Laura's Portfolio
Classwork for BIMM143
Class 9: Structural Bioinformatics (pt.1)
Laura Lu (PID: A17844089)
The main database for structural biology is called the PDB. Let’s have a look at what it contains:
Download a CSV file from the PDB site (accessible from “Analyze” > “PDB Statistics” > “by Experimental Method and Molecular Type”.)
stats <- read.csv("Data Export Summary.csv")
stats
Molecular.Type X.ray EM NMR Integrative Multiple.methods
1 Protein (only) 176,204 20,299 12,708 342 218
2 Protein/Oligosaccharide 10,279 3,385 34 8 11
3 Protein/NA 9,007 5,897 287 24 7
4 Nucleic acid (only) 3,066 200 1,553 2 15
5 Other 173 13 33 3 0
6 Oligosaccharide (only) 11 0 6 0 1
Neutron Other Total
1 83 32 209,886
2 1 0 13,718
3 0 0 15,222
4 3 1 4,840
5 0 0 222
6 0 4 22
stats$Total
[1] "209,886" "13,718" "15,222" "4,840" "222" "22"
Oh, these are characters not numeric…
stats$Total
[1] "209,886" "13,718" "15,222" "4,840" "222" "22"
as.numeric( sub("," , "" ,stats$Total) )
[1] 209886 13718 15222 4840 222 22
library(readr)
stats <- read_csv("Data Export Summary.csv")
Rows: 6 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): Molecular Type
dbl (4): Integrative, Multiple methods, Neutron, Other
num (4): X-ray, EM, NMR, Total
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
stats
# A tibble: 6 × 9
`Molecular Type` `X-ray` EM NMR Integrative `Multiple methods` Neutron
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Protein (only) 176204 20299 12708 342 218 83
2 Protein/Oligosacch… 10279 3385 34 8 11 1
3 Protein/NA 9007 5897 287 24 7 0
4 Nucleic acid (only) 3066 200 1553 2 15 3
5 Other 173 13 33 3 0 0
6 Oligosaccharide (o… 11 0 6 0 1 0
# ℹ 2 more variables: Other <dbl>, Total <dbl>
n.total <- sum(stats$Total)
n.total
[1] 243910
Q1. What percentage of structures in the PDB are solved by X-ray and Electron Microscopy? Give your answers to 2 significant figures.
n.xray <- sum(stats$`X-ray`)
round(n.xray/ n.total * 100)
[1] 81
n.xray <- sum(stats$`X-ray`)
precent.xray <- n.xray / n.total * 100
precent.xray
[1] 81.48087
There are 81.48 percent Xray structures in the PDB
Q2. What proportin of structures in the PDB are protein?
round( stats$Total[1]/n.total * 100, 2)
[1] 86.05
library(readr)
stats <- read_csv("Data Export Summary.csv")
stats
# A tibble: 6 × 9
`Molecular Type` `X-ray` EM NMR Integrative `Multiple methods` Neutron
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Protein (only) 176204 20299 12708 342 218 83
2 Protein/Oligosacch… 10279 3385 34 8 11 1
3 Protein/NA 9007 5897 287 24 7 0
4 Nucleic acid (only) 3066 200 1553 2 15 3
5 Other 173 13 33 3 0 0
6 Oligosaccharide (o… 11 0 6 0 1 0
# ℹ 2 more variables: Other <dbl>, Total <dbl>
Q3. Type HIV in the PDB website search box on the home page and determine how many HIV-1 protease structures are in the current PDB?
4,866 Structures
Exploring PDB structures
Package for structural bioinformatics
library(bio3d)
hiv <- read.pdb("1hsg")
Note: Accessing on-line PDB file
hiv
Call: read.pdb(file = "1hsg")
Total Models#: 1
Total Atoms#: 1686, XYZs#: 5058 Chains#: 2 (values: A B)
Protein Atoms#: 1514 (residues/Calpha atoms#: 198)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 172 (residues: 128)
Non-protein/nucleic resid values: [ HOH (127), MK1 (1) ]
Protein sequence:
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPQITLWQRPLVTIKIGGQLKE
ALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTP
VNIIGRNLLTQIGCTLNF
+ attr: atom, xyz, seqres, helix, sheet,
calpha, remark, call
Let’s first use the Mol* viewer to explore this structure.
hiv <- read.pdb("1hsg")
Note: Accessing on-line PDB file
Warning in get.pdb(file, path = tempdir(), verbose = FALSE):
/var/folders/jd/9031898564z2k2xvgkt_58gw0000gn/T//RtmpiaPXM4/1hsg.pdb exists.
Skipping download
hiv
Call: read.pdb(file = "1hsg")
Total Models#: 1
Total Atoms#: 1686, XYZs#: 5058 Chains#: 2 (values: A B)
Protein Atoms#: 1514 (residues/Calpha atoms#: 198)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 172 (residues: 128)
Non-protein/nucleic resid values: [ HOH (127), MK1 (1) ]
Protein sequence:
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPQITLWQRPLVTIKIGGQLKE
ALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTP
VNIIGRNLLTQIGCTLNF
+ attr: atom, xyz, seqres, helix, sheet,
calpha, remark, call
And a view of the ligand (ball and stick) with catalytic ASP 25 amino-acids (spacefill) and the all important active site water molecule (spacefill):
PDB objects in R
head( hiv$atom )
type eleno elety alt resid chain resno insert x y z o b
1 ATOM 1 N <NA> PRO A 1 <NA> 29.361 39.686 5.862 1 38.10
2 ATOM 2 CA <NA> PRO A 1 <NA> 30.307 38.663 5.319 1 40.62
3 ATOM 3 C <NA> PRO A 1 <NA> 29.760 38.071 4.022 1 42.64
4 ATOM 4 O <NA> PRO A 1 <NA> 28.600 38.302 3.676 1 43.40
5 ATOM 5 CB <NA> PRO A 1 <NA> 30.508 37.541 6.342 1 37.87
6 ATOM 6 CG <NA> PRO A 1 <NA> 29.296 37.591 7.162 1 38.40
segid elesy charge
1 <NA> N <NA>
2 <NA> C <NA>
3 <NA> C <NA>
4 <NA> O <NA>
5 <NA> C <NA>
6 <NA> C <NA>
Extract the sequence
pdbseq(hiv)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
"P" "Q" "I" "T" "L" "W" "Q" "R" "P" "L" "V" "T" "I" "K" "I" "G" "G" "Q" "L" "K"
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
"E" "A" "L" "L" "D" "T" "G" "A" "D" "D" "T" "V" "L" "E" "E" "M" "S" "L" "P" "G"
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
"R" "W" "K" "P" "K" "M" "I" "G" "G" "I" "G" "G" "F" "I" "K" "V" "R" "Q" "Y" "D"
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
"Q" "I" "L" "I" "E" "I" "C" "G" "H" "K" "A" "I" "G" "T" "V" "L" "V" "G" "P" "T"
81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 1
"P" "V" "N" "I" "I" "G" "R" "N" "L" "L" "T" "Q" "I" "G" "C" "T" "L" "N" "F" "P"
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
"Q" "I" "T" "L" "W" "Q" "R" "P" "L" "V" "T" "I" "K" "I" "G" "G" "Q" "L" "K" "E"
22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
"A" "L" "L" "D" "T" "G" "A" "D" "D" "T" "V" "L" "E" "E" "M" "S" "L" "P" "G" "R"
42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61
"W" "K" "P" "K" "M" "I" "G" "G" "I" "G" "G" "F" "I" "K" "V" "R" "Q" "Y" "D" "Q"
62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
"I" "L" "I" "E" "I" "C" "G" "H" "K" "A" "I" "G" "T" "V" "L" "V" "G" "P" "T" "P"
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
"V" "N" "I" "I" "G" "R" "N" "L" "L" "T" "Q" "I" "G" "C" "T" "L" "N" "F"
chainA_seq <- pdbseq( trim.pdb(hiv, chain="A") )
I can interactively view these PDB objects in R with the new bio3dview package. This is not yet on CRAN.
To install this I can setup pak package and use it to install bio3dview from Github. In my console I first run
install.packages(“pak”) pak::pak(“bioboot/bio3dview”)
library(bio3dview)
view.pdb(hiv)
file:////private/var/folders/jd/9031898564z2k2xvgkt_58gw0000gn/T/RtmpiaPXM4/file146cc79b55df5/widget146cc722bbe3f.html screenshot completed
Change some settings
sel <- atom.select(hiv, resno=25)
view.pdb(hiv, highlight = sel,
highlight.style = "spacefill",
colorScheme = "chain",
col=c("blue","orange"),
backgroundColor = "pink")
file:////private/var/folders/jd/9031898564z2k2xvgkt_58gw0000gn/T/RtmpiaPXM4/file146cc76bba882/widget146cc1a342bb4.html screenshot completed
Predict protein flexibility
We can run a bioinformatics calculation to predict protein dynamics - i.e. functional motions.
We will use the nma() function:
adk <- read.pdb("6s36")
Note: Accessing on-line PDB file
PDB has ALT records, taking A only, rm.alt=TRUE
adk
Call: read.pdb(file = "6s36")
Total Models#: 1
Total Atoms#: 1898, XYZs#: 5694 Chains#: 1 (values: A)
Protein Atoms#: 1654 (residues/Calpha atoms#: 214)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 244 (residues: 244)
Non-protein/nucleic resid values: [ CL (3), HOH (238), MG (2), NA (1) ]
Protein sequence:
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDKI
VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG
YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG
+ attr: atom, xyz, seqres, helix, sheet,
calpha, remark, call
m <- nma(adk)
Building Hessian... Done in 0.078 seconds.
Diagonalizing Hessian... Done in 0.998 seconds.
plot(m)
Generate a “trajectory” of predicted motion
mktrj(m, file="ADK_nma.pdb")