Sixth Residue Research Articles

Disordered structural ensembles of vasopressin and oxytocin and their mutants.

Vasopressin and oxytocin are intrinsically disordered cyclic nonapeptides belonging to a family of neurohypophysial hormones. Although unique in their functions, these peptides differ only by two residues and both feature a tocin ring formed by the disulfide bridge between first and sixth cysteine residues. This sequence and structural similarity are experimentally linked to oxytocin agonism at vasopressin receptors and vasopressin antagonism at oxytocin receptors. Yet single- or double-residue mutations in both peptides have been shown to have drastic impacts on their activities at either receptor, and possibly the ability to bind to their neurophysin carrier protein. In this study we perform molecular dynamics simulations of the unbound native and mutant sequences of the oxytocin and vasopressin hormones to characterize their structural ensembles. We classify the subpopulations of these structural ensembles on the basis of the distributions of radius of gyration and secondary structure and hydrogen-bonding features of the canonical tocin ring and disordered tail region. We then relate the structural changes observed in the unbound form of the different hormone sequences to experimental information about peptide receptor binding, and more indirectly, carrier protein binding affinity, receptor activity, and protease degradation. This study supports the hypothesis that the structural characteristics of the unbound form of an IDP can be used to predict structural or functional preferences of its functional bound form.

Continuous stimulation of the plant immune system by the peptide elicitor PIP-1 is required for phytoalexin biosynthesis in tobacco cells.

The peptide elicitor PIP-1 (YGIHTH-nh2) induced various defense responses in tobacco cells. Types of defense responses induced by PIP-1 were different based on its concentration range: oxidative burst (an early response) was induced at low micromolar levels, but phytoalexin production (a late response) required about 10-50-fold higher concentrations than those required for oxidative burst. We assumed that rapid decreases in the PIP-1 concentration due to enzymatic hydrolysis in the culture media could cause this difference. To examine the potential impact of such degradation particularly on induction of phytoalexin biosynthesis, we designed a degradation-resistant analogue, MePIP-1, in which the amide bond between the fifth and sixth residues was N-methylated. MePIP-1 was considerably more stable than PIP-1 and induced significant phytoalexin production upon treatment at low micromolar levels. Further investigation of the mechanism of action of MePIP-1 showed a requirement of continuous elicitor stimulation for 3-6 h for the phytoalexin production, which is likely to be regulated by long-lasting MAP kinase activation.

Asn441 plays a key role in folding and function of the Na + /I – symporter (NIS)

The Na(+)/I(-) symporter (NIS) is a plasma membrane glycoprotein that mediates active I(-) transport in the thyroid, the first step in the biosynthesis of the iodine-containing thyroid hormones T3 and T4. Several NIS mutants have been identified as a cause of congenital I(-) transport defect (ITD), and their investigation has yielded valuable mechanistic information on NIS. Here we report a thorough characterization of the ITD-causing NIS mutation in which the sixth intracellular loop residues 439-443 are missing. This mutant protein was intracellularly retained, incompletely glycosylated, and intrinsically inactive. Engineering 5 Ala at positions 439-443 partially recovered cell surface targeting and activity (∼15%). Strikingly, NIS with the sequence 439-AANAA-443, in which Asn was restored at position 441, was targeted to the plasma membrane and exhibited ∼95% the transport activity of WT NIS. Based on our NIS homology model, we propose that the side chain of N441, a residue conserved throughout most of the SLC5 family, interacts with the main chain amino group of G444, capping the α-helix of transmembrane segment XII and thus stabilizing the structure of the molecule. Our data provide insight into a critical interhelical interaction required for NIS folding and activity.

Probing the Protein Folding Code through the Polymer Properties of Low-Complexity Sequences

Converting primary structure into the tertiary structure of a protein remains an unsolved problem. Many proteins with highly divergent amino acid sequences have similar structures. Given the redundancy of the folding code, distinguishing signal from noise is an inherent problem. Rather than using the sequences of structurally characterized proteins to discern the code, we have adopted a strategy of first understanding the behavior of low complexity sequences using thermodynamic, kinetic and computational methods. We have inserted homopolymers of alanine, glycine and glutamine ranging from 6 to 30 residues into the N-terminus of yeast iso-1-cytochrome c. To maintain solubility, every sixth residue is lysine. Homopolymers of these amino acids are important because long repeats of these amino acids are often associated with Human disease. The homopolymers are inserted between a unique histidine and the heme allowing measurement of the thermodynamics and kinetics of His-heme loop formation under denaturing conditions ranging from 1.5 to 6 M guanidine hydrochloride (GdnHCl). Kinetic and thermodynamic loop formation data show that these homopolymers adhere closely to the expected linear dependence of loop formation probability on the logarithm of loop size predicted by the Jacobson-Stockmayer equation. Thus, the scaling exponent, ν3, and Flory's Characteristic ratio, Cn, are readily evaluated. In 6 M GdnHCl, all three hompolymers have similar ν3, but at lower GdnHCl concentrations, ν3 decreases for the Glycine-rich sequences relative to the Alanine-rich and Glutamine-rich sequences. Evaluation of Cn shows that chain stiffness follows the order: Glutamine-rich > Alanine-rich > Glycine-rich. We have also shown that insertion of aromatic amino acids into the Alanine-rich sequences significantly stabilizes His-heme loops, providing direct evidence that aromatic residues are structure-forming amino acids critical for biasing the conformational landscape of a polypeptide.

Isolation and Characterization of a Glucan-Type Polysaccharide from the Red Pine Mushroom, Lactarius deliciosus (Higher Basidiomycetes)

A novel glucan-type polysaccharide has been isolated from the fruiting bodies of the edible mushroom Lactarius deliciosus. Two successive extractions (cold aqueous extraction at 25°C and hot aqueous extraction at 100°C) were performed, and the same polysaccharide was obtained in both fractions. The purity of the polysaccharide was evaluated by size exclusion chromatography. The SEC chromatogram showed a unique peak with a molecular weight of approximately 150 kDa. Analysis of the chain composition revealed that the polysaccharide was composed of glucose. Methylation analysis and NMR experiments showed that the glucan-type carbohydrate contained a main chain consisting of α-(1→3)-Glcp units with α-(1→4)-linked branches every sixth glucose residue.

Conformational Properties of Polyglutamine Sequences in Guanidine Hydrochloride Solutions

Two sets of iso-1-cytochrome c variants have been prepared with N-terminal insertions of pure polyglutamine, i.e., PolyQ variants, or polyglutamine interrupted with lysine every sixth residue, i.e., Gln-rich variants. The polymer properties of these pure polyGln or Gln-rich sequences have been evaluated using equilibrium and kinetic His-heme loop formation methods for loop sizes ranging from 22 to 46 in 1.5, 3.0, and 6.0 M guanidine hydrochloride (GdnHCl). In 6.0 M GdnHCl, the scaling exponent, ν3, for the pure polyGln sequences, is ∼1.7—significantly less than ν3 ≈ 2.15 for the Gln-rich sequences. The stability of the His-heme loops becomes progressively greater for the pure polyGln sequences relative to the Gln-rich sequences as GdnHCl concentration decreases from 6.0 to 1.5 M. Thus, the context of the sequence effects the polymer properties of Gln repeats even in denaturing concentrations of GdnHCl. Comparison of data for the Gln-rich variants with previous results for Gly-rich and Ala-rich variants shows that ν3 ∼ 2.2 for the Gln-rich, Gly-rich, and Ala-rich sequences in 6.0 M GdnHCl, whereas ν3 remains unchanged at 3.0 M GdnHCl concentration for the Gln-rich and Ala-rich sequences but decreases to ∼1.7 for the Gly-rich sequences. Thus, the polymer properties of Gln-rich and Ala-rich sequences are less sensitive to solvent quality in denaturing solutions of GdnHCl than Gly-rich sequences. Evaluation of Flory’s characteristic ratio, Cn, for the Gln-rich and Ala-rich sequences relative to the Gly-rich sequences shows that Gln-rich sequences are stiffer than Ala-rich sequences at both 3.0 and 6.0 M GdnHCl.

Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion

The measles virus (MV) fusion (F) protein trimer executes membrane fusion after receiving a signal elicited by receptor binding to the hemagglutinin (H) tetramer. Where and how this signal is received is understood neither for MV nor for other paramyxoviruses. Because only the prefusion structure of the parainfluenza virus 5 (PIV5) F-trimer is available, to study signal receipt by the MV F-trimer, we generated and energy-refined a homology model. We used two approaches to predict surface residues of the model interacting with other proteins. Both approaches measured interface propensity values for patches of residues. The second approach identified, in addition, individual residues based on the conservation of physical chemical properties among F-proteins. Altogether, about 50 candidate interactive residues were identified. Through iterative cycles of mutagenesis and functional analysis, we characterized six residues that are required specifically for signal transmission; their mutation interferes with fusion, although still allowing efficient F-protein processing and cell surface transport. One residue is located adjacent to the fusion peptide, four line a cavity in the base of the F-trimer head, while the sixth residue is located near this cavity. Hydrophobic interactions in the cavity sustain the fusion process and contacts with H. The cavity is flanked by two different subunits of the F-trimer. Tetrameric H-stalks may be lodged in apposed cavities of two F-trimers. Because these insights are based on a PIV5 homology model, the signal receipt mechanism may be conserved among paramyxoviruses.

Prediction of substrate-binding site and elucidation of catalytic residue of a phytase from Bacillus sp.

The present study primarily deals with the identification of substrate-binding site and elucidation of catalytic residue of the phytase from Bacillus sp. (Genbank Accession No. EF536824) employing molecular modeling and site-directed mutagenesis. Homology-based modeling of the Bacillus phytase revealed β-propeller structure with twelve active-site aminoacid residues, viz., D75, R77, Y78, H138, Q140, D189, D190, E191, Y238, Y239, N346 and R348. Docking of substrate Ins(1,2,3,4,5,6)hexakisphosphate with the phytase model disclosed interaction of Y78 residue with the sixth position phosphate, while D75 and R77 residues revealed hydrogen bonding with the fifth position phosphate of the phytate. Analysis of hydrolysis products of phytate indicated the sequential removal of alternate phosphates, resulting in the formation of final product Ins triphosphate. Mutant phytases Y78A/F, derived from site-directed mutagenesis, exhibited complete loss of enzyme activity despite substrate binding, thereby suggesting the intrinsic role of Y78 residue in the catalytic activity. The Bacillus mutant phytases can be used to generate enzyme crystals complexed with phytate and lower Ins phosphates for indepth analysis of substrate binding and catalytic activity of the enzyme.

Functional Extension of Amino Acid Triads from the Fourth Transmembrane Segment (S4) into Its External Linker in Shaker K+ Channels

The highly conserved fourth transmembrane segment (S4) is the primary voltage sensor of the voltage-dependent channel and would move outward upon membrane depolarization. S4 comprises repetitive amino acid triads, each containing one basic (presumably charged and voltage-sensing) followed by two hydrophobic residues. We showed that the triad organization is functionally extended into the S3-4 linker right external to S4 in Shaker K(+) channels. The arginine (and lysine) substitutes for the third and the sixth residues (Ala-359 and Met-356, respectively) external to the outmost basic residue (Arg-362) in S4 dramatically and additively stabilize S4 in the resting conformation. Also, Leu-361 and Leu-358 play a very similar role in stabilization of S4 in the resting position, presumably by their hydrophobic side chains. Moreover, the double mutation A359R/E283A leads to a partially extruded position of S4 and consequently prominent closed-state inactivation, suggesting that Glu-283 in S2 may coordinate with the arginines in the extruded S4 upon depolarization. We conclude that the triad organization extends into the S3-4 linker for about six amino acids in terms of their microenvironment. These approximately six residues should retain the same helical structure as S4, and their microenvironment serves as part of the "gating canal" accommodating the extruding S4. Upon depolarization, S4 most likely moves initially as a sliding helix and follows the path that is set by the approximately six residues in the S3-4 linker in the resting state, whereas further S4 translocation could be more like, for example, a paddle, without orderly coordination from the contiguous surroundings.

An invertebrate [hydroxyproline]-modified neuropeptide: Further evidence for a close evolutionary relationship between insect adipokinetic hormone and mammalian gonadotropin hormone family

An octapeptide of the adipokinetic hormone (AKH) peptide family is identified in the corpora cardiaca of the stink bug, Nezara viridula, by ESI-MSN (electrospray ionization multistage MS). This is the second AKH in N. viridula and it has a hydroxyproline residue at position 6, whereas the major AKH (known as Panbo-RPCH) has Pro as the sixth amino acid residue. The correct sequence assignment of [Hyp6]-Panbo-RPCH is confirmed by retention time and MS spectra of the synthetic peptide. Various extraction procedures were followed to ascertain whether the hydroxylation is an artefact of extraction, or whether it is due to a true post-translational modification at the prohormone level. The proline hydroxylation is unique for invertebrate neuropeptides, while it has been described in the vertebrate gonadotropin-releasing hormone (GnRH). The current finding is another piece of evidence that AKH and GnRH form a peptide superfamily and are closely related evolutionarily. Biologically, [Hyp6]-Panbo-RPCH is active in vivo as an AKH, causing hyperlipaemia in the stink bug at low doses, indicating again that it is an endogenous, mature and functional hormone in this insect species.

Trace Representation and Linear Complexity of Binary $e$th Power Residue Sequences of Period $p$

Let p = ef + 1 be an odd prime for some e and e and let f, be the finite field with Fp elements. In this paper, we explicitly describe the trace representations of the binary characteristic sequences (of period p) of all the cyclic difference sets D which are some union of cosets of eth powers He in Fp* (=Δ Fp\{0}) for e ≤ 12. For this, we define eth power residue sequences of period p, which include all the binary characteristic sequences mentioned above as special cases, and reduce the problem of determining their trace representations to that of determining the values of the generating polynomials of cosets of He in Fρ* at some primitive pth root of unity, and some properties of these values are investigated. Based on these properties, the trace representation and linear complexity not only of the characteristic sequences of all the known eth residue difference sets, but of all the sixth power residue sequences are determined. Furthermore, we have determined the linear complexity of a nonconstant eth power residue sequence for any e to be either p - 1 or p whenever (e, (p-1)/n) = 1, where n is the order of 2 mod p.

The carboxy-terminal tail ofAeromonas sobriaserine protease is associated with the chaperone

ASP is the only bacterial protease in the kexin group of the subtilisin family. Previous studies have revealed that the ORF2 protein encoded at the 3' end of the asp operon is required for ASP to change from a nascent form into an active form in the periplasm. However, the mechanism by which ORF2 makes contact and interacts with ASP in the maturation process remains unknown. The present study examined the effect of mutations in the carboxy-terminal region of ASP on the ASP maturation process. Both deletion-mutation and amino acid-substitution studies have demonstrated that the histidine residue at position 595 (His-595), the sixth residue from the carboxyl terminus of ASP, is highly involved in the generation of active ASP molecules. An analysis by pull-down assay revealed that mutation at His-595 reduces the efficacy of nascent ASP to transition into active ASP by reducing the ability of ASP to make contact and interact with ORF2. Thus, it appears likely that nascent ASP in the periplasm interacts with ORF2 via the carboxy-terminal region, and His-595 of ASP appears to be an indispensable residue in this interaction.

A Biological Role for the Gonadotrophin‐Releasing Hormone (GnRH) Metabolite, GnRH‐(1‐5)

Gonadotrophin-releasing hormone (GnRH) was first isolated in the mammal and shown to be the primary regulator of the reproductive system through its initiation of pituitary gonadotrophin release. Subsequent to its discovery, this form of GnRH has been shown to be one of many structural variants found in the brain and peripheral tissues. Accordingly, the original form first discovered and cloned in the mammal is commonly referred to as GnRH-I. In addition to the complex regulation of GnRH-I synthesis, release and function, further evidence suggests that the processing of GnRH-I produces yet another layer of complexity in its activity. GnRH-I is processed by a zinc metalloendopeptidase EC 3.4.24.15 (EP24.15), which cleaves the hormone at the covalent bond between the fifth and sixth residue of the decapeptide (Tyr(5)-Gly(6)) to form GnRH-(1-5). It was previously thought that the cleavage of GnRH-I by EP24.15 represents the initiation of its degradation. Here, we review the evidence for the involvement of GnRH-(1-5), the metabolite of GnRH-I, in the regulation of GnRH-I synthesis, secretion and facilitation of reproductive behaviour.

Structural and Functional Roles of the Conserved Cysteine Residues of the Redox-regulated Import Receptor Mia40 in the Intermembrane Space of Mitochondria

Oxidative folding drives the import of proteins containing twin CXnC motifs into the intermembrane space of mitochondria. This import pathway employs a disulfide relay system whose key components are the redox-regulated import receptor Mia40 and the thiol oxidase Erv1. Mia40 contains six cysteine residues in a CPC-CX9C-CX9C arrangement in a highly conserved domain. We show that this domain is sufficient for the function of Mia40. By analysis of Mia40 cysteine mutants we demonstrate that the cysteine residues have distinct roles and are not equally important for Mia40 function. The second cysteine residue is essential for viability of yeast cells. It is required for the interaction of Mia40 with Erv1 in a disulfide intermediate and forms a redox-sensitive disulfide bond with the first cysteine residue. Both cysteine residues are required for the oxidation of the substrate, Tim10, in a reconstituted system comprised of Mia40 and Erv1. Mutants with amino acid exchanges in the third and sixth cysteine residues have severe defects in growth and in the import of intermembrane space proteins. These Mia40 variants are not tightly folded. We conclude that the cysteine residues of the twin CX9C motif have a structural role and stabilize Mia40. In particular, the disulfide bond formed by the third and sixth cysteine residues apparently supports a conformation crucial for the function of Mia40. Furthermore, the disulfide bond in the CPC segment mediates the redox reactions with the thiol oxidase Erv1 and substrate proteins in mitochondria.

Pompanopeptins A and B, new cyclic peptides from the marine cyanobacterium Lyngbya confervoides

A new 3-amino-6-hydroxy-2-piperidone (Ahp) containing peptolide, pompanopeptin A ( 1), and a novel N-methyl-2-amino-6-(4′-hydroxyphenyl)hexanoic acid ( N-Me-Ahpha) containing cyclic pentapeptide connected with a sixth amino acid residue via a rare ureido linkage, pompanopeptin B ( 2), were isolated from the marine cyanobacterium Lyngbya confervoides collected from the southeastern coast of Florida. Their planar structures were determined by a combination of NMR spectroscopic analysis and mass spectrometry. The absolute configurations were established using advanced Marfey's method and chiral HPLC analysis of the chemical degradation products. Compound 1 selectively inhibited trypsin over elastase and chymotrypsin, with an IC 50 value of 2.4 μM; selectivity is conferred by an arginine residue in the cyclic core.

Identification and functional analysis of the fusaricidin biosynthetic gene of Paenibacillus polymyxa E681

Fusaricidin, a peptide antibiotic consisting of six amino acids, has been identified as a potential antifungal agent from Paenibacillus polymyxa. Here, we report the complete sequence of the fusaricidin synthetase gene ( fusA) identified from the genome sequence of a rhizobacterium, P. polymyxa E681. The gene encodes a polypeptide consisting of six modules in a single open-reading frame. Interestingly, module six of FusA does not contain an epimerization domain, which suggests that the sixth amino acids of the fusaricidin analogs produced by P. polymyxa E681 may exist as an l-form, although all reported fusaricidins contain d-form alanines in their sixth amino acid residues. Alternatively, the sixth adenylation domain of the FusA may directly recognize the d-form alanine. The inactivation of fusA led to the complete loss of antifungal activity against Fusarium oxysporum. LC/MS analysis confirmed the incapability of fusaricidin production in the fusA mutant strain, thus demonstrating that fusA is involved in fusaricidin biosynthesis. Our findings suggested that FusA can produce more than one kind of fusaricidin, as various forms of fusaricidins were identified from P. polymyxa E681.

Factor Analysis Scale of Generalized Amino Acid Information as the Source of a New Set of Descriptors for Elucidating the Structure and Activity Relationships of Cationic Antimicrobial Peptides

AbstractFactor Analysis Scale of Generalized Amino Acid Information (FASGAI), as a new set of amino acid descriptors, reflecting hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility, and electronic properties, was derived from multi‐dimensional properties of 20 coded amino acids. Quantitative Structure–Activity Relationship (QSAR) analyses on 101 cationic Antimicrobial Peptides (AMPs) with 15 residues were then performed using FASGAI representation, Genetic Algorithm (GA) selection features, and Partial Least Squares (PLS) modeling. It was found that electronic properties of the tenth residue, bulky properties of the seventh residue, hydrophobicity of the twelfth residue, electronic properties of the third residue were highly positively correlated to antibacterial activity, whereas, hydrophobicity of the sixth residue, compositional characteristics of the sixth residue, and hydrophobicity of the tenth residue were highly negatively correlated to antibacterial activity. Analysis of variance demonstrated that a specific sequence rather than an overall sequence of AMPs may be responsible for high activity. Favorable results showed that FASGAI descriptors cherish many distinguished advantages such as plentiful structural information, easy manipulation, straightforward physicochemical meaning, and high characterization competence, and GA for parameter selection is valid in QSAR of antimicrobial peptides studied. These have thus pointed us further into the potential direction of investigation on structures and functions of other various functional peptides.

The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch

In previous studies, it was reported that DNA fragments with the sequence d(gcGXYAgc) (where X = A or G and Y = A, T or G) form a stable base-intercalated duplex (Bi-duplex) in which the central X and Y residues are not involved in any base-pair interactions but are alternately stacked on each other between the two strands. To investigate the structural stability of the Bi-duplex, the crystal structure of d(gcGAACgc) with a point mutation at the sixth residue of the sequence, d(gcGAAAgc), has been determined. The two strands are associated in an antiparallel fashion to form two types of bulge-containing duplexes (Bc-duplexes), I and II, both of which are quite different from the Bi-duplex of the parent sequence. In both Bc-duplexes, three Watson-Crick G.C base pairs constitute the stem regions at the two ends. The A(4) residues are bulged in to form a pair with the corresponding A(4) residue of the opposite strand in either duplex. The A(4).A(4)* pair formation is correlated to the orientations of the adjacent A(5) residues. A remarkable difference between the two Bc-duplexes is seen at the A(5) residue. In Bc-duplex I, it is flipped out and comes back to interact with the G(3) residue. In Bc-duplex II, the A(5) residue extends outwards to interact with the G(7) residue of the neighbouring Bc-duplex I. These results indicate that trans sugar-edge/Hoogsteen (sheared-type) G(3).A(6)* base pairs are essential in the formation of a Bi-duplex of d(gcGXYAgc). On the other hand, the alternative conformations of the internal loops containing two consecutive bulged A residues suggest molecular switching.

Induction of macrophage migration through lactose‐insensitive receptor by elastin‐derived nonapeptides and their analog

Elastin, one of the extracellular matrix components, is present in tissues requiring extensibility and resilience such as the aorta, lungs, ligaments and skin. Degradation of elastin is observed in diseases such as atherosclerosis, emphysema and metastasis. It has been suggested that degraded elastin-derived peptides interact with a variety of cell types and are involved in development of diseases. Two nonapeptides, Ala-Gly-Val-Pro-Gly-Leu-Gly-Val-Gly (AGVPGFGVG) and Ala-Gly-Val-Pro-Gly-Phe-Gly-Val-Gly (AGVPGFGVG), exist in hydrophobic regions of elastin. In this paper, we characterized these elastin-derived nonapeptides by macrophage migration assay. Both nonapeptides induced a maximal migration at 10(-8) M and elicited the same degree of responsiveness. To investigate the role of the sixth residue of the nonapeptides, seven analog peptides in which Leu or Phe is substituted by Ile, Val, Ala, Gly, Pro, Lys or Glu were synthesized and their macrophage migration activity tested. Among the nonapeptide analogs, only Ala-Gly-Val-Pro-Gly-Ile-Gly-Val-Gly induced the migration of macrophages at the optimal concentration of 10(-9) M and its responsiveness was the same as that of parent nonapeptide AGVPGFGVG. Results of the deactivation tests and the effect of lactose on macrophage migration showed that a lactose-insensitive receptor which mainly recognizes Ala-Gly-Val-Pro-Gly-Ile-Gly-Val-Gly is presumably present on the membrane of macrophages in addition to the elastin-binding protein (EBP) sensitive to lactose. These results suggest that Leu, Phe and Ile residues at the sixth position of elastin-derived nonapeptides are crucial for inducing macrophage migration and in particular, Ile residue is important for the recognition by receptor insensitive to lactose.

A new sequence representation as applied in better specificity elucidation for human immunodeficiency virus type 1 protease

Factor analysis scales of generalized amino acid information (FASGAI) involving hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility, and electronic properties were derived from 516 property parameters of 20-coded amino acids, and was then employed to represent sequence structures of 746 peptides with 8 amino acid residues. Cleavage site prediction models for human immunodeficiency virus type 1 protease by linear discriminant analysis and support vector machine with radial basis function kernel were constructed to identify if they could be cleaved or not, and were further utilized to investigate the cleavage specificity. These diversified properties, including the bulky properties, secondary conformation characteristics, electronic properties, and hydrophobicity at the first, the second, the fourth, the fifth, and the sixth residue, are possibly important factors in determining HIV PR cleavage or not. Particularly, maximal positive and negative influences result from the bulky properties of different sites. Further results from analysis of variance also likely reflect that the HIV PR recognizes diversified key properties of various sites in the octameric sequences. Satisfactory results show that FASGAI can not only be used to represent sequence structures of various functional peptides, but alsoprovide a potential feasible measure for exploring relationship between protein motif sequences and their functions.