Wenxiang: a web-server for drawing wenxiang diagrams

doi:10.4236/ns.2011.310111

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Vol.3, No.10, 862-865 (2011) Natural Science

http://dx.doi.org/10.4236/ns.2011.310111

Wenxiang: a web-server for drawing wenxiang diagrams

Kuo-Chen Chou1*, Wei-Zhong Lin2,3, Xuan Xiao1,3

1Gordon Life Science Institute, San Diego, California, USA; *Corresponding Author: [email protected]

2Information Science and Technology School, Donghua University, Shanghai, China;

3Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.

Received 15 September 2011, revised 16 October 2011; accepted 23 October 2011.

ABSTRACT

The wenxiang diagram was proposed to repre-

sent α-helices in a 2D (two dimensional) space

(Chou, K.C., Zhang, C.T., Maggiora, G.M. Proteins:

Struct., Funct., Genet., 1997, 28, 99-108). It has

the capacity to provide more information in a 2D

plane about each of the constituent amino acid

residues in an α-helix, and is particularly useful

for studying and analyzing amphiphilic helices.

To meet the increasing requests for getting the

program of generating wenxiang diagrams, a

user-friendly web-server called “Wenxiang” has

been established. It is accessible to the public at

the web-site http ://www. jci- bioinfo.cn/w enxiang2

or http://icpr.j ci.edu.cn/bioinfo/w enxiang2. Further-

more, for the convenience of users, here we

provide a step-to-step guide for how to use the

Wenxiang web-server to generate the desired

wenxiang diagrams.

Keywords: Amphiphilic Helix; Helix-Helix

Interaction; Hydrophobic; Hydrophilic; 2D Diagram;

Wenxiang Diagram; Helical Wheel Diagram

1. INTRODUCTION

The α-helix is one of the most basic and fundamental

elements in protein structure [1]. Owing to their regular-

ity, α-helices have had an immense influence on our un-

derstanding of protein structure. Also, owing to their

elasticity, many marvelous biological functions of pro-

teins can be revealed through the low-frequency accor-

dion-like motions of α-helices (see, e.g., [2-4] and a

comprehensive review [5]).

Using graphical or diagrammatic approaches to study

biological systems can provide an intuitive picture or

useful insights for helping analyzing their complicated

mechanisms, as demonstrated by many studies on a se-

ries of important biological topics, such as enzyme-

catalyzed reactions [6-9], protein folding kinetics [10,11],

inhibition of HIV-1 reverse transcriptase [12-14], inhibi-

tion kinetics of processive nucleic acid polymerases and

nucleases [15], drug metabolism systems [16], protein

attribute prediction [17,18], protein sequence evolution

[19], among many others.

Since the “pen-and-paper space” and most of the “pub-

lication space” are two-dimensional (2D) space, it is

desirable to represent the 3D structures of α-helices on a

2D plane. In this regard, two different kinds of diagrams

are usually used to represent α-helices. One is called the

“helical wheel diagram” [20], and the other called “wen-

xiang diagram” [21]. The name of the latter came from

the fact that it looks like a coil-like incense used in China

to repel mosquitoes, i.e., Chinese “蚊香” (pronounced as

“wenxiang”). For its shape and appearance, click the link

http://wapedia.mobi/zh /%E8%9A%8A%E9%A6%99.

According to its original definition [21], a 2D wen-

xiang diagram is generated by a conical projection of an

α-helix onto a plane perpendicular to its axis (Figure 1).

For a rigorous definition of an α-helix’s axis, see [22]. In

the 2D wenxiang diagram each amino acid residue is

represented by a circle with a letter to indicate its single

character code, while its location in the 2D plane is de-

fined by both an angle around the helix’s axis and the

distance from the center, the intersection point between

the 2D plane and the helix’s axis, as elaborated in [21].

As a 2D representation, the wenxiang diagram has the

following features: (i) able to show the relative locations

of the amino acids in an alpha-helix regardless how long

it is; (ii) able to indicate the direction of an alpha-helix;

and (iii) having the capacity to provide more information

about each of the constituent amino acid residues in an

α-helix [21].

With these features, the wenxiang diagram can pro-

vides an intuitive and easily visualizable picture in a 2D

space that characterizes the disposition of different resi-

due types in an α-helix.

As is known, except for transmembrane helices,

α-helices in globular proteins are generally amphiphilic,

i.e., consist of two types of residues, hydrophobic and

hydrophilic, with the number of each type being roughly

K. C. Chou et al. / Natural Science 3 (2011) 862-865

863

Figure 1. Conical projection of a helix H onto a plane

perpendicular to the helix H. The dashed lines represent

the radiating lines from the apex A. The image of helix H

on the projection plane is within the ring area R: the

closer the part of helix H is from the apex A, the further

away its image is from the center of the ring R.

equal. Wenxiang diagrams are particularly useful to help

gain insights into the interactions among amphiphilic

helices or between proteins that contain amphiphilic he-

lices [23,24].

Recently we have received many requests for the pro-

gram of generating wenxiang diagrams. To address these

requests in a unified manner, we have established a web-

server by which one can easily generate the wenxiang

diagram for any α-helix according to its amino acid se-

quence, as described below.

2. EQUIPMENT

You need a computer with access to the Internet and a

web browser.

3. PROCEDURE

You should follow the guide below to generate the

wenxiang diagram for an α-helix.

1) Go to the web page at http://www.jci-bioinfo.cn/

wenxiang2 or http://icpr.jci.edu.cn/bioinfo/wenxiang2, and

you will see the top page of the Wenxiang web-server

on your computer screen, as shown in Figure 2.

2) Click the Read Me button to see the user’s instruc-

tions, which can be elaborated via the following steps.

3) Either type or copy and paste the α-helix amino

acid sequence (in single letter code) into the input box at

the lower centre of Figure 2. If you are not sure about

the input format, click on the button Example right

above the input box to see the format of an acceptable

input sequence.

4) Click on the Black & White button to generate a

black-and-white wenxiang diagram (Figure 3), where

hydrophobic residues are shown by “black-filled circles

with white characters” while hydrophilic residues by

“open circles with black characters”. It will take about

20 seconds before the desired diagram is completely

shown on the screen.

5) Or alternatively, click the button Color to generate

a color wenxiang diagram (Figure 4), where hydropho-

bic residues are shown by “red-filled circles with white

characters” while hydrophilic residues by “blue-filled

circles with black characters.

Figure 2. A screenshot of the top page of the Wenxiang

web-server at http://www.jci-bioinfo.cn/wenxiang2 or

http://icpr.jci.edu.cn/bioinfo/wenxiang2.

Figure 3. The black-and-white wenxiang diagram gener-

ated by clicking the Black & White button of the

web-server for the input sequence taken from the Exam-

ple; the “black-filled circles with white characters” rep-

resent the hydrophobic residues, while the “open circles

with black characters” hydrophilic residues.

K. C. Chou et al. / Natural Science 3 (2011) 862-865

864

Figure 4. The color wenxiang diagram generated by

clicking the Color button of the web-server for the same

input sequence as in Figure 3. The “red-filled circles

with white characters” represent hydrophobic residues,

while the “blue-filled circles with black characters” rep-

resent the hydrophilic residues.

Figure 5. The black-and-white wenxiang diagram gener-

ated by clicking the Black & White button of the

web-server for the input sequence XXAEAVQQ-

LNHTIVNAAHELHETLGX that contains invalid codes

in its 1st, 2nd and last positions. The three “open circles”

represent the three invalid codes at the 1st, 2nd, and last

positions, respectively.

6) To save the wenxiang diagram, click it with the right

mouse button.

7) Click on the Citation button to find the relevant

papers that document the detailed development of

wenxiang diagram and some of its applications.

Figure 6. The color wenxiang diagram generated by

clicking the Color button of the web-server for the same

input sequence in Figure 5. The three “yellow-filled cir-

cles” represent the three invalid codes at the 1st, 2nd, and

last positions of the sequence, respectively.

4. DISCUSSION

The valid codes for a native α-helix should be within

the 20 characters ACDEFGHIKLMNPQRSTVWY, which

represent 20 native amino acids, respectively.

If your sequence contains some invalid codes, after

clicking the Black & White button, a warning message

will occur on the screen. If you still want to generate the

wenxiang diagram, just click the OK button. However,

the wenxiang diagram thus generated will contain some

“open circles” with each corresponding to one of the

invalid codes. For example, for the input sequence

XXAEAVQQLNHTIVNAAHELHETLGX where the first

two codes and the last one are invalid, the wenxiang

diagram thus generated will look like the one shown in

Figure 5.

The similar situation will also occur when clicking the

Color button to generate the color wenxiang diagram for

the above invalid sequence, in which case each of the

invalid codes will be shown by a “yellow-filled circle”

as shown in Figure 6.

The wenxiang diagrams thus generated for non-native

helices that contain invalid codes may give you some

flexibility for studying hypothetical α-helices.

5. ACKNOWLEDGEMENTS

This work was supported by the grants from the National Natural

Science Foundation of China (No. 60961003), the Key Project of Chi-

nese Ministry of Education (No. 210116), and the Department of Edu-

cation of Jiangxi Province (No. GJJ11557).

K. C. Chou et al. / Natural Science 3 (2011) 862-865

865

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