patterns (e.g., as in ] and the ], image). The process by which MAs are formed has been termed ], a term especially applied in non-biologic contexts. A wide variety of physical/biophysical, chemical/biochemical, and computational methods exist for the study of MA; given the scale (molecular dimensions) of MAs, efforts to elaborate their composition and structure and discern mechanisms underlying their functions are at the forefront of modern structure science. |
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== Roles == |
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== Roles == |
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] is a ] that utilizes ] on ]s to ] RNA into proteins]] |
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], an extraordinarily complex nucleoprotein MA. All ribosomes functions as ] biological ]s, using RNA and protein structure and ] to catalytically ] the information content contained in ] molecules into the linear sequences of proteins, which then fold into their functional 3D structures.{{cn}} The graphic presents the ] and membrane targeting stages of ], showing the mRNA as a black arc, the ] subunits in green and yellow, tRNAs in dark blue, proteins such as ] and other factors involved in light blue,{{cn}} the growing polypeptide chain as a black thread growing vertically from the curve of the nRNA. At end of the graphic, the polypeptide produced is extruded through a light blue SecY pore<ref name=pmid16212506>{{cite journal | vauthors = Osborne AR, Rapoport TA, van den Berg B | title = Protein translocation by the Sec61/SecY channel | journal = Annual Review of Cell and Developmental Biology | volume = 21 | pages = 529–50 | date = 2005 | pmid = 16212506 | doi = 10.1146/annurev.cellbio.21.012704.133214 }}</ref> into the gray interior of the ], encompassed by a lipid bilayer represented graphically here as a thicker black barrier.{{cn}}]] |
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The complexes of macromolecules that are referred to as MAs occur ubiquitously in nature, where they are involved in the construction of viruses and all living cells. In addition, they play fundamental roles in all basic life processes (], ], ], intra- and inter-cellular exchange of material between compartments, etc.). In each of these roles, complex mixtures of become organized in specific structural and spatial ways. While the individual macromolecules are held together by a combination of covalent bonds and ''intra''molecular non-covalent forces (i.e., associations between parts within each molecule, via ]s, ], and ]s such as ]s), by definition MAs themselves are held together solely via the ] forces, except now exerted ''between'' molecules (i.e., ]s).{{cn|date=March 2019}} |
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The complexes of macromolecules that are referred to as MAs occur ubiquitously in nature, where they are involved in the construction of viruses and all living cells. In addition, they play fundamental roles in all basic life processes (], ], ], intra- and inter-cellular exchange of material between compartments, etc.). In each of these roles, complex mixtures of become organized in specific structural and spatial ways. While the individual macromolecules are held together by a combination of covalent bonds and ''intra''molecular non-covalent forces (i.e., associations between parts within each molecule, via ]s, ], and ]s such as ]s), by definition MAs themselves are held together solely via the ] forces, except now exerted ''between'' molecules (i.e., ]s).{{cn|date=March 2019}} |
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== MA scales and examples == |
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== MA scales and examples == |
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The images above give an indication of the compositions and scale (dimensions) associated with MAs, though these just begin to touch on the complexity of the structures; in principle, each living cell is composed of MAs, but is itself an MA as well. In the examples and other such complexes and assemblies, MAs are each often millions of ]s in molecular weight (megadaltons, i.e., millions of times the weight of a single, simple atom), though still having measurable component ratios (]) at some level of precision. As alluded to in the image legends, when properly prepared, MAs or component subcomplexes of MAs can often be crystallized for study by ] and related methods, or studied by other physical methods (e.g., ], ]). |
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The images above give an indication of the compositions and scale (dimensions) associated with MAs, though these just begin to touch on the complexity of the structures; in principle, each living cell is composed of MAs, but is itself an MA as well. In the examples and other such complexes and assemblies, MAs are each often millions of ]s in molecular weight (megadaltons, i.e., millions of times the weight of a single, simple atom), though still having measurable component ratios (]) at some level of precision. As alluded to in the image legends, when properly prepared, MAs or component subcomplexes of MAs can often be crystallized for study by ] and related methods, or studied by other physical methods (e.g., ], ]). |
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], with 30 copies of each of its coat proteins, the Small (S, yellow) and the Large (L, green), along with 2 molecules of ] ] (RNA-1 and RNA-2, not shown). The assembly is symmetric and is approximately 280 Å (28 nm) across.]] |
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] MAs. Yellow-orange indicates ] lipid tails; black and white spheres represent PL polar regions (''v.i.''). Bilayer/liposome dimensions (obscured in graphic): hydrophobic and polar regions, each ~30 Å (3.0 nm) "thick"—the polar from ~15 Å (1.5 nm) ''on each side''.<ref>http://blanco.biomol.uci.edu/Bilayer_Struc.html</ref><ref>Experimental system, dioleoyl] bilayers. The hydrophobic hydrocarbon region of the lipid is ~30 Å (3.0 nm) as determined by a combination of neutron and X-ray scattering methods; likewise, the polar/interface region (glyceryl, phosphate, and headgroup moieties, with their combined hydration) is ~15 Å (1.5 nm) ''on each side'', for a total thickness about equal to the hydrocarbon region. See S.H. White references, preceding and following.</ref><ref>{{cite journal| author = Wiener MC & White SH | year = 1992 | title = Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. | journal = Biophys. J. | volume = 61 | pages = 434-447 | url = https://www.ncbi.nlm.nih.gov/pubmed/1547331?dopt=AbstractPlus | accessdate = October 9, 2019}}{{primary source inline}}</ref><ref>Hydrocarbon dimensions vary with temperature, mechanical stress, PL structure and coformulants, etc. by single- to low double-digit percentages of these values.{{cn}}</ref>]] |
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], with 30 copies of each of its coat proteins, the small coat protein (S, yellow) and the large coat protein (L, green), which, along with 2 molecules of ] ] (RNA-1 and RNA-2, not visible) constitute the virion. The assembly is highly ], and is ~280 Å (28 nm) across at its widest point.{{verification needed}}{{cn}}]] |
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]s were among the first studied MAs; other biologic examples include ribosomes (partial image above), proteasomes, and translation complexes (with ] and ] components), procaryotic and eukaryotic transcription complexes, and ] and other biological ]s that allow material passage between cells and cellular compartments. ]s are also generally considered MAs, though the requirement for structural and spatial definition is modified to accommodate the inherent ] of membrane ]s, and of proteins within ]s. |
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]s were among the first studied MAs; other biologic examples include ribosomes (partial image above), proteasomes, and translation complexes (with ] and ] components), procaryotic and eukaryotic transcription complexes, and ] and other biological ]s that allow material passage between cells and cellular compartments. ]s are also generally considered MAs, though the requirement for structural and spatial definition is modified to accommodate the inherent ] of membrane ]s, and of proteins within ]s. |
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== Research into MAs == |
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== Research into MAs == |
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The study of MA structure and function is challenging, in particular because of their megadalton size, but also because of their complex compositions and varying dynamic natures. Most have had standard chemical and biochemical methods applied (methods of ] and ], chemical and ] characterization, etc.). In addition, their methods of study include modern ] approaches, computational and atomic-resolution structural methods (e.g., ]), ] (SAXS) and ] (SANS), force spectroscopy, and ] and ]. ] was recognized with the 1982 ] in Chemistry for his work on structural elucidation using electron microscopy, in particular for protein-nucleic acid MAs including the ] (a structure containing a 6400 base ] molecule and >2000 coat protein molecules). The crystallization and structure solution for the ribosome, MW ~ 2.5 MDa, an example of part of the protein synthetic 'machinery' of living cells, was object of the 2009 ] in Chemistry awarded to ], ], and ]. |
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The study of MA structure and function is challenging, in particular because of their megadalton size, but also because of their complex compositions and varying dynamic natures. Most have had standard chemical and biochemical methods applied (methods of ] and ], chemical and ] characterization, etc.). In addition, their methods of study include modern ] approaches, computational and atomic-resolution structural methods (e.g., ]), ] (SAXS) and ] (SANS), force spectroscopy, and ] and ]. ] was recognized with the 1982 ] in Chemistry for his work on structural elucidation using electron microscopy, in particular for protein-nucleic acid MAs including the ] (a structure containing a 6400 base ] molecule and >2000 coat protein molecules). The crystallization and structure solution for the ribosome, MW ~ 2.5 MDa, an example of part of the protein synthetic 'machinery' of living cells, was object of the 2009 ] in Chemistry awarded to ], ], and ]. |
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== Non-biologic counterparts == |
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== Non-biologic counterparts == |
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Finally, biology is not the sole domain of MAs. The fields of ] and ] each have areas that have developed to elaborate and extend the principles first demonstrated in biologic MAs. Of particular interest in these areas has been elaborating the fundamental processes of ]s, and extending known machine designs to new types and processes. |
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Finally, biology is not the sole domain of MAs. The fields of ] and ] each have areas that have developed to elaborate and extend the principles first demonstrated in biologic MAs. Of particular interest in these areas has been elaborating the fundamental processes of ]s, and extending known machine designs to new types and processes. |
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The complexes of macromolecules that are referred to as MAs occur ubiquitously in nature, where they are involved in the construction of viruses and all living cells. In addition, they play fundamental roles in all basic life processes (protein translation, cell division, vesicle trafficking, intra- and inter-cellular exchange of material between compartments, etc.). In each of these roles, complex mixtures of become organized in specific structural and spatial ways. While the individual macromolecules are held together by a combination of covalent bonds and intramolecular non-covalent forces (i.e., associations between parts within each molecule, via charge-charge interactions, van der Waals forces, and dipole-dipole interactions such as hydrogen bonds), by definition MAs themselves are held together solely via the noncovalent forces, except now exerted between molecules (i.e., intermolecular interactions).
The images above give an indication of the compositions and scale (dimensions) associated with MAs, though these just begin to touch on the complexity of the structures; in principle, each living cell is composed of MAs, but is itself an MA as well. In the examples and other such complexes and assemblies, MAs are each often millions of daltons in molecular weight (megadaltons, i.e., millions of times the weight of a single, simple atom), though still having measurable component ratios (stoichiometries) at some level of precision. As alluded to in the image legends, when properly prepared, MAs or component subcomplexes of MAs can often be crystallized for study by protein crystallography and related methods, or studied by other physical methods (e.g., spectroscopy, microscopy).
The study of MA structure and function is challenging, in particular because of their megadalton size, but also because of their complex compositions and varying dynamic natures. Most have had standard chemical and biochemical methods applied (methods of protein purification and centrifugation, chemical and electrochemical characterization, etc.). In addition, their methods of study include modern proteomic approaches, computational and atomic-resolution structural methods (e.g., X-ray crystallography), small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), force spectroscopy, and transmission electron microscopy and cryo-electron microscopy. Aaron Klug was recognized with the 1982 Nobel Prize in Chemistry for his work on structural elucidation using electron microscopy, in particular for protein-nucleic acid MAs including the tobacco mosaic virus (a structure containing a 6400 base ssRNA molecule and >2000 coat protein molecules). The crystallization and structure solution for the ribosome, MW ~ 2.5 MDa, an example of part of the protein synthetic 'machinery' of living cells, was object of the 2009 Nobel Prize in Chemistry awarded to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath.
