remembering Secondary Structures Does everyone know what the backbone and residue/side chains are? Clear about 1, 2 3 structures?

Transcription

1 remembering Secondary Structures add blast Does everyone know what the backbone residue/side chains are? Clear about 1, 2 3 structures? Heteropolymer - + Mostly in regular secondary structure + - Secondary structure can be defined by phi psi angles or by hydrogen bond patterns. A connected sequence amino must have the right phi-psi angles to make the secondary structure. Gennis-protein structure

2 .*1..*+/'-+3+//+-'27+'-T$PX<$^l#$Th$R+5)+"8(/+G1,34+"15 =*+4'G<[h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move around not quite 1 C >N C >N C2 >N6 8.&#&#')P('4.01'44#/8-$=/7'5?#.4'Q$A%9'4#/$-$A%#.%$&#.2#'9.QK8.&# %/9$($-0-/-@%/9$(('4.01'4/-/%%/4.&'4.0'45?#'#'9.2$98#''9.4&$H'-3(/A$ _$7$,%%9'&8(.&&'-=:U08$(0`5IaY'.9$-0"#$(9'4F5](.4#$ACb-.7'(4.&:/3 c.(>.-.$.-"#$(9/&&'47.99'kc.(>.-.$e+ #&&%+VV2&.5.&25c.(>.-.$5UDbVd2A>VD'A/V8#''9V8#''9,%%5#&A95 C1 >N5 What s the pattern? Ci>Ni+? Gennis %T notice up-down-up-down Each side can have different properties the amino are on the outside 1f3c the boxes show amino

3 Motifs : Mruzin et at JMB 1995 (Cyrus Chothia) Cath: Orengo et al Structure 1997 (Janet Thornton) Each starts with domains Homolog - Phylogenetically related - derived from a common ancestor gene. (PFAM-genes; e/cathstructures). ifications are descriptive; Structural diversity comes from evolution - we use classification to deduce evolutionary relationships. Ortholog - retain the same function Paralog - function has diverged Family: related with similar function Superfamily: related with different functions Gennis: structure Gennis: structure Generally with very similar sequences you have a very similar fold. There are RARE cases where this is not true (even with different folds under different conditions) Proteins with similar fold can have different sequence. Fold is more conserved than sequence & convergent evolution can lead to similar folds. Proteins are made domains. A domain is a structural an evolutionary unit. They have 50-0 residues. Compact folded unit, quasi-independent structurally functionally Domains that are or come from a common ancestor. similar sequence - family diverged sequence but similar fold function - superfamily Chothia Gough (Biochem J (09) 9, 15-28

4 SCIENCE VOL JUNE 03 Fig. 2. An example a supradomain. The P-loop containing NTP hydrolase domain the Translation Proteins domain (5) occur in prokaryotic eukaryotic translation factors that hydrolyze guanosine triphosphate (GTP). GTP hydrolysis in the P-loop domain drives the conformational change in the Translation Proteins domain, which is then transmitted onto the ribosome. The supradomain occurs in 35 different domain architectures, 6 these are given here. The nset at left shows a protein known structure, which contains the supradomain. IF, initiation actor; EF, elongation factor; RF, factor; trna, transfer RNA. Figure 3. Glycosyl Hydrolases (A C) (A) (1/3)-b-glucanase (Varghese et al., 1994) represents the basic (Trans) glycosidases superfamily (c.1.8). Homologous catalytic domains are found in (B) b-glucuronidase (C) b-galactosidase. (B) In b-glucuronidase (Jain et al., 1996), the catalytic domain is 3 (in red) is joined by two other domains: 1 restricts the binding site, 2 links 1 to 3. (C) b-galactosidase.the first three domains have the same structure as b-glucuronidase (Jacobson et al., 1994). Domain 4 links domain 3 to 5, which contributes to the active site. Bashton Chothia: structure 15: (07) Dominant mechanisms that produce new are Duplication the genes old divergence these sequences to produce modified functions combination genes to further modify properties Many are multi-domain. Chothia Gough (Biochem J (09) 9, CATH : α,β,αβ Architecture: gross arrangement 2 structure independent connectivity Topology: Fold family linking 2 structure Fold=Topology 3 Homologous superfamily structure similar function similar 2386 Sequence family >35% identity domains : α,β,αβ,α+β Fold same 2 structure elements same topology not related Superfamily Common evolutionary origin low seq identity 1962 Family >30% identical or >15% with same function 92 ification: based on structure sequence (C-level): secondary structure composition contacts. The first, most general level the classification, class, describes the relative content α helices β sheets in a similar way to that described by Levitt Chothia [29], except that we only define three major classes mainly α, mainly β α β. Although the latter class can be sub- divided into alternating α/β α+β, in CATH, this information is considered at a lower level describing topology. Architecture (A-level): description the gross arrangement secondary structures, independent connectivity This level distinguishes structures in the same class with different architectures, but does not distinguish between different topologies (connectivities). The architectural groupings can sometimes be rather broad as they describe general features protein-fold shape, for example, the number layers in an α-β swich. A given architecture will contain structures with diverse connectivities (see Figure 2) which will be distinguished at the next level down (topology). For example, in the α-β class (C = 3), there are two common architectures each containing a large number different fold. One is the barrel- like architecture (A = ) adopted, (egtim-barrel folds). These have an inner β barrel an outer layer α helices (Figure 2). Alternatively, the three-layer α-β swich architecture (A = 40) consists a central β sheet which is covered by a layer α helices on both sides the sheet (Figure 2). Topology (T-level): fold Structures which are grouped at the T-level have the same overall fold, which means that they have a similar number arrangement secondary structures that the connectivity linking their secondary structure elements is the same. In this paper, the words fold topology have the same meaning. Proteins with the same CAT numbers have the same class, architecture topology but do not necessarily belong to the same homologous superfamily.within a given topology level, the structures are similar, but may have diverse functions. Homologous superfamily (H-level): highly similar structures functional similarity At the H-level, structures are grouped by their high structural similarity similar functions, which suggest that they may have evolved from a common ancestor, particularly, where there are resemblances in core packing or putative active sites. Using the example the mainly α.non-bundle. globin-like folds the erythrocruorins, colicins, phycocya- nins domain 1 diptheria toxin all have the same CAT number (1..340), but are differentiated by their H numbers,, 30 40, respectively (see Figure 3). Sequence family (S-level): significant sequence similarity thus a high probability having similar structure/function Members which are clustered at this level (having the same CATHS number) have sequence identities >35% as such are presumed to have extremely similar structures functions they may be slightly different examples the same protein from different species belonging to the same sequence superfamily. Some have many protein domains found (9 take up % the human genome) others have few. There are in animals; bacteria Many are found in all kingdoms life. Chothia Gough (Biochem J (09) 9, 15-28

5 Structural ification Proteins Structural ification Proteins : :Structural Structuralification ification PDB PDB (1 (1Aug Aug1998). 1998) Domains. Domains ification ification Orengo :93 et at: Structure folds folds Structural ification Proteins Structural ification Proteins 25 : :Structural Structural ification ification : Structural ification PDB PDB (1(1Aug 1998) Domains. Domains ). 70Aug PDB (23 Feb 09) Domains Reference : Structural ification PDB (23 Feb 09) Domains. 1 Reference 113 folds folds : Structural ification folds PDB (23 Feb ification 09) Reference Domains. 6 : Structural surface 12 folds PDB (23Feb 09) Domains. 1 Reference ification ification CATH version 3.3 (class, architecture, topology, homology) contains domains, 2386 homologous 3 fold groups folds surface 12 folds surface surface surface surface : :Structural Structuralification ification Nucleic Acids Research 01 Alison L Cuff, Ian Sillitoe, Tony Lewis, Andrew B Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David Jones, Janet Thornton, Christine A Orengo ification ification ification ification PDB PDB ( (Oct Oct1997). 1997) Domains. Domains.1 1 ification : :Structural Structuralification ification PDB PDB ( (Oct Oct1997). 1997) Domains. Domains.1 1 folds ification folds ification ification : Structural ification folds folds PDB (26 Sep 07). Reference Domains : Structural ification : Structural 1.73 ification PDB PDB (26 Sep 07) Reference Domains (26 Sep 07). 971 Domains Reference : Structural ification PDB (26 Sep 07). 11 Reference Domains folds surface folds folds 459 surface folds Page 1 9 Copyright The scop / /scop@mrc-lmb.cam.ac.uk Copyright The scopauthors authors scop@mrc-lmb.cam.ac.uk Page 1 9 Copyright The Copyright Thescop scopauthors authors/ /scop@mrc-lmb.cam.ac.uk scop@mrc-lmb.cam.ac.uk June June09 09 June June09 09 PagePage PagePage PagePage Figure 2 Schematic representation the class (C), architecture (A) topology (T) level in the C ATH database. Helices are drawn in blue strs are drawn as magenta arrows. The barrel, three-layer swich roll architectures (A-level) are shown for the α β class. Two representatives from fold in the three-layer swich architecture are shown. Cuff... Orengo Structure 17, 51 62, August 12, 09 The structural universe as revealed by CATH Research Article CATH: classification protein structures Orengo et al. 97 Figure 3 C ATH numbering scheme for representative structures from the globin-like fold family in the mainly α class. Four the seven levels within the C ATH database are shown, associated with C lass, Architecture, Topology, Homology. Each level is associated with a unique number. The (A), (T) (H) levels are numbered in bins ten to allow expansion the database. Architecture 1 Mainly α 2 Mainly β 3 4 Non-bundle α β Bundle Few SS 30 Few SS Topology Homology Variant surface glycoprotein Glucoamylase, domain 2 4 Globin-like 500 Although 5993 protein chains (80 domains) were selected for CATH from the September 1996 the PDB, sequence comparisons showed that approximately three quarters these were nearly identical (see Figure 1, Tables 1 2). CATH grouped the 80 domain structures into 21 non-identical (N-level). By assuming that with more than 35% sequence similarity adopt the same fold share a common evolutionary ancestor, this number can be reduced to 68 sequence (S-level). More distant relatives were added to these by searching for significantly high structural similarity related biological functions, thereby reducing the number homologous to 645 (H-level). If a lower degree structural similarity is allowed, these further group to give a total 505 1hlm Casein kinase δ.. 1cpc chain A col chain A 40 1ddt domain through overlap a large motif containing five β strs. This is not currently done in C ATH, as both are commonly referred to as separate folds in the literature. Mainly α.non-bundle.globin-like.1cpc chain A somewhat broad category, the fold within this barrel architecture all share a common structural feature comprising a single β sheet. Similarly, the three-layer α β swich architecture also represents a large grouping folds varying sizes (containing β sheets having from 4 to 17 β-strs). Again, all the folds within this architecture can be simply usefully described as having a central β sheet with layers α helices on each its sides (see Figure 2). Wherever possible, we have used architectural descriptions commonly cited in the literature. For a majority the folds (>80%) this was a simple straightforward process the architectural categories assigned agreed well with those given in other publicly available databases (e.g. [17]). For more complex shapes, no architecture was assigned, these folds were all placed in a single complex bin until alternative assignment methods are developed. Such methods will probably describe shape according to the diverse motifs contained within the fold the ways in which these motifs are combined in 3D space. The variety architectures that can easily be assigned by visual inspection is shown, for each class, in Figure 4. For mainly α only the familiar four-helix bundle architecture is easily distinguishable. Other helix arrangements Overview architectures The CATH architecture level is a subjective grouping folds having similar shape, regardless differences in scale or numbers secondary structures. For example, both the 5-stred barwin-like β-barrel folds the 17-stred porin-like β-barrel folds are assigned to the same general β-barrel architecture. Although this is a Illustration motif overlaps in the mainly β swich architecture. Each structure shown can be related to the central tenascin structure by a motif containing at least four β strs (although these are not sequential in the transthyretin structure) up to seven β strs in plastocyanin the -76 immunoglobulin variable domain structures. It can be seen that this results in the possible merging the immunoglobulin fold family (2rhe) the jelly-roll fold family (1tnfA) Figure 9 βlactamase, domain 2 5 fold (T-level), within which similarity may be a result divergent or convergent evolution. These fold are further grouped within CATH, automatically according to class manually according to their architecture giving a total 3 major classes 28 different architectures (see Table 1). Figure 1 shows the annual increase in structures structural for each level in the CATH hierarchy. 1TTF.pdb SHEET 1 SHEET 2 SHEET 3 SHEET 1 SHEET 2 SHEET 3 SHEET GLU A 9 THR A SER A 17 ASP A 23-1 O SER A 21 N GLU A THR A 56 SER A 60-1 N ALA A 57 O ILE A 2 4 GLN A 46 PRO A TYR A 31 GLU A 38-1 N TYR A 36 O GLN A VAL A THR A 76-1 N VAL A 75 O TYR A ILE A 88 THR A 94-1 N ILE A 88 O VAL A 72

6 14 Figure 9 Illustration motif overlaps in the mainly β swich architecture. Each structure shown can be related to the central tenascin structure by a motif containing at least four β strs (although these are not sequential in the transthyretin structure) up to seven β strs in plastocyanin the immunoglobulin variable domain structures. It can be seen that this results in the possible merging the immunoglobulin fold family (2rhe) the jelly-roll fold family (1tnfA) through overlap a large motif containing five β strs. This is not currently done in C ATH, as both are commonly referred to as separate folds in the literature. 10 Bron Tooze Figure 4 prediction (from sequence) methods. It would therefore seem more useful to subclassify these regions fold space according to more sophisticated criteria for structural similarity, in order to generate smaller containing closer relatives. These criteria would be based on recognising similarities within the cores the protein structures belonging to a particular family setting tolerances on the number allowed secondary structure indels. With this aim, a suite programs (CORA, COnsensus Residues Attributes) for analysing structural has been developed (CAO, unpublished data) will be applied to all the superfold within the CATH database. It is planned that future s CATH will assign structures to fold within the superarchitectures according to the diagnostics generated by CORA. Interestingly, an analysis the distribution domain structures in non-homologous multidomain showed that only 8.1% these domains occur also as single domain only 5% recur in other multidomain. Identification multidomains recurrence folds within multidomain Until we improve our understing structural constraints on secondary structure packing, the ideal a completely automatic approach generating self-consistent reproducible hierarchies at all levels is not feasible. Some approaches avoid this problem by clustering on the basis overlapping helices, strs or small common motifs, regardless 3D arrangement. Such motif-based classifications, however, are generally less useful for revealing global structural relationships between evolutionary related. We chose, therefore, to use an By applying the consensus domain boundary assignment procedure to all N-representatives (7 ) in the September 1996 version CATH, 74% the total number single domains (515) could be assigned automatically 21% the total number multidomain (272). Of those remaining unassigned, at least one the methods gave acceptable boundary assignments, needing no or only minor adjustments. Research Article CATH: classification pro Future developments: automatic architecture assignment The CATH architectural groupings are currently broad, general, categories that represent a preliminary classification which should significantly aid a future, more detailed analysis common architectural features. Although, these groups are assigned manually, other publicly available classifications have adopted a similar pragmatic approach, using a combination automatic manual approaches where appropriate (, DIAL [17,27]). Research Article CATH: classification protein structures Orengo et al. Research Article CATH: classification protein structures Orengo et al. 11 Research Article CATH: classification protein structures Orengo et al architectures identified for the mainly α, mainly β α β classes Research Article CATH: classification protein structures O rengo et al. 11 M O LS C RIPT [33] representations the architectures identified for the mainly α, mainly β α β classes (PD B codes are given in parentheses). architectures identified for the mainly α, mainly β α β classes M O LS C RIPT [33] representations the architectures identified for the mainly α, mainly β α β classes (PD B codes are given in parentheses). more pround disturbances to the architecture. This is structures in these regions fold space. This means because, in addition to the ability to exp by adding on similar motifs (which may arise from gene duplica for these architectures it is perhaps more more pround disturbances appropriate to the architecture. This isa continuum structures these regions fold space. This means tion), layer-based architectures can further accommodate to consider inprotein folds. This to the ability to exp by adding evolutionary changes by allowing thebecause, layers in to addition slide relais particularly apparent in the layer-based swich archion similar motifs (which may arise from gene duplica- for these architectures it is perhaps more M O LS C RIPT [33] representations the architectures identified for the mainly α, mainly β α β classes more pround disturbances to the architecture. This is because, in addition to the ability to exp by adding on similar motifs (which may arise from gene duplication), layer-based architectures can further accommodate evolutionary changes by allowing the layers to slide relative to each other. This mechanism would not be available to complex architectures possessing a more diffuse hydrophobic core. structures in these reg that it becomes harder to for these archite appropriate to consider a c is particularly apparent in tectures the mainly β within the α β three-laye is possible to generate a using the simple criteria M O LS C RIPT [33] representations the architectures identified for the mainly α, mainly β α β classes (PD B codes are given in parentheses). M O LS C RIPT [33] representations the architectures identified fold for the mainly α, β doll α βeffect classes (PD B codes are given in parentheses). Overlap between : themainly Russian (SSAP score > = 70) Each new structure added The recurrence common motifs within many the last by a simple extension superfolds major architectures gives rise to an overlap more pround disturbances to the architecture. This is structures in these regions fold space. This means more pround disturbances to the architecture. This is structures in these regions fold space. This means because, in addition to the ability to exp by adding because, in addition to the ability to exp by adding on similar motifs (which may arise from gene duplica for these architectures it is perhaps more on similar motifs (which may arise from gene duplica for these architectures it is perhaps more tion), layer-based architectures can further accommodate appropriate to consider a continuum protein folds. This tion), layer-based architectures can further accommodate appropriate to consider a continuum protein folds. This evolutionary changes by allowing the layers to slide relais particularly apparent in the layer-based swich archievolutionary changes by allowing the layers to slide relais particularly apparent in the layer-based swich architive to each other. This mechanism would not be availtectures the mainly β α β classes. For example, tive to each other. This mechanism would not be availtectures the mainly β α β classes. For example, able to complex architectures possessing a more diffuse within the α β three-layer doubly wound architectures, it able to complex architectures possessing a more diffuse within the α β three-layer doubly wound architectures, it hydrophobic core. is possible to generate a very large family structures hydrophobic core. is possible to generate a very large family structures using the simple criteria a good structural comparison using the simple criteria a good structural comparison Overlap between fold : the Russian doll effect (SSAP score > = 70) reasonable overlap (> = 60%). Overlap between fold : the Russian doll effect (SSAP score > = 70) reasonable overlap (> = 60%). Each new structure added to a family will be related to the The recurrence common motifs within many the Each new structure added to a family will be related to the The recurrence common motifs within many the last by a simple extension one or more βαβ motifs superfolds major architectures gives rise to an overlap last by a simple extension one or more βαβ motifs superfolds major architectures gives rise to an overlap

7 Atpase 1BMF-Bovine ATPase F1 Chain A all Left hed superhelix P-loop containing nucleoside trip hydrolase Vogal et al: Current Opinion in Structural Biology 04: 14: 8-216