[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-seo-326834-105":3,"detail-sidebar-cat-0-en-105":81,"doc-detail-326834-en":130},{"code":4,"msg":5,"data":6},0,"ok",{"site_id":7,"language":8,"slug":9,"title":10,"keywords":11,"description":12,"schema_data":13,"social_meta":74,"head_meta":76,"extra_data":78,"updated_unix":80},105,"en","secondary-structure-in-protein-analysis-protein-analysis","Secondary Structure in Protein Analysis - Protein Analysis","","Secondary Structure in Protein Analysis explains how protein conformations are organized beyond a simple amino-acid chain. It describes native folds and the secondary-structure motifs that dominate protein architecture, including alpha-helices, 310-helices, beta-strands, polyproline II helices, turns, and V-loops. The text details backbone covalent and geometric constraints, introduces dihedral angles (phi and psi) as degrees of freedom, and classifies protein structure into primary, secondary, and tertiary levels. It further outlines helix formation principles, hydrogen-bond patterns, helical turns per residue, and helix-cap end effects.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & Report",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/secondary-structure-in-protein-analysis-protein-analysis/326834/",4,{"url":32,"name":10,"@type":35,"image":36,"author":41,"headline":10,"publisher":44,"fileFormat":47,"inLanguage":8,"description":12,"dateModified":48,"datePublished":49,"encodingFormat":47,"isAccessibleForFree":50,"interactionStatistic":51},"DigitalDocument",{"url":37,"@type":38,"width":39,"height":40},"https://docshare.wps.com/thumbnails/secondary-structure-in-protein-analysis-protein-analysis/326834.png","ImageObject",300,407,{"name":42,"@type":43},"Miles","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-10-23","2026-09-21",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",7,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"What are the main elements of protein secondary structure mentioned in the text?","Question",{"text":63,"@type":64},"The text lists three major repetitive elements: α-helix, β-strand, and polyproline II helix, plus one minor repetitive element, the 310-helix. It also identifies two major nonrepetitive elements: turns and V-loops.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"How is protein secondary structure described geometrically?",{"text":68,"@type":64},"The backbone conformation is characterized by two dihedral angles per residue, called phi (f) and psi (c). These angles determine the specific secondary-structure patterns.",{"name":70,"@type":61,"acceptedAnswer":71},"What role do hydrogen bonds play in forming an α-helix?",{"text":72,"@type":64},"In an α-helix, each backbone N–H forms a hydrogen bond with a backbone carbonyl oxygen located four residues away in the sequence (i to i+4 relationship). The helical twist positions these groups to align hydrogen bonds roughly parallel to the helix axis.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},326834,1790192927,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,106,110,114,119,122,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & Novel",90,"story-novel",{"id":26,"doc_module":4,"doc_module_name":25,"category_name":89,"show_sort_weight":90,"slug":91},"Literature",80,"literature",{"id":33,"doc_module":4,"doc_module_name":25,"category_name":93,"show_sort_weight":94,"slug":95},"Exam",70,"exam",{"id":97,"doc_module":4,"doc_module_name":25,"category_name":98,"show_sort_weight":99,"slug":100},5,"Comic",60,"comic",{"id":102,"doc_module":4,"doc_module_name":25,"category_name":103,"show_sort_weight":104,"slug":105},6,"Technology",50,"technology",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":107,"show_sort_weight":108,"slug":109},"Healthcare",40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":112,"slug":113},8,30,"research-report",{"id":115,"doc_module":4,"doc_module_name":25,"category_name":116,"show_sort_weight":117,"slug":118},9,"Religion & Spirituality",20,"religion-spirituality",{"id":117,"doc_module":4,"doc_module_name":25,"category_name":120,"show_sort_weight":117,"slug":121},"World Cup","world-cup",{"id":123,"doc_module":4,"doc_module_name":25,"category_name":124,"show_sort_weight":123,"slug":125},10,"Lifestyle","lifestyle",{"id":127,"doc_module":4,"doc_module_name":25,"category_name":128,"show_sort_weight":97,"slug":129},19,"General","general",{"code":4,"msg":82,"data":131},{"doc_id":79,"user_id":132,"nickname":42,"user_avatar":133,"doc_module":4,"category_id":111,"category_name":29,"doc_title":10,"doc_description":12,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":55,"is_deleted":4,"is_public":22,"is_downloadable":22,"audit_status":22,"page_count":139,"language":140,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":12,"update_tm":144,"read_time":145,"preview_page_count":4},13056703019404,"https://ap-avatar.wpscdn.com/davatar_29158cc5080c5b710cf443261637dec0","s Secondary Structure in  \nProtein Analysis  \nGeorge D. Rose  \nThe Johns Hopkins University, Baltimore, Maryland, USA  \nProteins are linear, unbranched polymers of the 20 naturally occurring amino acid residues. Under physiological conditions, most proteins self-assemble into a unique, biologically relevant structure: the native fold. This structure can be dissected into chemically recognizable, topologically simple elements of secondary structure: a-helix, 310-helix, b-strand, polyproline II helix, turns, and V-loops. Together, these six familiar motifs account for ,95% of the total protein structure, and they are utilized repeatedly in mix-and-match patterns, giving rise to the repertoire of known folds. In principle, a protein’s threedimensional structure is predictable from its amino acid sequence, but this problem remains unsolved. A related, but ostensibly simpler, problem is to predict a protein’s secondary structure elements from its sequence.  \nProtein Architecture  \nA protein is a polymerized chain of amino acid residues, each joined to the next via a peptide bond. The backbone of this polymer describes a complex path through three-dimensional space called the “native fold” or “protein fold.”  \nCOVALENT STRUCTURE  \nAmino acids have both backbone and side chain atoms. Backbone atoms are common to all amino acids, while side chain atoms differ among the 20 types. Chemically, an amino acid consists of a  \ncentral, tetrahedral carbon atom, (), linked covalently to (1) an amino group (–NH2 ), (2) a carboxyl group (–COOH),(3) a hydrogen atom (–H) and (4) the side chain (–R) . Upon polymerization, the amino group loses an –H and the carboxy group loses an –OH; the remaining chemical moiety is called an“amino acid residue” or, simply, a “residue.” Residues in this polymer are linked via peptide bonds, as shown in Figure 1 .  \nDEGREES OF FREEDOM IN THE BACKBONE  \nThe six backbone atoms in the peptide unit [Ca(i)–CO– NH–Ca(i þ 1)] are approximately coplanar, leaving only two primary degrees of freedom for each residue. By convention, these two dihedral angles are called fand c (Figure 2) . The protein’s backbone conformation is described by the f,c-specification for each residue.  \nCLASSIFICATION OF STRUCTURE  \nProtein structure is usually classified into primary, secondary, and tertiary structure. “Primary structure”corresponds to the covalently connected sequence of amino acid residues.“Secondary structure” corresponds to the backbone structure, with particular emphasis on hydrogen bonds. And “tertiary structure” corresponds to the complete atomic positions for the protein.  \nSecondary Structure  \nProtein secondary structure can be subdivided into repetitive and nonrepetitive, depending upon whether the backbone dihedral angles assume repeating values. There are three major elements (a-helix, b-strand, and polyproline II helix) and one minor element (310-helix) of repetitive secondary structure (Figure 3) . There are two major elements of nonrepetitive secondary structure (turns and V-loops) .  \nREPETITIVE SECONDARY STRUCTURE: THE a-HELIX  \nWhen backbone dihedral angles are assigned repeating f,c-values near (2608, 2408 ), the chain twists into aright-handed helix, with 3.6 residues per helical turn. First proposed as a model by Pauling, Corey, and Branson in 1951, the existence of this famous structure was experimentally confirmed almost immediately by  \nEncyclopedia of Biological Chemistry, Volume 4. q 2004, Elsevier Inc. All Rights Reserved. 1  \n2 SECONDARY STRUCTURE IN PROTEIN ANALYSIS  \nFIGURE 1 (A) A generic amino acid. Each of the 20 naturally occurring amino acids has both backbone atoms (within the shaded rectangle) and side chain atoms (designated R) . Backbone atoms are common to all amino acids, while side chain atoms differ among the 20 types. Chemically, an amino acid consists of a tetrahedral carbon atom (–C–), linked covalently to (1) an amino group (–NH2),(2) a carboxyl group (–COOH),(3) a hydrogen atom (–H), a","cbCaijlUswLxe77W","https://ap.wps.com/l/cbCaijlUswLxe77W","pdf",11505019,503,"English","# Secondary structure in protein analysis\n## Protein architecture\n## Covalent structure\n## Degrees of freedom in the backbone\n## Classification of structure\n## Secondary structure\n## Repetitive secondary structure: the α-helix\n## Repetitive secondary structure: the 310-helix","[{\"question\":\"What are the main elements of protein secondary structure mentioned in the text?\",\"answer\":\"The text lists three major repetitive elements: α-helix, β-strand, and polyproline II helix, plus one minor repetitive element, the 310-helix. It also identifies two major nonrepetitive elements: turns and V-loops.\"},{\"question\":\"How is protein secondary structure described geometrically?\",\"answer\":\"The backbone conformation is characterized by two dihedral angles per residue, called phi (f) and psi (c). These angles determine the specific secondary-structure patterns.\"},{\"question\":\"What role do hydrogen bonds play in forming an α-helix?\",\"answer\":\"In an α-helix, each backbone N–H forms a hydrogen bond with a backbone carbonyl oxygen located four residues away in the sequence (i to i+4 relationship). The helical twist positions these groups to align hydrogen bonds roughly parallel to the helix axis.\"}]","Secondary Structure in Protein Analysis - Protein Analysis | PDF",1789975500,1268]