Rules of thumb when looking at a multiple alignment (MA)

Slides:

Advertisements

Similar presentations

Introduction to bioinformatics Lecture 9 Multiple sequence alignment (3)

Advertisements

Blast to Psi-Blast Blast makes use of Scoring Matrix derived from large number of proteins. What if you want to find homologs based upon a specific gene.

Protein Structure – Part-2 Pauling Rules The bond lengths and bond angles should be distorted as little as possible. No two atoms should approach one another.

©CMBI 2001 The amino acids in their natural habitat.

The amino acids in their natural habitat. Topics: Hydrogen bonds Secondary Structure Alpha helix Beta strands & beta sheets Turns Loop Tertiary & Quarternary.

Trans peptide bond 180 °. 2e Structure Regular pattern of H-bonding Involves backbone (not side chains) C=O … H-N Several consecutive residues.

Strict Regularities in Structure-Sequence Relationship

1 Levels of Protein Structure Primary to Quaternary Structure.

Sequence analysis course Lecture 7 Multiple sequence alignment 3 of 3 Optimizing progressive multiple alignment methods.

1-month Practical Course Genome Analysis Lecture 5: Multiple Sequence Alignment Centre for Integrative Bioinformatics VU (IBIVU) Vrije Universiteit Amsterdam.

The following slides present some answers….. Please don’t peek before doing the exercise!

1-month Practical Course Genome Analysis Lecture 5: Multiple Sequence Alignment Centre for Integrative Bioinformatics VU (IBIVU) Vrije Universiteit Amsterdam.

The relative orientation observed for  helices packed on ß sheets.

Protein Structure Elements Primary to Quaternary Structure.

Protein Structure Lecture 2/26/2003. beta sheets are twisted Parallel sheets are less twisted than antiparallel and are always buried. In contrast, antiparallel.

Pair-wise alignment quality versus sequence identity (Vogt et al., JMB 249, ,1995)

The structural organization within proteins Kevin Slep June 13 th, 2012.

Lecture 10: Protein structure

Introduction to Protein Structure

3-Dimensional Structure of Proteins 4 levels of protein structure:

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

Neural Networks for Protein Structure Prediction Brown, JMB 1999 CS 466 Saurabh Sinha.

Alpha/Beta Structures Branden & Tooze, Chapter 4.

The α-helix forms within a continuous strech of the polypeptide chain 5.4 Å rise, 3.6 aa/turn  1.5 Å/aa N-term C-term prototypical  = -57  ψ = -47 

Bioinformatics Ayesha M. Khan 9 th April, What’s in a secondary database?  It should be noted that within multiple alignments can be found conserved.

Manually Adjusting Multiple Alignments Chris Wilton.

Sequence Based Analysis Tutorial March 26, 2004 NIH Proteomics Workshop Lai-Su L. Yeh, Ph.D. Protein Science Team Lead Protein Information Resource at.

Medical Natural Sciences Year 2: Introduction to Bioinformatics Lecture 9: Multiple sequence alignment (III) Centre for Integrative Bioinformatics VU.

Protein backbone Biochemical view:

Introduction to bioinformatics Lecture 7 Multiple sequence alignment (1)

V diagonal lines give equivalent residues ILS TRIVHVNSILPSTN V I L S T R I V I L P E F S T Sequence A Sequence B Dot Plots, Path Matrices, Score Matrices.

V diagonal lines give equivalent residues ILS TRIVHVNSILPSTN V I L S T R I V I L P E F S T Sequence A Sequence B Dot Plots, Path Matrices, Score Matrices.

Marlou Snelleman 2012 Protein structure. Overview Sequence to structure Hydrogen bonds Helices Sheets Turns Hydrophobicity Helices Sheets Structure and.

Mir Ishruna Muniyat. Primary structure (Amino acid sequence) ↓ Secondary structure （ α -helix, β -sheet ） ↓ Tertiary structure （ Three-dimensional.

Protein Structure and Properties

The heroic times of crystallography

Introduction to bioinformatics 2008 Lecture 8

Figure 3.14A–D Protein structure (layer 1)

Aligning Sequences You have learned about: Data & databases Tools

Introduction to bioinformatics 2007 Lecture 10

Amino acids R-groups non-polar polar acidic basic proteins

Secreted Fringe-like Signaling Molecules May Be Glycosyltransferases

Volume 8, Issue 3, Pages (March 2000)

Sequence Based Analysis Tutorial

Multiple sequence alignment Why?

Antimicrobial peptides: broad-spectrum antibiotics from nature

بیوشیمی : پروتئین ها و لیپیدها

1-month Practical Course

The 20 amino acids.

Levels of Protein Structure

Homology modelling by distance geometry

The 20 amino acids.

David R Buckler, Yuchen Zhou, Ann M Stock Structure

Volume 14, Issue 2, Pages (February 2006)

Protein Structure INTRODUCTION OF PROTIEN. Organic compounds containing C,H,O,N,P,S Comprise 50% of dry weight of cell. Made up of Amino acids. Protein.

Volume 5, Issue 7, Pages (July 1997)

Volume 124, Issue 5, Pages (March 2006)

Volume 2, Issue 7, Pages (July 1994)

Qian Steven Xu, Rebecca B. Kucera, Richard J. Roberts, Hwai-Chen Guo

Predicting protein structure and function

Ideas of Order for Amyloid Fibril Structure

Introduction to bioinformatics lecture 9

Lecture 10 Secondary Structure Prediction

Introduction to bioinformatics Lecture 8

Hideki Kusunoki, Ruby I MacDonald, Alfonso Mondragón Structure

Volume 12, Issue 11, Pages (November 2004)

Three protein kinase structures define a common motif

Green Fluorescent Protein

Green Fluorescent Protein

Looking at periodicity in protein sequence and structure

Presentation transcript:

Rules of thumb when looking at a multiple alignment (MA) Hydrophobic residues are internal Gly (Thr, Ser) in loops MA: hydrophobic block -> internal -strand MA: alternating (1-1) hydrophobic/hydrophilic => edge -strand MA: alternating 2-2 (or 3-1) periodicity => -helix MA: gaps in loops MA: Conserved column => functional? => active site

Rules of thumb when looking at a multiple alignment (MA) … cont. Active site residues are together in 3D structure Helices often cover up core of strands Helices less extended than strands => more residues to cross protein -- motif is right-handed in >95% of cases (with parallel strands) MA: ‘inconsistent’ alignment columns and match errors! Secondary structures have local anomalies, e.g. -bulges

Amino acid properties

Amino acid hydrophobicity scale hydrophilic

Burried and Edge strands Parallel -sheet Anti-parallel -sheet

Periodicity patterns within secondary structures Burried -strand Edge -strand -helix = hydrophilic = hydrophobic

TOPS diagrams Circle = helix Triangle = strand

-- motif is right-handed in >95% of cases LH RH

Flavodoxin-cheY example: 5() 1fx1 -PKALIVYGSTTGNT-EYTAETIARQLANAG-YEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACF FLAV_DESDE MSKVLIVFGSSTGNT-ESIaQKLEELIAAGG-HEVTLLNAADASAENLADGYDAVLFgCSAWGMEDL------EMQDDFLSLF-EEFNRFGLAGRKVAAf FLAV_DESVH MPKALIVYGSTTGNT-EYTaETIARELADAG-YEVDSRDAASVEAGGLFEGFDLVLLgCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACf FLAV_DESSA MSKSLIVYGSTTGNT-ETAaEYVAEAFENKE-IDVELKNVTDVSVADLGNGYDIVLFgCSTWGEEEI------ELQDDFIPLY-DSLENADLKGKKVSVf FLAV_DESGI MPKALIVYGSTTGNT-EGVaEAIAKTLNSEG-METTVVNVADVTAPGLAEGYDVVLLgCSTWGDDEI------ELQEDFVPLY-EDLDRAGLKDKKVGVf 2fcr --KIGIFFSTSTGNT-TEVADFIGKTLGA---KADAPIDVDDVTDPQALKDYDLLFLGAPTWNTG----ADTERSGTSWDEFLYDKLPEVDMKDLPVAIF FLAV_AZOVI -AKIGLFFGSNTGKT-RKVaKSIKKRFDDET-MSDA-LNVNRVS-AEDFAQYQFLILgTPTLGEGELPGLSSDCENESWEEFL-PKIEGLDFSGKTVALf FLAV_ENTAG MATIGIFFGSDTGQT-RKVaKLIHQKLDG---IADAPLDVRRAT-REQFLSYPVLLLgTPTLGDGELPGVEAGSQYDSWQEFT-NTLSEADLTGKTVALf FLAV_ANASP SKKIGLFYGTQTGKT-ESVaEIIRDEFGN---DVVTLHDVSQAE-VTDLNDYQYLIIgCPTWNIGEL--------QSDWEGLY-SELDDVDFNGKLVAYf FLAV_ECOLI -AITGIFFGSDTGNT-ENIaKMIQKQLGK---DVADVHDIAKSS-KEDLEAYDILLLgIPTWYYGE--------AQCDWDDFF-PTLEEIDFNGKLVALf 4fxn -MK--IVYWSGTGNT-EKMAELIAKGIIESG-KDVNTINVSDVNIDELL-NEDILILGCSAMGDEVL-------EESEFEPFI-EEIS-TKISGKKVALF FLAV_MEGEL MVE--IVYWSGTGNT-EAMaNEIEAAVKAAG-ADVESVRFEDTNVDDVA-SKDVILLgCPAMGSEEL-------EDSVVEPFF-TDLA-PKLKGKKVGLf FLAV_CLOAB -MKISILYSSKTGKT-ERVaKLIEEGVKRSGNIEVKTMNLDAVD-KKFLQESEGIIFgTPTYYAN---------ISWEMKKWI-DESSEFNLEGKLGAAf 3chy ADKELKFLVVDDFSTMRRIVRNLLKELGFN--NVEEAEDGVDALNKLQAGGYGFVI---SDWNMPNM----------DGLELL-KTIRADGAMSALPVLM T 1fx1 GCGDS-SY-EYFCGA-VDAIEEKLKNLGAEIVQD---------------------GLRIDGD--PRAARDDIVGWAHDVRGAI-------- FLAV_DESDE ASGDQ-EY-EHFCGA-VPAIEERAKELgATIIAE---------------------GLKMEGD--ASNDPEAVASfAEDVLKQL-------- FLAV_DESVH GCGDS-SY-EYFCGA-VDAIEEKLKNLgAEIVQD---------------------GLRIDGD--PRAARDDIVGwAHDVRGAI-------- FLAV_DESSA GCGDS-DY-TYFCGA-VDAIEEKLEKMgAVVIGD---------------------SLKIDGD--PE--RDEIVSwGSGIADKI-------- FLAV_DESGI GCGDS-SY-TYFCGA-VDVIEKKAEELgATLVAS---------------------SLKIDGE--PD--SAEVLDwAREVLARV-------- 2fcr GLGDAEGYPDNFCDA-IEEIHDCFAKQGAKPVGFSNPDDYDYEESKS-VRDGKFLGLPLDMVNDQIPMEKRVAGWVEAVVSETGV------ FLAV_AZOVI GLGDQVGYPENYLDA-LGELYSFFKDRgAKIVGSWSTDGYEFESSEA-VVDGKFVGLALDLDNQSGKTDERVAAwLAQIAPEFGLS--L-- FLAV_ENTAG GLGDQLNYSKNFVSA-MRILYDLVIARgACVVGNWPREGYKFSFSAALLENNEFVGLPLDQENQYDLTEERIDSwLEKLKPAV-L------ FLAV_ANASP GTGDQIGYADNFQDA-IGILEEKISQRgGKTVGYWSTDGYDFNDSKA-LRNGKFVGLALDEDNQSDLTDDRIKSwVAQLKSEFGL------ FLAV_ECOLI GCGDQEDYAEYFCDA-LGTIRDIIEPRgATIVGHWPTAGYHFEASKGLADDDHFVGLAIDEDRQPELTAERVEKwVKQISEELHLDEILNA 4fxn G-----SY-GWGDGKWMRDFEERMNGYGCVVVET---------------------PLIVQNE--PDEAEQDCIEFGKKIANI--------- FLAV_MEGEL G-----SY-GWGSGEWMDAWKQRTEDTgATVIGT----------------------AIVNEM--PDNA-PECKElGEAAAKA--------- FLAV_CLOAB STANSIAGGSDIA---LLTILNHLMVKgMLVYSG----GVAFGKPKTHLGYVHINEIQENEDENARIfGERiANkVKQIF----------- 3chy VTAEAKK--ENIIAA---------AQAGAS-------------------------GYVV-----KPFTAATLEEKLNKIFEKLGM------ G Iteration 0 SP= 136944.00 AvSP= 10.675 SId= 4009 AvSId= 0.313

Building flavodoxin RH