PFAM

PFAM is a database of Hidden Markov Models of protein families and domains, maintained at the Sanger Centre in Cambridge1651. The concept of PFAM is comparable to that of the PROSITE profile section. Similar to the profiles, the HMMs in PFAM have been derived by the iterative refinement procedure mentioned in Sect. 5.2.4. Unlike the PROSITE profiles, which all have been created manually by the curators, the HMMs in PFAM are generated semi-automatically, which accounts for a slightly lower sensitivity. However, this lack is more than compensated for by the facilitated update procedure, allowing the database to grow much faster than PROSITE and to have a shorter generation cycle. Currently, PFAM holds 2727 entries. 

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Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

Tribology performances and applications of ordered molecular films have been a long-standing research subject in SKLT, the workplace for the authors of this book. Hu and Luo [42] prepared SAMs of fluoroalkylsilane (FAS) and poly-fluorealkylmethacrylate (PFAM) on the magnetic head of computer hard disk drivers. Experiment results show that the molecular films greatly improve the performance of the... 

The Influence of the PFAM Concentration on the Film Thickness, the Water Contact Angle, and the Surface Topography... 

The apparatus for the PFAM film coating on the slider surface is shown in Fig. 1 (a). The film thickness was measured by the TOF-SIMS as shown in Fig. 1 (b). It used a pulsed primary Ga+ ion beam to impact the surface of the PFAM film with an inset energy of 15 keV, an extractor current of 2 fj,A, beam current of 600 pA, a pulse width of 17.5 ns, and a frequency of 10 kHz, respectively. The positive TOF-SIMS spectra on the slider surface is shown in Fig. 2 where the peaks at m/z 31, 50, 69, 100, and 131 in Fig. 2(a) correspond to the positive secondary ion fragments of CF+, CFj, C2F4, and C3F5, respectively. The peak at m/z 469 apparent in Fig. 2(b) corresponds to the ion C12H7F 15O2H+ which is the characteristic ion of PFAM molecules. Therefore, the positive TOF-SIMS spectra demonstrates the existence of PFAM film [24,25]. The thickness of the PFAM film can be determined... 

The values of the water contact angle of the PFAM film on the slider surface also increased with the concentration of PFAM solutions (Fig. 5 [26]). The water contact angle increased up to 121 ° at 200 ppm from the initial values of 88.4° without the PFAM film, indicating that the PFAM had covered the slider surface well. For N-Hexane, the contact angle was only about 48°, but the contact area was much larger than that on the slider surface without the PFAM film as shown in Fig. 6. 

Fig. 2— Positions of the positive TOF-SIMS spectra of PFAM thin film on slider, showing the most characteristic fragments (a) positive, m/z=0-150 (b) positive, m/z=460-475.

Figure 8 shows the stiction of the sliders at the different stages of the CSS test from the initial cycle to the final cycle, with the PFAM films prepared at different concentrations [26]. There was a 2 h parking after every 5,000 CSS and a 24 h parking at the end of the final 20,000 CSS. Without PFAM film, the stiction increased with the increase of the... 

Fig. 3- Relation between the PFAM film thickness and CF number.

CSS number or the testing time. At 5 K CSS after a 2 h stop, the stiction increased slightly with the number of flying cycles. At the last cycle after the 24 h stop, the stiction increased to 5.712 g [Fig. 8(a)]. When the PFAM film was formed on the slider surface, even if the concentration was only 50 ppm, the stiction became stable in the whole CSS process [Fig. 8(fc)]. In the case of 500 ppm, the stiction value became much lower and stable than that in other concentrations [Fig. 8(c)]. At the concentration of 1,000 ppm, the stiction in every 5 K CSS remained quite small. However, it increased to 6.484 g after the 24 h stop, which was much larger than that in other conditions. 

To evaluate wear properties of the PFAM film, the friction after 20 K flying cycles was measured by Yang et al. [28] and Hu et al. [26] as shown in Fig. 9. Each cycle of the takeoff and landing process was performed within 2 min. The existence of the PFAM film has no influence on the normal takeoff and landing of the slider. In the case of 50 ppm and 500 ppm, the PFAM film maintained a low friction at the last cycle in a CSS test. The maximum friction value of the latter is less than 2 g, which is about one-third of that of the bare... 

Fig. 5—The thickness and water-contact angle of PFAM thin film as a function of solution concentration.

It can be concluded that the concentrations of the PFAM solution is an important factor for the PFAM film formed on the slider surface to affect the stiction and friction in the CSS tests. If the concentration is controlled around 500 ppm, an ideal surface topography, good hydrophobic nature, a preferred film thickness, and better frictional and anti-wear properties can be obtained. 

Fig. 8—Stiction profiles of (a) bare slider and PFAM thin film in different concentrations (b) 50 ppm (c) 500 ppm (d) 1,000 ppm.

The N-terminal domain of the OCP is an orthogonal alpha-helical bundle, subdivided into two four-helix bundles (Figure 1.3a and c). These subdomains are composed of discontinuous segments of the polypeptide chain (gray and white in Figure 1.3c). To date, the OCP N-terminal domain is the only known protein structure with this particular fold (Pfam 09150). The hydroxyl terminus of the 3 -hydroxyechinenone is nestled between the two bundles. The C-terminal domain (dark... 

Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2000 28[l] 263-266. 

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

The specific format for cross references to the PROSITE and Pfam protein domain and family databases is ... 

DR PROSITE PFAM ACCESSION NUMBER ENTRY NAME STATUS. 

ACCESSION NUMBER" stands for the accession number of the PROSITE or Pfam pattern, profile or HMM entry "ENTRY NAME" is the name of the entry and "STATUS" is one of the following ... 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

Using the domain databases should be considered an important early step in the analysis of any protein. Several of the domain databases are reviewed next. The reader should be aware that the authors are a part of the Pfam consortium and although we have tried to be impartial, the following will almost certainly be a biased view. 

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